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Evolutionary genetics of the family Placobranchidae (Mollusca: Gastropoda: Opisthobranchia: Sacoglossa)

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Title:
Evolutionary genetics of the family Placobranchidae (Mollusca: Gastropoda: Opisthobranchia: Sacoglossa)
Physical Description:
Book
Language:
English
Creator:
Bass, Anna Lee
Publisher:
University of South Florida
Place of Publication:
Tampa, Fla
Publication Date:

Subjects

Subjects / Keywords:
Phylogeny
Population genetics
Mitochondrial DNA
Nuclear DNA
Cladogenesis
Dissertations, Academic -- Biology -- Doctoral -- USF   ( lcsh )
Genre:
bibliography   ( marcgt )
theses   ( marcgt )
non-fiction   ( marcgt )

Notes

Abstract:
ABSTRACT: Members of the family Placobranchidae have been the focus of numerous studies because of their interesting physiological adaptations (kleptochemistry and kleptoplasty) and ecological associations with marine algae. More than 100 species have been described since the 1800's, but no determination of phylogenetic relationships in the family has occurred. DNA sequences from two mitochondrial genes (large subunit ribosomal and cytochrome c oxidase subunit I) and one nuclear gene (Histone 3) were used to reconstruct relationships among 34 nominal species within the Placobranchidae. Strong support for terminal nodes was found using Bayesian phylogenetic methods; however, a "soft" polytomy was detected at internal nodes. In general, the results confirm the paraphyly of Elysia. Proposals for the designation of the genera, Thallepus Swainson, 1840 and Tridachia Deshayes, 1857 and delineation of species are presented.^ How intrinsic factors affect speciation rates in groups of animals has been a central focus in evolutionary biology. Adaptive radiation associated with food choice has been postulated for the opisthobranch order Sacoglossa. An increase in the rate of cladogenesis was detected within the family Placobranchidae and intrinsic factors such as larval development, kleptoplasty and food choice were investigated as potential key innovations. Ancestral state reconstruction of characters suggests that food choice played a dominant role in influencing speciation rate within the family Placobranchidae. Life history strategy may play an important role in structuring genetic variation throughout the geographic range of a species. Members of the sacoglossan family Placobranchidae Gray, 1840, exhibit variation in life history strategies such as feeding preference and degree of kleptoplasty that could be influential in population structuring.^ ^Three species, Elysia subornata Verrill, 1901, Elysia tuca Marcus and Marcus, 1967, and Elysia crispata Mörch, 1863 were sampled from several locations in an attempt to quantify genetic variation as indicated by cytochrome c oxidase subunit I gene sequencing. Elysia crispata exhibited the highest degree of population subdivision followed by Elysia tuca and Elysia subornata. Nucleotide and haplotype diversity also revealed the same general ranking of species. Preliminary conclusions suggest that diversity in feeding preference and degree of kleptoplasty play significant roles in population subdivision of these species.
Thesis:
Dissertation (Ph.D.)--University of South Florida, 2006.
Bibliography:
Includes bibliographical references.
System Details:
System requirements: World Wide Web browser and PDF reader.
System Details:
Mode of access: World Wide Web.
Statement of Responsibility:
by Anna Lee Bass.
General Note:
Title from PDF of title page.
General Note:
Document formatted into pages; contains 143 pages.
General Note:
Includes vita.

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Source Institution:
University of South Florida Library
Holding Location:
University of South Florida
Rights Management:
All applicable rights reserved by the source institution and holding location.
Resource Identifier:
aleph - 001930872
oclc - 213467075
usfldc doi - E14-SFE0001725
usfldc handle - e14.1725
System ID:
SFS0026043:00001


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E vol ut i ona r y G e ne t i c s O f T he F a m i l y P l a c obr a nc hi da e ( M ol l us c a : G a s t r opoda : O pi s t hobr a nc hi a : S a c ogl os s a ) by A nna L e e B a s s A di s s e r t a t i on s ubm i t t e d i n pa r t i a l f u l f i l l m e nt of t he r e qui r e m e nt s f or t he de g r e e of D oc t or of P hi l os ophy D e pa r t m e nt of B i ol ogy C ol l e ge of A r t s a nd S c i e nc e s U ni ve r s i t y of S ou t h F l o r i da C o M a j or P r of e s s or : D r E a r l M c c oy P h. D C o M a j or P r of e s s or : D r S t e phe n K a r l P h D D r S i dne y P i e r c e P h D D r J a m e s G a r e y, P h. D D a t e of A ppr ova l : S e pt e m be r 29, 2006 K e yw or ds : phyl oge ny, popul a t i on ge ne t i c s m i t oc h ondr i a l dna nuc l e a r dna c l a doge ne s i s C opyr i ght 2006 A nna L e e B a s s

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D E D I C A T I O N I de di c a t e t hi s di s s e r t a t i on t o m y pa r e nt s R obe r t a a nd R obe r t B a s s M y m ot he r i ns t i l l e d i n m e a gr e a t r e s pe c t f or di ve r s i t y a nd a pp r e c i a t i on f or be a ut y. A l t hough m os t of t he t i m e he r vi e w w a s or i e nt e d t ow a r ds hum a n be i ngs i t w a s e a s y e xt e ndi ng t hi s a ppr e c i a t i on a nd r e s pe c t t o ot he r a ni m a l s I t ha nk he r f or t he a bi l i t y t o s e e t hi s M y f a t he r ha s be e n a g r e a t s our c e of s t r e ngt h t ha t ha s s uppor t e d m e t h r ough good a nd ba d t i m e s H e t r i e d hi s be s t t o t e a c h m e m a t h a nd i n d oi ng s o i ns t i l l e d i n m e a g r e a t a ppr e c i a t i on f or t he pow e r of i t E ve n t hough m y pa r e nt s do not r e a l l y unde r s t a nd m y f a s c i na t i on w i t h bi ol ogy t he y ha ve a l w a ys s uppor t e d m y c hoi c e t o pur s ue bi ol ogi c a l s t udi e s T he y ha ve be e n a c ons i s t e nt s our c e of f un di ng t hr oughout m y c a r e e r a nd I t ha nk t he m f or t ha t F o r t he s e r e a s ons a nd m a ny o t he r ot he r s I de di c a t e t hi s di s s e r t a t i on t o t he m T hus t he y ar e t o ov e r c om e t he t e m pt at i on t o c at e g or i z e t hi ngs t oo qui c k l y s o t he y m ay k e e p t he i r pe r c e pt i ons ne ut r al and v i e w e v e nt s and pe o pl e as t he y ac t ual l y ar e F r om t he I t t y B i t t y B uddha by N i c ol a D i xon ( 2002 )

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A C K N O W L E D G E M E N T S I w i s h t o t ha nk m y c om m i t t e e S t e phe n K a r l E a r l M c C oy, S i dne y P i e r c e a nd J a m e s G a r e y. F l or e nc e T hom a s w a s a f or m e r c om m i t t e e m e m be r w ho pr ovi de d e xc e l l e nt gui da nc e a nd s uppor t ove r t he ye a r s T ha nks t o e v e r yone f or t he i r gui da nc e a nd s uppor t I pa r t i c ul a r l y w a nt t o t ha nk m y l a b m a t e s A ndr e y C a s t r o, C a i t l i n C ur t i s K e nne t h H a ye s T oni a S c hw a r t z E m i l y S e ve r a nc e a nd C e c e l i a P uc hul e t e gui w ho m a de s i gni f i c a nt i nt e l l e c t ua l c ont r i but i ons dur i ng m y t e n ur e a t U S F I a l s o w a nt t o t ha nk t he m f or t he i r pa t i e nc e hum or a nd ge ne r a l g r oovi ne s s T he y m a de m y gr a dua t e c a r e e r a n e nj oya bl e e xpe r i e nc e a nd I know t ha t I c oul d not h a ve done i t w i t hout t he m O t he r B i ol ogy gr a dua t e s t ude nt s T e r r y C a m pbe l l T a t i a n a C or ne l i s e n, M a r k D r i s c ol l J e f f H a nt e n, M a r y H a r m on S e a n K i na ne A l l i s on M e y e r s B r e nt N i c hol s a nd K r i s t e n P e nne y, a l s o c ont r i but e d t o t hi s di s s e r t a t i on e i t he r t hr ough f i e l d, s t a t i s t i c a l or m a i nt e na nc e of s a ni t y a s s i s t a n c e N one of t hi s w o r k c oul d ha ve be e n c onduc t e d w i t h out t he pe opl e w ho r e s ponde d t o m y r e que s t s f or he l p w i t h t he c ol l e c t i on of t he s e a s l ug s pe c i m e ns I n pa r t i c ul a r C l a y C a r l s on a nd P a t t y J o H of f qui c kl y a nd unw a ve r i ng l y s uppl i e d s a m pl e s f r om G ua m I a l s o t ha nk t he f ol l ow i ng f o r e i t he r s e ndi ng m e s pe c i m e ns or he l pi ng m e c ol l e c t s pe c i m e ns i n F l or i da a nd t he B a ha m a s : V i c t or B on i t o, C hr i s & J a ne B ow e n, A ndr e y C a s t r o, L uc a s C e r ve r a N i c k C ur t i s A nne D upont P a ul i ne F i e ne D a ni e l G e i ge r K e nne t h

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H a ye s N i s hi na M a s a yo s hi S a ndr a M i l l e n, M i ke M i l l e r R obe r t O m s C or y P i t t m a n V i c t or R a pha e l L u i z R oc ha E m i l y S e ve r a nc e a nd C ynt hi a T r ow br i dge O t he r pe r s ons w ho ha ve c ont r i but e d t o m y gr ow t h a s a bi ol ogi s t t e a c he r a nd pe r s on a r e J odi & A l e xa ndr a N e t t l e t on, J ohnny E l R a dy, T he r e s a & J i m D e m a s t e s M a r i l yn M ye r s on, S us a n M e i e r s R a c he l C r a w f or d M a t t G a r ve y, a nd M r O 'M a l l e y. T he y a l w a ys of f e r e d e nc our a ge m e nt a nd s uppor t a nd t ha nks i s s i m pl y i ns uf f i c i e nt T he D e pa r t m e nt o f B i ol ogy ha s a w onde r f ul s t a f f a nd I g r a t e f ul l y t ha nk J a ne t G a ut hi e r P a t H om e r K a t hl e e n H ot c hki s s B e t t y L or a a m R a y M a r t i ne z D a w n M c G ow a n, C hr i s t i ne S m i t h, R obi n S yl ve s t e r a nd T ot ka T z a ne va T r a ve l a nd r e s e a r c h f undi ng w e r e pr ovi de d by t he C onc hol ogi s t s of A m e r i c a P A D I D e pa r t m e nt of B i ol ogy T ha r pe F e l l ow s hi ps a nd R obe r t a & R obe r t B a s s F i na l l y I w i s h t o t ha nk D us t i n B i nge a nd D a ni e l M a j c hr z a k, m e m be r s of t he R e s e a r c h C om put i ng C or e F a c i l i t y a t t he U ni ve r s i t y o f S ou t h F l o r i da f o r t he i r pa t i e nc e a nd a s s i s t a nc e w hi l e I w a s l e a r ni n g how t o us e L i nux c om put i ng l a ngua g e

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N ot e t o R e a de r : T he o r i gi na l o f t hi s doc um e nt c on t a i ns c ol or t ha t i s ne c e s s a r y f or unde r s t a ndi ng t he da t a T he or i gi na l di s s e r t a t i on i s on f i l e w i t h t he U S F l i b r a r y i n T a m pa F l o r i da

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i T A B L E O F C O N T E N T S L i s t of T a bl e s i i i L i s t of F i gur e s i v A bs t r a c t vi O ve r vi e w 1 C ha pt e r 1: P hyl oge ne t i c R e l a t i ons hi ps W i t hi n T he F a m i l y P l a c obr a nc hi da e 5 I nt r oduc t i on 5 M a t e r i a l s a nd M e t hods 9 R e s ul t s 16 V a r i a t i on a t t he i ndi vi dua l l e ve l 1 6 S a t ur a t i on t e s t s f or pr ot e i n c odi ng ge ne s 17 D i ve r ge nc e l e ve l s 18 P hyl oge ny 20 N uc l e ot i de s ubs t i t ut i on pa t t e r ns a nd r e l a t i ve r a t e s 21 T ot a l e vi de nc e phyl oge ny 22 D i s c us s i on 27 D i ve r ge nc e l e ve l s a m ong t a xonom i c c a t e gor i e s a n d w i t hi n s pe c i e s va r i a t i on 27 P hyl oge ny of t he P l a c obr a nc hi da e a nd a s s oc i a t e d f a m i l i e s 29 G e ne pe r f or m a nc e i n phyl oge ne t i c r e c ons t r uc t i on 31 R e f e r e nc e s 33 C ha pt e r 2: E vi de nc e o f I nc r e a s e d C l a doge ne s i s i n t he F a m i l y P l a c obr a nc hi da e 65 I nt r oduc t i on 65 M a t e r i a l s a n d M e t hods 67 R e s ul t s 72 C ha r a c t e r t r a c i ng 73 L i ne a ge s t hr ough t i m e 75 D i s c us s i on 75 R e f e r e nc e s 82

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i i C ha pt e r 3: C om pa r a t i ve P opul a t i on G e ne t i c S t r uc t ur e A m ong T hr e e S pe c i e s of P l a c obr a nc hi ds 100 I nt r oduc t i on 100 M a t e r i a l s a nd M e t hods 103 R e s ul t s 108 E l y s i a t uc a 108 E l y s i a c r i s pat a 110 E l y s i a s ubor nat a 114 D i s c us s i on 117 E l y s i a s ubor nat a va r i a t i on 117 E l y s i a c r i s pat a va r i a t i on 120 W i t hi n a nd a m ong popu l a t i on va r i a t i on 121 R e f e r e nc e s 128 A bout t he A ut hor E nd P a ge

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i i i L I S T O F T A B L E S T a bl e 1. 1 L i s t o f s pe c i e s us e d i n t he phyl oge ne t i c a na l ys i s 44 T a bl e 1. 2 M ode l s of e vol ut i on us e d i n e s t i m a t e s of di ve r ge nc e a t va r i ous t a xonom i c l e ve l s 47 T a bl e 1. 3 M a xi m um l i ke l i hood e s t i m a t e s of di ve r g e nc e ba s e d on m t D N A 48 T a b l e 1. 4 M a xi m um l i ke l i hood e s t i m a t e s of di ve r g e nc e ba s e d on H i s t one 3. 49 T a bl e 1. 5 B a ye s i a n pa r a m e t e r e s t i m a t e s f r om t he G T R + I + G 50 T a bl e 2. 1 S a c ogl os s a n f a m i l i e s ge ne r a a nd num be r of s pe c i e s c ur r e nt l y r e c ogni z e d. 91 T a bl e 2. 2 T a xonom i c l i s t of s pe c i e s us e d i n t he ph yl oge ne t i c a na l ys i s 92 T a bl e 2. 3 C ha r a c t e r m a t r i x f o r s pe c i e s us e d i n t he a nc e s t r a l s t a t e r e c ons t r uc t i ons f or t h r e e l i f e hi s t or y t r a i t s 94 T a bl e 3. 1 P r i m e r s us e d i n a m pl i f i c a t i on of t hr e e s pe c i e s of s a c ogl os s a n s 134 T a bl e 3. 2 C yt oc hr om e c oxi da s e s ubuni t I ha pl ot y pe s by l oc a t i on f o r s pe c i e s of s a c ogl os s a ns 135 T a bl e 3. 3 H a pl ot ype a nd nuc l e ot i de di ve r s i t y e s t i m a t e s + s t a nda r d de vi a t i ons f or t h r e e s pe c i e s of s a c ogl os s a n s 136 T a bl e 3. 4 S um m a r y of unc or r e c t e d p a nd m a xi m u m l i ke l i hood ( M L ) di s t a nc e s 137 T a bl e 3. 5 A c c e s s i on num be r s f or s e que nc e s of 16S a nd H i s t one 3 ge ne r e gi ons 138 T a bl e 3. 6 R e s ul t s of ove r a l l e s t i m a t e of S T a nd s e l e c t l i f e hi s t or y t r a i t s f or t hr e e s pe c i e s of s a c ogl os s a n s 139

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i v L I S T O F F I G U R E S F i gur e 1. 1 S a t ur a t i on a s i ndi c a t e d by non l i ne a r r e l a t i ons hi p be t w e e n unc or r e c t e d p di s t a nc e s ve r s us unc or r e c t e d p t r a ns ve r s i on di s t a nc e s f or 3 r d pos i t i ons o f A ) c ox 1 a nd B ) H i s t one 3 52 F i gur e 1. 2 M a xi m um l i ke l i hood e s t i m a t e s of s e que nc e di ve r ge nc e ba s e d on m t D N A 53 F i gur e 1. 3 M a xi m um l i ke l i hood e s t i m a t e s of s e que nc e di ve r ge nc e ba s e d on H i s t one 3. 54 F i gur e 1. 4 B a ye s i a n phyl ogr a m f o r m t D N A 55 F i gur e 1. 5 B a ye s i a n phyl ogr a m f o r H i s t one 3 56 F i gur e 1. 6 P r opor t i on of nuc l e ot i de s A ) by ge ne f o r a l l t hr e e ge ne s a nd B ) by pos i t i on f or t he pr ot e i n c odi ng ge ne s 57 F i gur e 1. 7 R e l a t i ve r a t e s of e vol ut i on A ) by ge ne a nd B ) by ge ne f or 16S a nd by pos i t i on f or t he pr ot e i n c odi ng ge ne s 58 F i gur e 1. 8 R e l a t i ve r a t e s de r i ve d f r om t he i ns t a nt a ne ous r a t e m a t r i x f or a l l ge ne s ge ne r a t e d f r om G T R + I + G by ge ne m ode l s e t t i ngs 59 F i gur e 1. 9 B a ye s i a n phyl ogr a m of G T R + I + G m od e l f or t he c om bi ne d m t D N A a nd nuc D N A da t a s e t s 60 F i gur e 1. 10 M a xi m um pa r s i m ony c l a dogr a m o f c o nc a t e na t e d m t D N A a nd nuc D N A da t a s e t s 61 F i gur e 1. 11 M a xi m um pa r s i m ony phy l ogr a m of c o nc a t e na t e d m t D N A a nd nuc D N A da t a s e t s w i t h br a nc h l e ngt hs pr opor t i ona l t o una m bi guous c ha nge s 62 F i gur e 1. 12 B a ye s i a n phyl ogr a m of a s ubs a m pl e of t a xa us e d t o t e s t l ong br a nc h di vi s i on by m ul t i pl e s hor t br a nc he s 63

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v F i gur e 1. 13 P o r t i on o f B a ye s i a n phyl ogr a m ba s e d on t ot a l e vi de nc e ( F i gur e 1 9) 64 F i gur e 2. 1 B a ye s i a n phyl ogr a m ba s e d on c onc a t e n a t e d m t D N A a nd nuc D N A da t a s e t s 95 F i gur e 2. 2 M os t pa r s i m oni ous r e c ons t r uc t i on o f l a r va l de ve l opm e nt on t he B a ye s i a n phyl oge ny. 96 F i gur e 2. 3 M os t pa r s i m oni ous r e c ons t r uc t i on o f l e ve l of kl e pt opl a s t y on t he B a ye s i a n phyl oge ny. 97 F i gur e 2. 4 M os t pa r s i m oni ous r e c ons t r uc t i on o f f o od c hoi c e on t he B a ye s i a n phyl oge ny. 98 F i gur e 2. 5 N P R S t r a ns f or m e d ul t r a m e t r i c t r e e w i t h a s c a l e ba r pr opo r t i ona l t o s m oot he d r a t e o f s ubs t i t ut i on. 99 F i gur e 3. 1 R e s ul t s of N e i ghbor J oi ni ng ( N J ) a na l ys i s of E l y s i a t uc a c ox 1 ha pl ot ype s f r om t he G ul f o f M e xi c o ( G O M ) F l o r i da K e ys ( F L K ) a nd t he B a ha m a s ( B A ) 140 F i gur e 3. 2 R e s ul t s of N e i ghbor J oi ni ng ( N J ) a na l ys i s of E l y s i a c r i s pat a c ox 1 ha pl ot ype s f r om F l or i da K e ys ( F L K ) B e l i z e B a ha m a s ( B A 1 & B A 2) a nd t he U ni t e d S t a t e s V i r gi n I s l a nds ( U S V I ) 141 F i gur e 3. 3 R e gr e s s i on of 3 r d pos i t i on t r a ns i t i ons ( ) a nd t r a ns ve r s i ons ( ) a ga i ns t unc or r e c t e d p di s t a nc e s f or E l y s i a c r i s pat a ha pl ot ype s a nd E l y s i a di om e de a 142 F i gur e 3. 4 R e s ul t s of N e i ghbor J oi ni ng ( N J ) a na l ys i s of E l y s i a s ubor nat a c ox 1 ha pl ot ype s f r om t he F l or i da K e ys ( F L K ) a nd I ndi a n R i ve r L a goon ( I R L ) 143

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vi E V O L U T I O N A R Y G E N E T I C S O F T H E F A M I L Y P L A C O B R A N C H I D A E ( M O L L U S C A : G A S T R O P O D A : O P I S T H O B R A N C H I A : S A C O G L O S S A ) A nna L B a s s A B S T R A C T M e m be r s of t he f a m i l y P l a c obr a nc hi da e ha ve be e n t he f oc us of num e r ous s t udi e s be c a u s e of t he i r i nt e r e s t i ng phys i ol ogi c a l a da pt a t i ons ( kl e pt oc he m i s t r y a nd kl e pt opl a s t y) a nd e c ol ogi c a l a s s oc i a t i ons w i t h m a r i ne a l ga e M or e t ha n 100 s pe c i e s ha ve be e n de s c r i be d s i nc e t he 1800's but no de t e r m i na t i on of phyl oge ne t i c r e l a t i ons hi ps i n t he f a m i l y ha s oc c ur r e d. D N A s e que nc e s f r om t w o m i t oc hondr i a l ge ne s ( l a r ge s ubuni t r i bos om a l a nd c yt oc hr om e c oxi da s e s ubuni t I ) a nd one nuc l e a r ge ne ( H i s t one 3) w e r e us e d t o r e c ons t r uc t r e l a t i ons hi ps a m ong 34 nom i na l s pe c i e s w i t hi n t he P l a c obr a nc hi da e S t r ong s u ppor t f or t e r m i na l node s w a s f ound us i ng B a ye s i a n phyl oge ne t i c m e t hods ; how e ve r a s of t pol yt om y w a s de t e c t e d a t i nt e r na l node s I n ge ne r a l t he r e s ul t s c onf i r m t he pa r a phyl y o f E l y s i a P r opos a l s f or t he de s i gna t i on of t he ge ne r a T hal l e pus S w a i ns on, 1 840 a nd T r i dac hi a D e s ha ye s 1857 a nd de l i ne a t i on of s pe c i e s a r e pr e s e nt e d. H ow i nt r i ns i c f a c t or s a f f e c t s pe c i a t i on r a t e s i n gr o ups of a ni m a l s ha s be e n a c e nt r a l f oc us i n e vol ut i ona r y bi ol ogy A da pt i ve r a di a t i on a s s oc i a t e d w i t h f ood c hoi c e ha s be e n pos t ul a t e d f or t he opi s t hobr a nc h or de r S a c ogl os s a A n i nc r e a s e i n t he r a t e o f c l a doge ne s i s w a s de t e c t e d w i t hi n t he f a m i l y P l a c o br a nc hi da e a nd i nt r i ns i c f a c t or s s uc h a s

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vi i l a r va l de ve l opm e nt k l e pt opl a s t y a nd f ood c hoi c e w e r e i nve s t i ga t e d a s pot e nt i a l ke y i nnova t i o ns A nc e s t r a l s t a t e r e c ons t r uc t i on of c ha r a c t e r s s ugge s t s t ha t f ood c hoi c e pl a ye d a dom i na nt r ol e i n i n f l ue nc i ng s pe c i a t i on r a t e w i t hi n t he f a m i l y P l a c obr a nc hi da e L i f e hi s t or y s t r a t e gy m a y pl a y a n i m por t a nt r ol e i n s t r uc t ur i ng ge ne t i c va r i a t i on t hr ougho ut t he ge ogr a phi c r a nge o f a s pe c i e s M e m be r s of t he s a c ogl os s a n f a m i l y P l a c obr a nc hi da e G r a y, 1840 e xhi bi t va r i a t i on i n l i f e hi s t or y s t r a t e gi e s s uc h a s f e e di ng pr e f e r e nc e a nd de gr e e o f kl e pt opl a s t y t ha t c oul d be i nf l ue nt i a l i n popul a t i on s t r uc t ur i ng T h r e e s pe c i e s E l y s i a s ubor nat a V e r r i l l 1901, E l y s i a t uc a M a r c us a nd M a r c us 1967 a nd E l y s i a c r i s pat a M r c h, 1863 w e r e s a m pl e d f r om s e ve r a l l oc a t i ons i n a n a t t e m pt t o qua nt i f y ge ne t i c va r i a t i on a s i ndi c a t e d by c yt oc hr o m e c oxi da s e s ubuni t I ge ne s e que nc i ng E l y s i a c r i s pat a e xhi bi t e d t he hi ghe s t de gr e e of popul a t i on s ubdi vi s i on f ol l ow e d by E l y s i a t uc a a nd E l y s i a s ubor nat a N u c l e ot i de a nd ha pl ot ype di ve r s i t y a l s o r e ve a l e d t he s a m e ge ne r a l r a nki ng of s pe c i e s P r e l i m i na r y c onc l us i ons s ugge s t t ha t di ve r s i t y i n f e e di ng pr e f e r e nc e a nd de gr e e of kl e pt opl a s t y pl a y s i gni f i c a nt r ol e s i n popul a t i on s ubdi vi s i on of t he s e s pe c i e s

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1 O V E R V I E W A l t hough t he e a r t h i s dom i na t e d by w a t e r s pe c i a t i on ha s ge ne r a l l y be e n e xa m i ne d i n l i ght o f p r oc e s s e s obs e r ve d i n t he t e r r e s t r i a l e nvi r onm e nt w i t h m a ny of t he e a r l y di s c us s i on s of s pe c i a t i on c e nt e r e d on i s l a nd popul a t i ons or t e r r e s t r i a l s pe c i e s ( M a yr 1942) T he s e e m i ngl y c ont i guous na t ur e o f t he m a r i ne r e a l m i s r e f l e c t e d i n t he doc um e nt e d s pe c i e s di ve r s i t y. B r i ggs ( 1994 ) obs e r ve d t ha t t he num be r o f s pe c i e s i n t he m a r i ne e nvi r onm e nt i s m a ny f e w e r t ha n t ha t i n t e r r e s t r i a l e nvi r onm e nt s a l t hough us e of t he e ne r gy s t a bi l i t y a r e a t he or y of bi odi ve r s i t y w o ul d pr e di c t t he oppos i t e t r e nd B r i ggs s ugge s t e d t ha t t he a ppa r e nt di s c r e pa nc y i n f r e que nc y of m ul t i c e l l ul a r o r ga ni s m s ( 12 m i l l i on + 1 m i l l i on f o r l a nd ve r s us < 200, 000 f or s e a ) i s a r e s ul t of e s t i m a t i on m e t hods O ne of t he s e m e t hods i nvol ve s e xt r a pol a t i on f r o m a gi ve n s a m pl e a r e a a nd t he ot he r i s t he e xpe r t opi ni on m e t hod T he s e ge ne r a l obs e r va t i ons on num be r s of m ul t i c e l l ul a r or ga ni s m s i n t e r r e s t r i a l ve r s us m a r i ne e nvi r onm e nt s c a n l e a d one t o be l i e ve t ha t s pe c i a t i on m a y be l i m i t e d i n t he m a r i ne r e a l m A l t hough f e w m ol e c ul a r s t udi e s of pl a nkt oni c pe l a gi c s pe c i e s ha ve be e n unde r t a ke n ( s e e N or r i s 2000 ) pe l a gi c or ga ni s m s a r e pr e s um e d t o be hom oge nous popul a t i ons be c a us e of t he pot e nt i a l f or m i xi ng a nd t r a ns por t i n a nd a c r os s t he oc e a n. T hi s a s s um pt i on i s ba s e d on t he p r e m i s e t ha t pl a nkt oni c or ga ni s m s or l a r va e a r e c a pa bl e of hi gh di s pe r s a l r a t e s r e s ul t i ng i n s i gni f i c a nt ge ne f l ow t ha t pr e ve nt s l oc a l a da pt a t i on a nd s pe c i a t i on. T he p l a nkt ot r ophi c l a r va e e qua l s hi gh l e ve l s of ge ne f l ow pa r a di g m ha s be e n c ha l l e nge d by num e r ous r e s e a r c he r s ( B ur t on,

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2 1983; H e dge c oc k, 1986) L a r va l de ve l opm e nt a l m ode a nd r e s ul t a nt pr e di c t i ons o f di s pe r s a l pot e nt i a l i s j us t one e xa m pl e o f a c ont e m por a r y i nf l ue nc e on s pe c i a t i on i n t he m a r i ne e nvi r onm e nt a nd ne gl e c t s t he i m po r t a nc e o f hi s t or i c a l i n f l ue nc e s s uc h a s vi c a r i a nt e ve nt s ( M a yr 1942 ; M c C oy & H e c k 19 7 6; B r i ggs 1995 ) M a r i ne i nve r t e br a t e s a r e e xt r e m e l y di ve r s e i n t e r m s of t he i r a da pt a t i ons t o m a r i ne l i f e T he i r ha bi t a t s s pa n m a ny e xt r e m e s i n s a l i ni t y t e m pe r a t ur e a nd f l ow r e gi m e s A s i m pl e ne c e s s i t y s uc h a s f ood a c qui s i t i on m a y be c om e di f f i c ul t i n t he m a r i ne e nvi r onm e nt i f l oc om ot i on i s l i m i t e d a nd pr e y a r e s e a s ona l R e pr oduc t i on i n t he a qua t i c r e a l m pr e s e nt s ne w c ha l l e nge s a nd num e r ous e xa m pl e s of m e t hods t o ove r c om e r e pr oduc t i ve i m pe di m e nt s a r e a ppa r e nt s uc h a s m a s s s pa w ni ng i n ge ne r a l a nd c ha nge s i n ga m e t e buoya nc y s pe c i f i c a l l y. T he phys i ol ogi c a l a nd be ha vi or a l c ons e que nc e s of l i f e i n t he m a r i ne e nvi r on m e nt i m pl y t ha t t he pot e nt i a l f o r l oc a l a da pt a t i on a nd r e pr oduc t i ve i s ol a t i on a r e hi gh; t he r e by, i nc r e a s i ng s pe c i a t i on r a t e s a nd l i m i t i ng g l oba l l y di s t r i but e d s pe c i e s G l oba l l y di s t r i but e d t a xa a r e c om m on a m ong m a r i ne i nve r t e br a t e s a s a r e t a xa e xhi bi t i ng r e s t r i c t e d di s t r i but i ons S om e l a r ge s c a l e que s t i ons be c om e a ppa r e nt w he n a t t e m pt i ng t o e xa m i ne s pe c i a t i on i n t he m a r i ne e nv i r onm e nt A r e ge ol ogi c a l pr oc e s s e s t he m a i n de t e r m i na nt of s pe c i a t i on i n t he m a r i ne e nvi r onm e nt ? W ha t a r e t he r e l a t i ve r ol e s of l i f e hi s t or y t r a i t s a nd be ha vi or s i n t he pr o m ot i on/ pr e ve nt i on o f s pe c i a t i on? C a n one i de nt i f y ke y i nnova t i ons i n m a r i ne i nve r t e br a t e s t ha t m a y l e a d t o i nc r e a s e d r a t e s of s pe c i a t i on? A pot e nt i a l m ode l f or a t e s t of t he i m por t a nc e of l i f e hi s t or y t r a i t s on s pe c i a t i on c a n be f ound i n t he P hyl um M ol l us c a A di ve r s e p hyl um M ol l us c a i s t he s e c ond l a r ge s t a ni m a l phyl um i n t e r m s o f num be r s o f s pe c i e s T h e di ve r s i t y r a nge s f r om t he r a pt or i a l

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3 pr e da t or s of C e pha l opoda t o t he s e de nt a r y bi va l ve m ol l us c s T he C l a s s G a s t r opoda dom i na t e s t hi s phyl um a t nu m e r ous t a xonom i c l e v e l s a nd c ont a i ns a t l e a s t 40, 000 de s c r i be d s pe c i e s ( P e c he ni k, 2000) A l t hough r e pr e s e nt i ng onl y a s m a l l por t i on of t hi s di ve r s i t y, t he S ubc l a s s O pi s t hobr a nc hi a i nc l ude s s om e of t he m os t f l a m boya nt ( nudi br a nc hs ) a nd unde r s t udi e d ( pt e r opods ) s pe c i e s T he or de r S a c ogl os s a i s pa r t i c ul a r l y i nt e r e s t i ng i n t e r m s of t he s e c onda r y l os s of t he s he l l i n m a ny of t he f a m i l i e s a nd t he s ubs e que nt c ha nge s i n phys i ol ogy a nd be ha vi or t h a t m a y ha ve a c c om pa ni e d t hi s l os s ( M a r i n & R os 2004 ) I n t he f i r s t c ha pt e r I us e m ol e c ul a r da t a f r o m t w o m i t oc hondr i a l ( c yt oc hr o m e c oxi da s e s ubuni t I a nd l a r ge r i bo s om a l s ubuni t ) a nd one nuc l e a r ( H i s t one 3) ge ne t o r e c ons t r uc t phyl oge ne t i c r e l a t i ons hi ps a m ong t a xa w i t hi n t he f a m i l y P l a c obr a nc hi da e I n t he s e c ond c ha pt e r I t e s t f o r a c ha nge i n t he r a t e of c l a doge ne s i s w i t h a s ubs e t of s pe c i e s us e d t o r e c ons t r uc t t he phyl oge ny of t he f a m i l y. I n a ddi t i on t o a n e xa m i na t i on of t he r a t e of c l a doge ne s i s I us e c ha r a c t e r m a ppi ng t o a c c e s s t he e vol ut i on of l i f e hi s t or y t r a i t s s uc h a s l a r va l de ve l opm e nt a l t ype l e ve l of kl e pt opl a s t y a nd f ood c hoi c e I n t he t hi r d c ha pt e r I c om pa r e s e ve r a l s pe c i e s of pl a c obr a nc hi ds t o e xa m i ne t he e f f e c t of l i f e hi s t or y t r a i t s on popul a t i on s ubdi vi s i on a nd m i t oc hondr i a l D N A di ve r s i t y.

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4 R E F E R E N C E S B R I G G S J C 1994 S pe c i e s di ve r s i t y: l a nd a nd s e a c om pa r e d. Sy s t e m at i c B i ol ogy 43: 1 30 135. B R I G G S J C 1995 G l obal B i oge ogr aphy E l s e vi e r S c i e nc e B V A m s t e r da m B U R T O N R S 1983. P r ot e i n po l ym or phi s m s a nd ge ne t i c di f f e r e nt i a t i on o f m a r i ne i nve r t e br a t e popul a t i ons M ar i ne B i ol ogy L e t t e r s 4: 193 206 H E D G E C O C K D 1986. I s ge ne f l ow f r om pe l a gi c l a r va l di s pe r s a l i m por t a nt i n t he a da pt a t i on a nd e vol ut i on of m a r i ne i nve r t e br a t e s ? B ul l e t i n of M ar i ne Sc i e nc e 39: 550 564. M A R I N A & R O S J 2004. C he m i c a l de f e ns e s i n s a c ogl os s a n opi s t hobr a nc hs : t a xonom i c t r e nds a nd e vol ut i ve i m pl i c a t i ons Sc i e n t i a M ar i na, 68( S uppl 1 ) : 227 241. M A Y R E 1 942. Sy s t e m at i c s and t he O r i gi n o f Sp e c i e s C ol um bi a U ni ve r s i t y P r e s s N e w Y or k M C C O Y E D & H E C K K L 1976. B i oge ogr a p hy of c o r a l s s e a gr a s s e s a nd m a ngr ove s : a n a l t e r na t i ve t o t he c e nt e r of o r i gi n c o nc e pt Sy s t e m at i c Z ool ogy 25: 201 210. N O R R I S R D 2000. P e l a gi c s pe c i e s di ve r s i t y, bi o ge ogr a phy, a nd e vol ut i on P al e obi ol ogy 26 : 236 258 P E C H E N I K J A 2000. B i ol ogy of t he I nv e r t e br at e s 4 t h E di t i on. M c G r a w H i l l C om pa ni e s I nc B os t on.

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5 C H A P T E R 1: P H Y L O G E N E T I C R E L A T I O N S H I P S W I T H I N T H E F A M I L Y P L A C O B R A N C H I D A E I N T R O D U C T I O N W i t hi n t he P hyl um M ol l us c a t he G a s t r opoda a r e n um e r i c a l l y dom i na nt a t va r i ous t a xonom i c l e ve l s a nd c ont a i ns a t l e a s t 40, 000 de s c r i be d s pe c i e s ( P e c he ni k, 2000) A l t hou gh r e pr e s e nt i ng onl y a s m a l l po r t i on o f t hi s di ve r s i t y, t he O pi s t hob r a nc hi a i nc l ude s s om e of t he m os t f l a m boya nt ( nudi br a nc hs ) a nd un de r s t udi e d ( pt e r opods ) s pe c i e s T he c l a de S a c ogl os s a i s pa r t i c ul a r l y i nt e r e s t i ng i n t e r m s of t he s e c onda r y l os s of t he s he l l i n m a ny of t he f a m i l i e s a nd t he s ubs e que nt c ha nge s i n phys i ol ogy a nd be ha vi or t ha t m a y ha ve a c c om pa ni e d t hi s l os s ( J e ns e n, 1996, C i m i no & G hi s e l i n, 1998) W i t hi n t he S a c ogl os s a t he f a m i l y P l a c obr a nc hi da e G r a y, 184 0 e xhi bi t s a di ve r s e a r r a y of a da pt a t i ons t ha t a r e i nt e r e s t i ng i n t e r m s o f bot h t he i r e vol ut i on a nd t he i r e c ol ogi c a l a s pe c t s A va r i e t y o f l a r va l l i f e hi s t or i e s a r e know n f or t he m e m be r s o f t he f a m i l y r a ngi ng f r o m be nt hi c e nc a ps ul a t e d ( or di r e c t de ve l opm e nt ) t o hi ghl y va gi l e pl a nkt oni c de ve l opm e nt D e N e gr i & D e N e gr i ( 1876) f i r s t not e d e vi de nc e of pl a nt pi gm e nt a t i on i n t he di ge s t i ve gl a nds of E l y s i a a nd T a yl or ( 1968) pr ovi de d da t a i ndi c a t i ng a s ym bi ot i c r e l a t i ons hi p be t w e e n t he s l ugs a nd a l ga e I n m a ny c a s e s w hi l e f e e di ng on t he i r pr e f e r r e d f ood s our c e s pe c i e s e xt r a c t a ddi t i ona l e ne r gy by c om m a nde e r i ng t he c hl or opl a s t s f r om t he a l ga e ( R um pho, S um m e r & M a nha r t 2000) T hi s r e l a t i ons hi p i s pr oba bl y m or e a ppr opr i a t e l y t e r m e d kl e pt opl a s t y, be c a us e t he pl a s t i ds a r e r e m ove d or s t ol e n f r om t he

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6 a l ga e ( W a ugh & C l a r k, 1986) S om e s pe c i e s of P l a c obr a nc hi da e s uc h a s E t uc a a nd E l y s i e l l a pus i l l a ( o r i gi na l l y de s c r i be d a s E l y s i a hal i m e dae ) a r e be l i e ve d t o f e e d s ol e l y on H al i m e da s pp. ( J e ns e n, 1983) w hi l e ot he r s m a y be m or e ge ne r a l i s t t ype f e e de r s s uc h a s E s e r c a w hi c h pr e ys on H al ophi l a T hal as s i a a n d H al odul e ( J e ns e n, 1993) T he s e obs e r va t i ons m a y be a r e s ul t o f l i m i t e d know l e dge of f ood c hoi c e but m a y a l s o r e f l e c t m or phol ogi c a l c ons t r a i nt s i n f e e di ng s t r uc t ur e s ( J e ns e n, 1993) I nf or m a t i on on s ys t e m a t i c r e l a t i ons hi ps a m ong s pe c i e s w oul d be a us e f ul f r a m e w or k f o r t e s t s of c ha r a c t e r e vol ut i on i n t hi s f a m i l y J e ns e n ( 1996) a nd M i kke l s on ( 1998) r e c ogni z e d t w o s ubc l a de s w i t hi n t he S a c ogl os s a t he O xynoa c e a a nd P l a c obr a nc ha c e a w i t h t he O xynoa c e a b e i ng m o r e ba s a l T he P l a c obr a nc hi da e ( = E l ys i i da e ) a r e pl a c e d w i t h i n t he s upe r f a m i l y P l a c obr a nc hoi de a a nd i n t e r m s o f num be r s of s pe c i e s a r e r i va l e d onl y by t he L i m a pont i i da e G r a y, 1847 R e l a t i ve t o ot he r f a m i l i e s i n t he or de r S a c ogl os s a t he num be r of s pe c i e s a s s i gne d t o P l a c obr a nc hi da e G r a y, 1840 i s l a r ge w i t h 60 100 n a m e d s pe c i e s ( J e ns e n, 1997) S i nc e t he 1800's m e m be r s o f t hi s f a m i l y ha ve be e n va r i o us l y di vi de d i nt o a s f e w a s ni ne a nd a s m a ny a s 14 ge ne r a ( s e e J e ns e n, 1992) S om e t a xo nom i c s c he m e s ha ve r e s ul t e d i n t he a s s i gnm e nt of m onot ypi c ge ne r a t o f a m i l y ( P l ak ob r anc hus oc e l l at us t o P l a c obr a nc hi da e s e ns u M a r c u s 1982) N o a t t e m pt s t o de t e r m i ne t h e phyl oge ne t i c r e l a t i ons hi ps a m ong s pe c i e s ha ve be e n c onduc t e d pa r t l y be c a us e of nu m e r ous t a xonom i c c onf us i ons a nd t he l a r ge num be r o f na m e d s pe c i e s I n a ddi t i on t o t he s e f a c t or s m a ny s pe c i e s de s i gna t i ons a r e ba s e d on a s i ngl e s pe c i m e n a nd m os t popul a t i o ns s e e m t o e xpe r i e nc e a l t e r na t i ng de ns i t i e s r a ngi ng f r om e xt r e m e l y num e r ous t o no a ni m a l s pr e s e nt ( e g. E l y s i a c hl or ot i c a ; B l e a kne y, 1996)

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7 A not he r f a c t or t ha t m os t l i ke l y ha s l e d t o t he l a c k of a f a m i l y phyl oge ny i s t ha t m e m be r s of P l a c obr a nc hi da e a r e c ons e r va t i ve i n t e r m s of e xt e r na l va r i a t i on i n body f o r m G e ne r a l l y, c ol or a t i on or pa t t e r ns of c ol or a r e gi ve n i n s pe c i e s de s c r i pt i ons but onl y f r om l i ve s pe c i m e ns a s pr e s e r va t i ve s de s t r oy a l l c ol or e xc e pt f or b l a c k pi gm e nt s C ol or how e ve r m a y not be a good i ndi c a t or of r e pr oduc t i ve i s ol a t i on, a s di e t m a y a l s o de t e r m i ne c ol or ( M a r c us 1980) O t he r c om m on c ha r a c t e r s a r e t he pr e s e nc e of pa pi l l a e on he a d, r h i nophor e s a nd pa r a podi a P e r i c a r di um s ha pe a nd l e ngt h, a nd pa t t e r n of dor s a l ve s s e l s a ppe a r t o be ve r y r e l i a bl e ( B e r gh, 1872; M a r c us & M a r c us 1970; C a r l s on & H of f 1978) but m a y be s ubj e c t t o a ge va r i a t i on a n d a r e a f f e c t e d by pr e s e r va t i on ( M a r c us 1980) R a dul a r t e e t h c ha r a c t e r i s t i c s a r e i n t he m a j or i t y of de s c r i pt i ons but m a y pr ove t o be t oo pl a s t i c w i t h t oot h s ha pe di r e c t l y a f f e c t e d by di e t ( J e ns e n, 1993 ) s uc h t ha t a c om pr e he ns i ve s t udy of m ul t i pl e i ndi vi dua l s i s n e c e s s a r y t o e nc om pa s s bot h i nt r a s pe c i f i c a nd ont oge ne t i c va r i a t i on ( B e r t s c h, 1976) M ol e c ul a r da t a m a y pr ovi de i nf or m a t i ve c ha r a c t e r s f or t he e l uc i da t i on o f s ys t e m a t i c r e l a t i ons hi ps i n pa r t i c ul a r t he que s t i on of ge ne r i c l e ve l a s s i gnm e nt s a nd w he t he r t a xonom y r e f l e c t s t he e vol ut i ona r y hi s t or y. I n a p r e vi ous s t udy, J e ns e n ( 1992) us e d i nt e r na l a n a t om i c a l c ha r a c t e r s ( s ha pe of pha r ynx, r e pr oduc t i ve s ys t e m s pr e s e nc e / a bs e nc e of pha r ynge a l pouc h) t o di f f e r e nt i a t e s pe c i e s G os l i ne r ( 1995) f oc us e d on ge ne r a w i t hi n t he f a m i l y a nd p r opos e d a phyl oge ny ba s e d on 12 m or phol ogi c a l c ha r a c t e r s f or t e n t a xo nom i c uni t s H i s a na l ys i s de f i ne d t w o m a j or c l a de s w i t hi n t he f a m i l y but f a i l e d t o r e s ol v e m a ny of t he r e l a t i ons hi ps w i t hi n t he ge nus E l y s i a G o s l i ne r ( 1995) c onc l ude d t ha t t he f a m i l y w a s pa r a phyl e t i c a nd s ugge s t e d t ha t onl y t he ge ne r i c na m e s P l ak obr anc hus T hur i di l l a a nd E l y s i a be r e t a i ne d r e s ul t i ng i n

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8 t he l os s of f ou r ge ne r i c l e ve l de s i gna t i ons ( T r i dac hi e l l a, T r i dac hi a, E l y s i e l l a a nd P at t y c l ay a ) A f e w s t udi e s ha ve us e d m i t oc hondr i a l D N A s e que nc e da t a t o e l uc i da t e r e l a t i ons hi ps w i t hi n t he O pi s t hobr a nc hi a ( M e di na & W a l s h, 2000; T hol l e s s on, 1999) M e di na & W a l s h ( 2000) e xa m i ne d e vol ut i ona r y r e l a t i ons hi ps i n t he c l a de A pl ys i om or pha a nd c onc l ude d t ha t bot h of t he m i t oc hondr i a l r i bos om a l ge ne s a nd t he c yt oc hr om e c oxi da s e s ubuni t I ge ne w e r e a pp r opr i a t e f or r e s ol ut i on w i t hi n t he or de r a nd a t t he ge nus or s pe c i e s l e ve l r e s pe c t i ve l y. B a s s & K a r l ( 2006 ) us e d t he m i t oc hondr i a l ge ne s 16S a nd c ox 1 a nd t he nuc l e a r ge ne H i s t one 3 t o e xa m i ne ge ne r i c l e ve l di vi s i ons a nd f ound s uf f i c i e nt r e s ol ut i on a t t he ge ne r i c l e ve l I n t hi s s t udy, m ol e c ul e s a r e us e d t o r e c ons t r uc t t he e vol ut i ona r y hi s t or y of t he m e m be r s of t he f a m i l y P l a c obr a nc hi da e A hi e r a r c hi c a l ge ne t i c di ve r s i t y a ppr oa c h t o t he de l i ne a t i on of t a xonom i c uni t s i s e xpl or e d i n a n a t t e m pt t o t a ke a dva nt a ge o f t he l a r ge a m ount of i n f or m a t i on a va i l a bl e w i t h t he us e of ge ne s s uc h a s c yt oc hr om e c oxi da s e s ubuni t 1 ( c ox 1 ) l a r ge r i bos om a l s ubuni t ( 16 S ) a n d H i s t one 3 ( H 3 ) T hi s t ype of a ppr oa c h a l l ow s us t o us e t he de gr e e of di ve r ge nc e w i t hi n t he f a m i l y a s a ya r ds t i c k f o r t a xonom i c hi e r a r c hi e s ( B a s s & K a r l 2006) A l t ho ugh t a xonom y i s a hum a n c ons t r uc t e vol ut i ona r y hi s t or y s houl d not be ne gl e c t e d i n ou r a t t e m pt s t o de l i ne a t e hi e r a r c hi c a l l e ve l s T he ut i l i t y of t he s e t hr e e ge ne s f or phyl oge ne t i c r e c ons t r uc t i on i s t e s t e d us i ng m or e e xt a nt s pe c i e s w i t hi n t he f a m i l y. M ol e c ul a r s ys t e m a t i s t s ha ve t a ke n t he a ppr oa c h of us i ng s i ngl e i ndi vi dua l s a nd f e w s t udi e s i nc l ude i nf or m a t i on on w i t hi n s pe c i e s va r i a t i on of di f f e r e nt ge ne s ( but s e e F unk, 1999 ) W hi l e r e s e a r c he r s hope t ha t t he y a r e us i ng a ge ne t ha t i s a ppr op r i a t e f or t he

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9 t i m i ng of di ve r ge nc e t he y a r e s t udyi ng, t he r e i s o f t e nt i m e s l i t t l e i nf o r m a t i on a va i l a bl e t o a s s e s s t hi s e xc e pt t he pe r f or m a nc e of a pa r t i c ul a r ge ne or ge ne s i n s pe c i f i c t a xa ( L i n & D a nf or t h, 2004) W hi l e c om pl e t e t a xon s a m pl i ng of a l l de s c r i be d s pe c i e s i s a va unt e d goa l i t i s not a l w a ys a n op t i on f or r a r e s pe c i e s s uc h a s s a c ogl os s a n s T o ove r c om e s om e of t he p r obl e m s t ha t c a n be a s s oc i a t e d w i t h i nc om pl e t e t a xon s a m pl i ng a nd t o de t e r m i ne t he unde r l yi ng di s t r i but i on o f va r i a t i on i n pa r t i c ul a r ge ne s m ul t i p l e i ndi vi dua l s w e r e s e que nc e d f or t he va r i ous ge ne s us e d i n t hi s s t udy. I n s om e c a s e s t he s a m pl i ng of popul a t i ons ha s be e n good i n t e r m s of m ul t i pl e i nd i vi dua l s f r om m ul t i pl e l oc a t i ons ( e g T r i dac hi a c r i s pat a ) w he r e a s i n s om e s pe c i e s ( e g. E l y s i a obt us a a nd ot he r s ) onl y one i ndi vi dua l w a s a va i l a bl e f or a na l ys i s T he goa l w a s t o de ve l op a n e s t i m a t e of w i t hi n s pe c i e s va r i a t i on w he r e pos s i bl e ke e pi ng i n m i nd t he ul t i m a t e goa l o f i de nt i f yi ng r e l a t i ons hi ps a t hi ghe r l e ve l s U l t i m a t e l y t he ut i l i t y of va r i ous ge ne s f or phyl oge ne t i c s t udi e s a nd f or popul a t i on l e ve l s t udi e s w i t hi n t hi s gr oup c a n be a s s e s s e d. T he c ha r a c t e r i s t i c s i n t e r m s of nuc l e ot i de s ubs t i t ut i ons r e l a t i ve r a t e s of e vol ut i on a m ong t he ge ne s a nd s a t ur a t i on pa t t e r ns a l s o a r e e xpl or e d M A T E R I A L S A N D M E T H O D S A t ot a l of 31 de s c r i be d a nd t w o unna m e d s pe c i e s f r om P l a c obr a nc hi da e t w o s pe c i e s f r om B os e l l i i da e t w o s pe c i e s i n a s i ngl e g e nus f r om L i m a pont i i da e a nd one s pe c i e s f r om O xynoi da e ( T a bl e 1. 1) w e r e c ol l e c t e d a ne s t he t i z e d w i t h M gC l 2 a nd s t or e d i n 95% E t O H I n T a bl e 1. 1 a nd t h r oughout t he t e x t B ouc he t & R oc r oi ( 2005) nom e nc l a t ur e ha s be e n f ol l ow e d. T he ge ne r i c l e ve l de s i gna t i ons pr i or t o G os l i ne r ( 1995) ha ve a l s o be e n us e d. S a m pl e s w e r e c ol l e c t e d be t w e e n 2000 a nd 2005. S a m pl e s f r om a

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10 m i ni m um of t w o popu l a t i ons w e r e c ol l e c t e d f o r E l y s i a or nat a, E pat i na E s ubor nat a, E t uc a, E t i m i da, P l ak obr anc hus oc e l l at us T hur i di l l a r at na a nd T r i dac hi a c r i s pat a T ot a l c e l l D N A w a s i s ol a t e d f r om a s m a l l por t i on o f t he a nt e r i or e nd o f t he a ni m a l s ubj e c t e d t o a non boi l i ng c he l e x m e t hod ( W a l s h e t a l 1991) a nd us e d i n s ubs e que nt pol ym e r a s e c ha i n r e a c t i on ( P C R ) a m pl i f i c a t i ons of t hr e e ge ne s A l l t r e a t e d s a m pl e s w e r e di l ut e d w i t h 1X T E ( 10 m M T r i s 1 m M E D T A ; pH 7. 5 ) a nd s t or e d a t 20 C S e gm e nt s of t w o m i t oc hondr i a l ge ne s ( ~ 700 bp o f c yt oc hr om e c oxi da s e s ubuni t I a nd ~ 450 bp o f t he l a r ge s ubuni t R N A ) a nd one nu c l e a r ge ne ( ~ 380 bp of H i s t one 3) w e r e P C R a m pl i f i e d w i t h pr i m e r pa i r s r e s pe c t i ve l y, L C O 1490 5 G G T C A A C A A A T C A T A A A G A T A T T G G 3 a nd H C O 2198 5 T A A A C T T C A G G G T G A C C A A A A A A T C A 3 ( F ol m e r e t a l 1994 ) 16S s a r 5 C G C C T G T T T A T C A A A A A C A T 3 a nd 16s a 5 C T C C G G T T T G A A C T C A G A T C 3 ( K e s s i ng e t a l 1989) a nd H 3F 5 A T G G C T C G T A C C A A G C A G A C V G C 3 a nd H 3R 5 A T A T C C T T R G G C A T R A T R G T G A C 3 ( C ol ga n, P onde r & E ggl e r 2000) A m pl i f i c a t i on r e a c t i ons ( 25 o r 50 L ) c ons i s t e d of 1X buf f e r ( E nz ypol L T D D e nve r C O ) 1 5 uni t s of E nz ypol P l us 2000 pol ym e r a s e ( E nz ypol L T D D e nve r C O ) 0 2 m M e a c h dN T P s 3. 0 m M M gC l 2 ( C O I a nd 16S ) or 1. 5 m M M gC l 2 ( H 3) 0. 5 M o f e a c h pr i m e r 1. 0 M B e t a i ne 0. 12 g/ L o f bovi ne s e r um a l bum e n, a nd 2 0 4. 0 L of t e m pl a t e T he c yc l i ng c ondi t i ons f or t he c ox 1 a nd 16S pr i m e r s c ons i s t e d of 1 m i n. a t 95 C f ol l ow e d by 3 5 45 c yc l e s of 30 s e c a t 95 C 45 s e c a t 48 C a nd 1 m i n a t 72 C w i t h a f i na l e xt e ns i on of 3 m i n. a t 72 C C yc l i ng c ondi t i ons f or t he H 3 pr i m e r s c ons i s t e d of 1 c yc l e of 4 m i n a t 95 C 1 m i n. a t 50 C a nd 1 m i n a t 72 C f ol l ow e d by 35 c yc l e s of 45 s e c a t 95 C 30 s e c a t 52 C a nd 45 s e c a t 72 C a nd a

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11 f i na l e xt e ns i on of 3 m i n a t 72 C A t e m pl a t e f r e e r e a c t i on w a s i nc l ude d f or t he d e t e c t i on of c ont a m i na t i on. A m pl i c ons w e r e pur i f i e d us i ng s t e r i l e na nopur e w a t e r a nd 30, 000 M W M i l l i por e f i l t e r s ( M i l l i po r e I nc B e df or d, M A ) or a Q I A qui c k P C R pur i f i c a t i on ki t ( Q i a ge n, I nc V a l e nc i a C A ) T he m a s s of t he a m pl i c ons w a s de t e r m i ne d by c om p a r i ng e t hi di um br om i de s t a i ni ng i nt e ns i t y o f 2 0 5 0 L o f e a c h pu r i f i e d r e a c t i on r e l a t i ve t o a s t a nda r d m a s s D N A l a dde r ( I nvi t r oge n L i f e T e c hnol ogi e s C a r l s ba d, C A ) C yc l e s e que nc i ng r e a c t i ons ( A m e r s ha m E T T e r m i na t or K i t A m e r s ha m B i os c i e nc e s C or p. B i s c a t a w a y, N J ) w e r e c onduc t e d w i t h a ppr oxi m a t e l y 100 ng of pur i f i e d P C R pr oduc t a c c or di ng t o m a nuf a c t ur e r 's s pe c i f i c a t i ons a nd f l uor e s c e nt l y l a b e l e d pr oduc t s w e r e s i z e s or t e d a nd vi s ua l i z e d us i ng a n A B I 310 G e ne t i c A na l yz e r ( A p pl i e d B i os ys t e m s I nc F os t e r C i t y C A ) T he s e que nc e s f r om bot h s t r a nds of t he a m pl i c on w e r e c om pa r e d a nd e di t e d ( w he n ne e de d) us i ng S e que nc he r ( v4 1; G e ne C ode s C or p A nn A r bor M I ) T he 16S ge ne r e gi on f r a gm e nt s w e r e c om pa r e d t o pr e vi ous l y a l i g ne d A pl ys i om or pha s e c onda r y s t r uc t ur e us i ng S e a vi e w ( G a ul t i e r G uoy & G a ut i e r 1996) a nd hype r va r i a bl e r e gi ons w he r e no one a l i gnm e nt a ppe a r e d s upe r i or t o a not he r w e r e e xc l ude d f r om f ur t he r a na l ys e s T he ope n r e a di ng f r a m e s f or t he c ox 1 a nd H 3 ge ne s w e r e us e d t o a i d i n p r ope r a l i gnm e nt W h e r e pos s i bl e ( s a m pl e s a va i l a bl e ) t hr e e or m or e i ndi vi dua l s w e r e s c or e d f or t he 16S a nd c ox 1 ge ne s ( T a bl e 1 1) F or s pe c i e s w he r e m ul t i pl e i ndi v i dua l s w e r e s e que nc e d t he f ol l ow i ng a ppr oa c h w a s t a ke n t o r e m ove m t D N A ha pl ot ype s not de e m e d us e f ul f o r t he f a m i l y l e ve l a na l ys i s I f i nt r a s pe c i f i c 16S s e que nc e s di f f e r e d a t m o r e t ha n t w o pol ym or phi c s i t e s i ndi vi d ua l s e que nc e s w e r e e xpor t e d f r o m S e que nc he r A l l ha pl ot ype s

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12 w e r e us e d i n a p d i s t a nc e ba s e d N J a na l ys i s t o de t e r m i ne i f ha pl ot ype s w e r e m onophyl e t i c G e nB a nk s e que nc e s f r om A pl y s i a c al i f or ni c a, A s c obul l a f r agi l i s a nd a S ys t e l l om m a t ophor a O nc hi de l l a c e l t i c a w e r e i nc l ude d a s out gr oups ( T a bl e 1. 1 ) T w o pol ym or phi c s i t e s w e r e us e d a s a c ut o f f f or i nc l us i on i n t he N J a na l ys i s be c a us e t hi s s m a l l a m ount of va r i a t i on s houl d not r e s ul t i n non m onophyl y of t he ha pl ot ype s F or t he c ox 1 f r a gm e nt s e xhi bi t i ng m or e t ha n t w o pol ym or phi c s i t e s w i t hi n s pe c i e s 74 i ndi vi dua l s e que nc e s r e pr e s e nt i ng 30 s pe c i e s ( no c ox 1 da t a f or E l y s i a t r i s i nuat a ) t w o unna m e d s pe c i e s t w o s pe c i e s f r om B os e l l i i da e a nd t w o s pe c i e s f r om L i m a pont i i da e w e r e us e d i n a N J a na l ys i s A s w i t h t he 16 S ha pl ot ype s i f c ox 1 ha pl ot ype s w e r e not m onophyl e t i c i ndi vi dua l s w e r e r e t a i ne d f or f ur t he r a na l ys i s I f t h e br a nc he s w e r e a s l ong a s ot he r pu t a t i ve s pe c i e s s pe c i e s de s i gna t i on s w e r e que s t i ona bl e or popul a t i on s a m pl i ng w a s gr e a t e r t ha n o r e qua l t o f i ve i ndi vi dua l s t he n t he s e i ndi vi dua l s w e r e a l s o r e t a i ne d f or f ur t he r a na l ys i s I n ot he r c a s e s t he de e pe s t br a nc h of t he ha pl ot ype c l us t e r w a s c ho s e n f or f ur t he r a na l ys i s T o e va l ua t e t he r e l a t i ve di ve r ge nc e l e ve l s a m ong t a xa t he be s t f i t m ode l o f e vol ut i on a s s e l e c t e d i n M ode l t e s t us i ng A ka i ke i n f or m a t i on c r i t e r i a ( v3. 7 ; P os a da & C r a nda l l 1998) w a s de t e r m i ne d f or bot h t he m i t oc hondr i a l D N A da t a s e t e xc l udi ng put a t i ve 3 r d pos i t i ons of t he c ox 1 f r a gm e nt a nd t h e nuc l e a r D N A da t a s e t P ut a t i ve t hi r d pos i t i ons of t he c ox 1 f r a gm e nt w e r e e xc l ude d a f t e r t he i nd i c a t i on of s a t ur a t i on a s e vi de nc e d by a non l i ne a r r e l a t i ons hi p i n a pl ot of t he num be r of s ub s t i t ut i ons ve r s us unc or r e c t e d pa i r w i s e pe r c e nt s e que nc e di f f e r e nc e I ndi vi dua l s pe c i e s f or w hi c h da t a w e r e m i s s i ng i n e i t he r o f t he m t D N A ge ne s w e r e e xc l ud e d f r om t he m ode l s e l e c t i on a nd f r o m

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13 di ve r ge nc e e s t i m a t e s E s t i m a t e s of di ve r ge nc e w e r e ge ne r a t e d u s i ng a m a xi m um l i ke l i hood e s t i m a t or w i t h P A U P ( v4. 0b10 ; S w of f or d, 1998 ) A B a ye s i a n f r a m e w or k w a s us e d t o a s s e s s r e l a t i ons hi ps a m ong t he s pe c i e s of i nt e r e s t ( M r B a ye s v3. 1. 2 ; H ue l s e nbe c k & R onqui s t 2001, R onqui s t & H ue l s e nbe c k, 2003) A l l a na l ys e s w e r e r un i n a n M P I e nvi r onm e nt ( A l t e ka r e t a l 2004 ) us i ng t he R e s e a r c h C om put i ng C or e F a c i l i t y ( R C C F ) a t t he U ni ve r s i t y of S ou t h F l o r i da T hr e e s e pa r a t e a na l ys e s w e r e c onduc t e d: 1) m t D N A da t a ( 16S a nd c ox 1 ) 2 ) nuc l e a r da t a ( H 3) a nd 3) c om bi ne d m t D N A a nd nu c l e a r da t a T he m t D N A da t a w e r e di vi de d i nt o 4 pa r t i t i ons : put a t i ve 1 s t 2 n d a nd 3 r d c odon pos i t i ons of c ox 1 a nd a l l pos i t i ons o f 16S e xc e pt f or hype r va r i a bl e r e gi ons F o r t he m t D N A da t a s e t t w o m ode l pe r m ut a t i ons w e r e t e s t e d 1) G e ne r a l t i m e r e ve r s i bl e a nd ga m m a di s t r i but i on ( G T R + G ) by ge ne f or 16S a nd by pos i t i on f o r c ox 1 a nd 2) G e ne r a l t i m e r e ve r s i bl e w i t h bot h i nva r i a nt s i t e s a nd s i t e s f ol l ow i ng a ga m m a di s t r i but i on ( G T R + I + G ) by ge ne f or 16S a nd by pos i t i on f or c ox 1 ge ne F o r t he nuc l e a r da t a s e t t w o m ode l s w e r e a l s o t e s t e d 1) G T R + I + G by pos i t i on a nd 2) G T R + G by pos i t i on. A ge ne r a l m ode l f or by g e ne f or H i s t one 3 w a s not t e s t e d be c a us e of t he i m pr ove m e nt i n l i ke l i hood s c or e s w he n a na l yz i ng pr ot e i n da t a by pos i t i on ( S ha pi r o, R a m ba ut & D r u m m ond, 2005) T he m o s t a ppr opr i a t e m ode l of e vol ut i on w a s s e l e c t e d by a ppl yi ng a l i ke l i hood r a t i o t e s t ( 2 # L nL t e s t e d w i t h a $ 2 di s t r i bu t i on; F e l s e ns t e i n, 1988) t o t he m a xi m um l i ke l i hood s c or e s pos t bur ni n. T he m ode l c ondi t i ons s e l e c t e d unde r t he s e s e pa r a t e a na l ys e s w e r e t he n us e d t o de f i ne t he m ode l f o r t he c om bi ne d da t a s e t I n a l l B a ye s i a n s e a r c he s t w o r uns of 1, 000 000 ge ne r a t i ons w e r e c onduc t e d s i m ul t a ne ous l y a nd s a m pl e d e ve r y 1, 00 0 ge ne r a t i ons T o a s s e s s c onve r ge nc e of t he M C M C s a m pl i ng r uns t he a ve r a ge s t a nda r d de vi a t i on of t he s pl i t f r e que nc i e s of

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14 t he t w o r uns w a s i ns pe c t e d a nd i f gr e a t e r t ha n 0 01 a n a ddi t i ona l one m i l l i on ge ne r a t i ons w e r e r un. T hi s pr oc e s s w a s r e pe a t e d unt i l t he a ve r a ge s t a nda r d de vi a t i on of t he s pl i t f r e que nc i e s of t he t w o r uns w a s l e s s t ha n 0. 01 T o de t e r m i ne t he bur ni n num be r t he pa r a m e t e r s of a l l i ndi vi dua l r uns w e r e s um m a r i z e d a nd t he i ni t i a l r uns be l ow t he a s ym pt ot e w e r e di s c a r de d. I n ge ne r a l onl y t he l a s t 1000 s a m pl e s of ge ne r a t i ons f r om bot h r uns w e r e us e d t o de t e r m i ne pa r a m e t e r a nd p os t e r i or pr oba bi l i t y va l ue s I n a ddi t i on t o a s s e s s i ng c onve r ge nc e dur i ng t he a na l ys i s t he c ha i n s w a p i nf or m a t i on f or e a c h i ndi vi dua l r un w a s e xa m i ne d a nd i f t he p r opor t i on of s uc c e s s f ul s t a t e e xc ha nge s be t w e e n c ha i ns w a s be t w e e n 10 a nd 70% t he n c onve r ge nc e w i t hi n t he i ndi vi dua l r uns w a s a s s um e d. M ode l pa r a m e t e r s pr opo r t i on of i nva r i a nt s i t e s ga m m a di s t r i but i on a nd nuc l e ot i de s ubs t i t ut i on r a t e s w e r e e s t i m a t e d i n de pe nde nt l y f or e a c h da t a s e t us i ng M r B a ye s va l ue s of f our c ha i ns a nd 0 1 f or t he c ha i n t e m pe r a t ur e pa r a m e t e r M ul t i pl e r uns s t a r t i ng f r om r a ndom t r e e s w e r e c onduc t e d t o ve r i f y c onve r ge nc e L e ve l s of s uppor t f o r node s w e r e c ons i de r e d hi gh i f t he pos t e r i or pr oba b i l i t y va l ue ( ppv) w a s > 95, m ode r a t e i f be t w e e n 80 94 a nd l ow i f < 79. T o de t e r m i ne t he r e l a t i ve r a t e s of e vol ut i on of t he t h r e e ge ne s a s e pa r a t e B a ye s i a n a na l ys i s of one m i l l i on ge ne r a t i ons w a s c onduc t e d on t he c om bi ne d da t a s e t us i ng a G T R pl us s i t e s pe c i f i c r a t e ( S S R ) m ode l ( L i n & D a nf or t h 2004, D a nf or t h, L i n & F a ng, 2005) M a xi m um pa r s i m ony a na l ys i s a s i m pl e m e nt e d i n P A U P ( v4 010b; S w o f f or d 1998) w a s a l s o us e d f or phyl oge ny r e c ons t r uc t i on pr i m a r i l y t o a ppl y t r a ns ve r s i on pa r s i m ony t o s i gni f i c a nt l y s a t ur a t e d s i t e s ( W oe s e e t a l 1991) A n i nc ong r ue nc e l e ngt h di f f e r e nc e ( I L D ) t e s t a s i m pl e m e nt e d i n P A U P w a s c onduc t e d t o de t e r m i ne i f t he da t a c oul d be c om bi ne d i nt o a s i ngl e m a xi m u m pa r s i m ony a na l ys i s ( F a r r i s e t a l 1994

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15 S w of f or d 1998) A he u r i s t i c s e a r c h i nc l udi ng 300 r a ndom s t e pw i s e a ddi t i ons w i t h T B R w a s r un on bot h t he c om bi ne d da t a s e t a nd a c om bi ne d da t a s e t w i t h t r a ns ve r s i ons of c ox 1 c ode d a s R Y ( P hi l l i ps & P e nny, 2003) B oot s t r a p s uppor t f o r i ndi v i dua l node s w a s ge ne r a t e d f r om 100 r e pl i c a t e s us i ng a f ul l he ur i s t i c s e a r c h ( F e l s e ns t e i n, 1985) A ha r d pol y t om y i n phyl oge ne t i c r e c ons t r uc t i ons i ndi c a t e s m ul t i pl e s i m ul t a ne ous s pe c i a t i on e ve nt s w hi l e s of t pol yt om i e s a r e c a us e d by t he l a c k o f una m bi guous c ha r a c t e r s T o e xpl or e t he i s s ue of a ha r d o r s of t p ol yt om y us i ng B a ye s i a n a na l ys i s a l i m i t e d s e t of t a xa w a s r un t o s e e i f s i gni f i c a nt phy l oge ne t i c s t r uc t ur e w a s pr e s e nt I n t hi s a na l ys i s t a xa w e r e c hos e n ba s e d on t he r e s ol ut i on of t e r m i na l c l a de s f ound i n a c om bi ne d da t a a na l ys i s A B a ye s i a n a na l ys i s us i ng t he s hor t e s t br a nc he s f r o m r e s ol ve d c l a de s w a s us e d t o t e s t i f t he r e w a s s i gni f i c a nt phyl oge ne t i c i nf or m a t i on pr e s e nt t o r e s ol ve t he pol yt om y. I f s i gni f i c a nt phyl oge ne t i c r e s ol ut i on i s i ndi c a t e d, t he n a s i gni f i c a nt num be r o f c ha r a c t e r s a r e a va i l a bl e f or p hyl oge ne t i c r e c ons t r uc t i on. I f no s i gni f i c a nt ph yl oge ne t i c r e s ol ut i on i s f ound, t he n s uf f i c i e nt phyl oge ne t i c c ha r a c t e r s a r e not a va i l a bl e f or r e s ol ut i on a t t hi s l e ve l I f s i gni f i c a nt phyl oge ne t i c r e s ol ut i on i s i ndi c a t e d t he n t w o s c e na r i os a r e pos s i bl e 1) l ong b r a nc h s ubdi vi s i on by m ul t i p l e s uc c e s s i ve b r a nc he s a nd 2) a ha r d pol yt om y. A s e c ond B a ye s i a n a na l ys i s us i ng t he l onge s t br a nc h w a s c hos e n t o t e s t i f s hor t b r a nc he s i n t he c om bi ne d a na l ys i s a r e di vi di ng m ul t i pl e l ong br a nc he s I f s i gni f i c a nt s t r uc t ur e i s i ndi c a t e d t he n m ul t i pl e s uc c e s s i ve br a nc he s a r e di vi di ng l ong br a nc he s I f no s i gni f i c a nt s t r uc t ur e i s i ndi c a t e d t he n a ha r d pol yt om y c a nnot be r e j e c t e d.

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16 R E S U L T S V ar i at i on at t he i ndi v i dual l e v e l F or s i x s pe c i e s no va r i a t i on a m ong 16S s e que nc e s w a s i de nt i f i e d a nd f or 10 i ngr oup s pe c i e s onl y on e i ndi vi dua l w a s a va i l a bl e f or a na l ys i s I n 12 s pe c i e s one or t w o pol ym or phi c s i t e s w e r e i de nt i f i e d a m ong i nd i vi dua l s a nd one i ndi vi dua l w a s c hos e n ba s e d on m a xi m um s e que nc e l e ngt h or r a ndom l y i f s e que nc e l e ngt h di d not di f f e r I n s i x c a s e s i ndi vi dua l s e xhi bi t e d m or e t ha n t w o pol ym o r phi c s i t e s a nd m ul t i pl e ge ogr a phi c a l l oc a t i ons w e r e s a m pl e d; t he r e f or e m ul t i p l e i ndi vi d ua l s w e r e us e d i n t he N J a na l ys i s T hi s pr oc e s s r e s ul t e d i n t he s e l e c t i on o f 56 i ndi vi d ua l s e que nc e s r e pr e s e nt i ng 31 de s c r i be d s pe c i e s w i t hi n P l a c obr a nc hi da e t w o unn a m e d s pe c i e s t w o s pe c i e s f r om B os e l l i i da e t w o s pe c i e s f r om L i m a pont i i da e a nd o ne s pe c i e s of O xynoi da e f or t he N J a na l ys i s of 16S I f t he ha pl ot ype s di d not c l us t e r t he y w e r e r e t a i ne d f or f ur t he r a na l ys i s T he r e s ul t i ng l i s t of i ndi vi dua l s r e t a i ne d f r om i ns pe c t i on of bot h t he 16S a nd c ox 1 ha pl ot ype s w a s m os t l y c onc or da nt i e de e pe s t l i ne a ge i n a l l c om pa r i s ons I n one c a s e t he de e pe s t br a nc h of t he c ox 1 N J t r e e di d not c oi nc i de w i t h t he s a m e i ndi vi dua l i n t he 16S a na l ys i s ( popul a t i ons of T r i dac hi a c r i s pat a ) I n t w o ot he r c a s e s w he r e t he de e pe s t l i ne a ge w a s not c onc or da nt E l y s i e l l a pus i l l a a nd E l y s i a c hl or ot i c a t he c ox 1 s e que nc e f r a gm e nt w a s s hor t e r o r 16 S s e que nc e da t a w e r e n ot a va i l a bl e f or t ha t i ndi vi dua l A t o t a l of 1165 nuc l e ot i de s ( 16S : 535 nt a l i gne d a n d c ox 1 : 630 nt ) w e r e c onc a t e na t e d f or a l l i nd i vi dua l s s e l e c t e d i n t hi s pr o c e s s r e s ul t i ng i n 56 i ndi vi dua l s e que nc e s ( 59 i nc l udi ng out g r oups ) T w o r e gi ons c om pr i s i ng a t ot a l of 87 pos i t i ons of t he 16S a l i gnm e nt w e r e hi ghl y va r i a bl e a nd w e r e e xc l ude d. T he s e i ndi vi dua l s w e r e t he n

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17 us e d i n a B a ye s i a n a na l ys i s ( 1. 5 m i l l i on ge ne r a t i on s ) t o c onf i r m t he m onophyl y o f s e l e c t e d ha pl opt ype s L e s s va r i a t i on w i t hi n s pe c i e s w a s i de nt i f i e d i n t he H 3 s e que nc e s F or 19 s pe c i e s onl y one i ndi vi dua l w a s s e que nc e d. F or 16 s pe c i e s w he r e m ul t i pl e i nd i vi dua l s w e r e s e que nc e d t he m a j or i t y of c a s e s ( 10/ 16) r e s ul t e d i n m or e t ha n one pol ym o r phi c s i t e a nd t he s e i ndi vi dua l s w e r e us e d i n t he a na l ys i s A t ot a l of 321 nuc l e ot i de s w a s a l i g ne d ( A pl y s i a c al i f or ni c a A Y 064472, a s a r e f e r e nc e s e que nc e ) f r om 47 i ndi vi dua l s r e pr e s e nt i ng 31 s pe c i e s of P l a c obr a nc hi da e one un na m e d s pe c i e s t w o s pe c i e s of B os e l l i i da e t w o s pe c i e s of L i m a pont i i da e a nd one s pe c i e s of O xynoi da e A r e pr e s e nt a t i ve of t he S ys t e l l om m a t ophor a O nc hi di um s p. w a s a l s o i nc l ude d a nd de s i gna t e d a s t he out gr oup. W i t hi n t he 31 s pe c i e s of P l a c obr a nc hi da e da t a f r o m m ul t i p l e popul a t i ons w e r e i nc l ude d. F o r e xa m pl e f or P l ak obr anc hus oc e l l at us of t he t h r e e i ndi vi dua l s s e que nc e d t w o w e r e f r om H a w a i i t he t hi r d w a s f r o m G ua m a nd t hr e e pol ym or phi c s i t e s w e r e i de nt i f i e d i n s e que nc e s f r om t he s e t w o l oc a t i ons T he onl y popul a t i on s a m pl e s not r e pr e s e nt e d i n t he a na l ys i s a r e f or E l y s i a t uc a H 3 w a s s uc c e s s f ul l y a m pl i f i e d a nd s e que nc e d f r om t w o i n di vi dua l s f r om t he F l o r i da K e ys onl y. Sat ur at i on t e s t s f or pr ot e i n c odi ng ge ne s S a t ur a t i on by pos i t i on w a s e xa m i ne d f o r t he c ox 1 a nd H 3 ge ne us i ng unc or r e c t e d p di s t a nc e s a nd a bs ol ut e di f f e r e nc e s N o e vi de nc e of s a t ur a t i on w a s f ound f or 1 s t a nd 2 n d pos i t i ons of e i t he r ge ne T o a s s e s s s a t ur a t i on a t 3 r d pos i t i ons unc or r e c t e d p di s t a nc e s f or 3 r d pos i t i on t r a ns ve r s i ons w e r e pl ot t e d a ga i ns t t he unc or r e c t e d p di s t a nc e s f or a l l pos i t i ons a nd s a t ur a t i on i n bot h ge ne s w a s i ndi c a t e d by t he a s ym pt ot i c c ur ve ( F i gur e 1. 1A a nd 1 1B ) W he n 3 r d pos i t i on t r a ns i t i ons a nd t r a ns ve r s i ons w e r e pl ot t e d i ndi vi dua l l y

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18 t he r e w a s a n i ndi c a t i on o f non s a t ur a t i on of t r a ns i t i ons a t va r i ous t a xonom i c l e ve l s I n 467 of 1540 c om pa r i s ons i nvol vi ng t he c ox 1 ge ne a nd i n 1042 o f 1176 c om pa r i s ons i nvol vi ng t he H 3 ge ne no s a t ur a t i on w a s i ndi c a t e d i n t e r m s of t r a ns i t i ons ve r s us t r a ns ve r s i ons F or t he c ox 1 ge ne m os t o f t he s e no n s a t ur a t e d c a s e s i nvol ve d i nt r a s pe c i f i c l e ve l c om pa r i s ons but s om e a l s o i nvol ve d uppe r l e ve l c om pa r i s ons F or t he H 3 da t a s e t w he r e t he num be r o f t r a ns ve r s i ons w a s gr e a t e r t ha n t r a ns i t i ons i e s a t ur a t i on ( 134 c om pa r i s ons ) no c l e a r pa t t e r n i nd i c a t i ng w hi c h t a xonom i c l e ve l t hi s w a s oc c ur r i ng a t w a s a va i l a bl e I n m os t c a s e s t he c om pa r i s ons i nv ol ve d de e pe r t a xonom i c l e ve l s s uc h a s or di na l bu t t he r e w e r e s ha l l ow e r l e ve l s r e p r e s e nt e d a s w e l l D i v e r ge nc e l e v e l s D i ve r ge nc e l e ve l s w e r e e s t i m a t e d i n m ul t i pl e w a ys I nt r a s pe c i f i c d i ve r ge nc e of t he 16S a nd c ox 1 da t a s e t s w e r e de t e r m i ne d bot h i nde pe nde nt l y a n d i n t he c onc a t e na t e d f or m a t T he ove r a l l a ve r a ge i nt r a s pe c i f i c d i ve r ge nc e i n 16S a l one w a s 0. 0211 + 0. 0172 ( r a nge : 0. 0000 0. 0527 ) ba s e d on a T r a ns ve r s i ona l m ode l w i t h i nva r i a nt s i t e s a nd s i t e s f ol l ow i ng a ga m m a di s t r i but i on ( T V M + I + G ) a s s e l e c t e d by A I C i n M ode l t e s t ( T a bl e 1 2) F or t he c ox 1 e s t i m a t e of di ve r ge nc e ba s e d on a T r a ns i t i ona l m ode l w i t h i nva r i a nt s i t e s a nd s i t e s f ol l ow i ng a ga m m a di s t r i but i on ( T I M + I + G ) a s s e l e c t e d by A I C i n M ode l t e s t a l l pos i t i ons w e r e i nc l ude d i n t he a na l ys i s a s s a t ur a t i on w a s not a n i s s ue a t t he w i t hi n s pe c i e s l e ve l T he ove r a l l i nt r a s pe c i f i c di ve r ge nc e w a s 0. 0329 + 0. 0388 ( r a nge : 0. 0035 0. 1098) T a xonom i c l e ve l s hi ghe r t ha n i n t r a s pe c i f i c l e ve l w e r e no t e xa m i ne d us i ng t he i ndi vi dua l da t a s e t s due t o a ppa r e nt s a t ur a t i on o f 3 r d pos i t i ons i n c ox 1 T he ove r a l l m ode l of e vol ut i on f or t he m t D N A da t a s e t w a s G T R + I + G ( T a bl e 1. 2) A ve r a ge e s t i m a t e s of di ve r ge nc e w e r e ge ne r a t e d a t va r i ous t a xonom i c l e ve l s

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19 r a ngi ng f r o m i nt r a s pe c i f i c t o be t w e e n c l a de s ( T a b l e 1. 3) B e c a us e of t he i m pa c t o f m i s s i ng da t a ( s i gni f i c a nt i nf l a t i on of di ve r ge nc e e s t i m a t e ) no e s t i m a t e of di ve r ge nc e i s a va i l a bl e f or O xynoi da e ve r s us ot he r s a c ogl os s a n f a m i l i e s a nd E l y s i a t r i s i nuat a w a s not i nc l ude d be c a us e of t he l a c k of c ox 1 da t a U nna m e d s pe c i e s w e r e a l s o r e m ove d f r om t hi s a na l ys i s T he a ve r a ge i nt r a s pe c i f i c di ve r ge nc e d = 0. 0135 + 0. 00 80 ( r a nge : 0. 0027 0. 0304 ) i s l e s s t ha n t he e s t i m a t e de r i ve d f r o m c o x 1 a l one w hi c h i s not s ur pr i s i ng a s 3 r d pos i t i ons w e r e not i nc l ude d i n t hi s e s t i m a t e I n t e r ge ne r i c d = 0. 0909 + 0 0162 ( r a nge : 0. 0546 0. 1175 ) a nd i nt e r f a m i l i a l d = 0 2383 + 0. 1084 ( r a nge : 0. 0975 0. 3672 ) a ve r a ge s w e r e di f f e r e nt but t he r a nge s of di ve r ge n c e a r e ove r l a ppi ng. A ve r a ge di ve r ge nc e s pl us t he s t a nda r d de vi a t i on a t va r i ous t a x onom i c l e ve l s a r e pr e s e nt e d i n F i gur e 1. 2 F o r t he m t D N A da t a s e t t he r e i s c l e a r c onc or da nc e be t w e e n t a xonom i c l e ve l pr e G os l i ne r ( 1995) a nd di ve r ge nc e e s t i m a t e s up t o t he f a m i l y l e ve l A t t hi s t a xonom i c l e ve l a nd a bove t he di ve r ge nc e s a r e not c ongr ue nt w i t h t a xonom y ( F i gu r e 1. 2) A l t hough 3 r d pos i t i ons of H i s t one 3 a r e s a t ur a t e d, t he s e pos i t i ons c oul d not be de l e t e d t o ge ne r a t e a m ode l of e vol ut i on. F e w ( 0 1) c ha nge s oc c ur a t 2 n d pos i t i on of H i s t one 3 r e s ul t i ng i n hi ghl y s ke w e d e s t i m a t e s of t he r e ve r s e m a t r i x of nuc l e ot i de c ha nge s T he r e f o r e a l l pos i t i ons w e r e us e d t o ge n e r a t e a G T R + I + G m ode l of e vol ut i on ( T a bl e 1 2) F or t he m a j or i t y of i nt r a s pe c i f i c c om pa r i s ons t he di ve r ge nc e l e ve l w a s l e s s t ha n 1% e xc e pt f or E l y s i a or nat a a nd P l ak obr anc hus oc e l l at us w i t h t he ove r a l l d = 0. 0117 + 0 0072 ( r a nge : 0 0045 0 0238) ( T a bl e 1 4) I nt e r ge ne r i c c om pa r i s ons w i t hi n t he P l a c obr a nc hi da e a ve r a ge d = 0 1942 + 0 0498 ( r a nge : 0. 1014 0. 2494 ) a nd i nt e r f a m i l i a l c om pa r i s ons a ve r a ge d = 0 2674 + 0. 0487 ( r a ng e : 0 2098 0 3240) e xhi bi t e d ove r l a p i n t e r m s of t he i r r a nge s W he n a ve r a ge di ve r ge nc e s a nd s t a nda r d de vi a t i ons a r e

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20 pl a c e d i n a c om pa r a t i ve c ont e xt ( F i gu r e 1 3) l e s s c onc or da nc e i s i ndi c a t e d a s w i t h t he m t D N A da t a s e t ( F i gur e 1 2) W i t h H i s t one 3 t he c onc or da nc e t o t a xonom i c l e ve l b r e a ks dow n a t t he ge ne r i c l e ve l P hy l oge ny F r om t he B a ye s i a n a na l ys e s of G T R + G a nd G T R + I + G m ode l s a ppl i e d t o t he c onc a t e na t e d m t D N A da t a s e t t he l a t t e r m ode l w a s c hos e n ba s e d on a l i ke l i hood r a t i o t e s t ( L R = 17 44; d f = 3, P < 0. 05 ) B e c a us e of di s c r e p a nc i e s a m ong s t udi e s a s t o t he s i s t e r gr oup of t he S a c ogl os s a ( but s e e G r a nde e t a l 200 4) or c om pl e t e l a c k o f r e s ol ut i on f ound by s om e a ut ho r s ( D a yr a t & T i l l i e r 2003) t h e c hoi c e of out g r oup w a s unc l e a r a l t hough S ys t e l l om m a t ophor a a ppe a r e d t o be ba s a l i n m os t ge ne t r e e s ( G r a nde e t a l 2004; V onne m a nn e t a l 2005) I ni t i a l l y m ul t i pl e opi s t hobr a nc hs w e r e us e d t o a s s e s s t he i m pa c t a nd r e s ol ut i on o f a l t e r na t i ve out gr oups T h e m t D N A a na l ys i s r e s ul t e d i n a pol yt om y be t w e e n a l l ot he r opi s t hobr a nc hs a nd t he S a c ogl os s a S ubs e que nt l y, m e m be r s of S ys t e l l om m a t ophor a a nd A pl ys i om or pha w e r e u s e d be c a us e H i s t one 3 da t a w e r e a va i l a bl e f or t he s e t a xa M i t oc hondr i a l D N A s upp or t e d t he m onophyl y of t he S a c ogl os s a us e d i n a l l a na l ys e s w he n S ys t e l l om m a t ophor a or A pl ys i om or pha w a s de s i gna t e d a s a n out gr oup a s di d t he us e of A s c obul l a f r agi l i s a nd O x y noe ant i l l ar um ( F i gur e 1. 4 ) F or t he H 3 da t a s e t a G T R + I + G by pos i t i on m ode l w a s c hos e n ba s e d on a L R t e s t ( L R = 54 84, df = 3, P < 0 05) N o t opol ogi c a l di f f e r e nc e s w e r e not e d i n t he phyl oge ni e s f r om t he G T R + G a nd G T R + I + G m ode l s F i gur e 1 5 i l l us t r a t e s t he l a c k of r e s ol ut i on a t de e pe r node s a m ong t he ope r a t i ona l t a xonom i c uni t s ( O T U s ) e xa m i ne d. T he r e i s s uppor t f or s om e node s w i t hi n t he phyl og e ny s uc h a s t he r e l a t i ons hi ps w i t hi n t he c l a de c om pr i s i ng t he t r i da c hi ds a nd E c anguz ua, E s e r c a, E c hl or ot i c a, a nd E v i r i di s

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21 T he m i t oc hondr i a l D N A da t a s e t pr ovi de d be t t e r a l be i t i nc om pl e t e phyl oge ne t i c r e s ol ut i on ( F i gu r e 1. 4 ) M os t of t he c ongr ue nc e a m ong t he m i t oc hond r i a l a nd nuc l e a r phyl oge ni e s i s obs e r va bl e a t t he s pe c i e s l e ve l F or e xa m pl e bot h phyl oge ni e s r e c ove r e d t he c l a de c om pr i s i ng t he t r i da c hi ds pl us E l y s i a c anguz ua, E s e r c a, E c hl or ot i c a a nd E v i r i di s I n t hi s i ns t a nc e H i s t one 3 pr ovi de d m o r e r e s ol ut i on t ha n t he m i t oc hond r i a l ge ne s T he c l a de c om p r i s i ng E or nat a E r uf e s c e ns E obt us a, E t r i s i nuat a, E c f j aponi c a a nd E l y s i a s p. 42 w a s a l s o r e c ove r e d i n b ot h phyl oge ni e s T he pos i t i on of E ni gr oc api t at a di f f e r e d i n t ha t i t g r oupe d, a l be i t a t l ow e r pos t e r i or p r oba bi l i t y va l ue s ( ppv) w i t h a not he r c l a de i n t he H i s t one 3 phyl oge ny. B e yond t he s e c l a de s t he onl y ot he r c ongr ue nc i e s not e d a r e a t t he popul a t i on l e ve l N uc l e ot i de s ubs t i t ut i on pat t e r ns and r e l at i v e r at e s T he pr opor t i on o f nuc l e ot i de s ( i nc l udi ng 95% c onf i de nc e i nt e r va l s ) f r o m t he G T R + I + G by ge ne m ode l i l l us t r a t e a n A T bi a s i n bot h m i t oc hondr i a l ge ne s w he n c om pa r e d t o t he nuc l e a r pr ot e i n c odi ng ge ne ( T a bl e 1. 5, F i gur e 1. 6A ) T he c om pos i t i on of t he r i bos om a l a nd pr o t e i n c odi ng ge ne s a r e s i m i l a r e xc e pt f o r di f f e r e nc e s i n A a nd T T he A T bi a s i n m i t oc hond r i a l D N A i s a l s o a ppa r e nt w he n pr ot e i n c odi ng ge ne s a r e c om pa r e d by pos i t i on ( F i gur e 1. 6B ) T hi r d pos i t i o ns of c ox 1 a r e s t r ongl y A T b i a s e d, a c c ount i ng f or 80 % of t he nuc l e ot i de s T hi s A T bi a s i s a l s o obs e r ve d i n 1 s t a nd 2 n d pos i t i ons but i s not a s s t r ong r e l a t i ve t o 3 r d pos i t i on s T he nuc l e a r p r ot e i n c odi ng ge ne e xhi bi t s a s i gni f i c a nt l y l ow e r pr opor t i on o f A T a t 3 r d pos i t i ons w i t h T hi ghe r t ha n A A t 1 s t a nd 2 n d pos i t i ons t he r e i s a r e ve r s a l of t hi s t r e nd w i t h m or e A s t ha n T s but i s s i gni f i c a nt l y di f f e r e nt a s i nd i c a t e d by t he 95% c on f i de nc e i nt e r va l s onl y f o r 1 s t pos i t i ons

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22 T he r e l a t i ve r a t e of e vol ut i on ( i nc l udi ng 95 % c onf i de nc e i nt e r va l s ) ge ne r a t e d us i ng G T R + S S R by ge ne a nd by pos i t i on m ode l s i ndi c a t e d t ha t bot h m i t oc hondr i a l ge ne s a r e f a s t e r t ha n t he nuc l e a r pr ot e i n c odi ng ge ne ( F i gur e 1. 7A & B ) T he 3 r d pos i t i ons of t he c ox 1 ge ne w hi c h e xhi bi t t he hi gh e s t r e l a t i ve r a t e o f m ut a t i on w he n c om pa r e d t o a l l ot he r pos i t i ons a ppe a r s t o be dr i vi ng t hi s di f f e r e nc e i n r e l a t i ve r a t e f or t he c ox 1 ge ne ( F i gur e 1. 7B ) B ot h m i t oc hondr i a l ge ne s e xhi bi t hi ghl y s ke w e d t r a ns i t i on t o t r a ns ve r s i on bi a s w he n t he r e l a t i ve r a t e s of t he s ubs t i t ut i on m a t r i x d e t e r m i ne d f or e a c h ge ne a r e e xa m i ne d ( F i gur e 1 8) T he nuc l e a r pr ot e i n c odi ng ge ne a l s o e xhi bi t s a t r a ns i t i on t o t r a ns ve r s i on bi a s but not a s hi gh a s i n t he m t D N A da t a s e t T he a l pha s ha pe ( % ) o f t he ga m m a pa r a m e t e r r a ng e d f r om 34. 12 98 02 f or 2 n d pos i t i ons i n bot h p r ot e i n c odi ng ge ne s a nd 1 s t pos i t i ons i n t he nuc l e a r pr ot e i n c odi ng ge ne ( T a bl e 1 5) A l l t hr e e e s t i m a t e s e xhi bi t e d l a r ge 95 % c onf i de nc e i nt e r va l s ( T a bl e 1 5) T he s e l a r ge s ha pe e s t i m a t e s i l l us t r a t e t he hi ghl y s ke w e d na t ur e of a m ong s i t e r a t e va r i a t i on f o r t he s e pos i t i ons of t he pr ot e i n c odi ng ge ne s ( T a bl e 1. 5 ) T h i s l a c k of va r i a t i on a l s o i s e vi de nc e d i n t he e s t i m a t e s of p r op or t i on of i nva r i a nt s i t e s ( P i nva r ) w hi c h a r e hi gh f or t he s e s a m e pos i t i ons T he s ke w e d na t ur e of a l pha i m pa c t s t he s w i t c hi ng a m ong t he c ha i ns dur i ng t he M ont e C a r l o M a r kov C ha i n s e a r c he s a s di f f e r e nt pe a ks i n t he pos t e r i or a r e e xpl or e d T ot al e v i de nc e phy l oge ny U s i ng t he m ode l s e t t i ngs ba s e d on t he s e pa r a t e a na l ys e s of m i t oc hondr i a l a nd nuc l e a r da t a s e t s t he c om bi ne d B a ye s i a n a n a l ys e s yi e l de d a phyl oge ny hi ghl y s uppor t e d a t va r i ous node s ( F i gu r e 1. 9 ) T he a ddi t i on of t he H i s t one 3 da t a di d not yi e l d a ny f u r t he r

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23 r e s ol ut i on of t he m t D N A phyl oge ny ( F i gu r e 1. 4 ) a t de e pe r node s ( r e d l i ne pol y t om y, F i gur e 1. 9 ) no r di d t he e xc l us i on of s i gni f i c a nt l y s a t ur a t e d s i t e s 3 r d pos i t i ons of c ox 1 ( t r e e not s how n) T h r e e m a i n di v i s i ons w e r e de t e c t e d i n t he s a m pl e s e xa m i ne d he r e i n O x y noe ant i l l ar um a nd A s c obul l a f r agi l i s f o r m e d a m or e ba s a l m onophyl e t i c g r oup r e pr e s e nt i ng t he s ubor de r O xynoa c e a T he r e pr e s e nt a t i ve s of t he s upe r f a m i l y L i m a pont i oi de a C os t as i e l l a k ur os hi m ae a nd C oc e l l i f e r a a l s o f or m e d a s e pa r a t e a nd m onophyl e t i c c l a de F i na l l y, a m onophy l e t i c s upe r f a m i l y P l a c obr a nc hoi de a w a s i de nt i f i e d c ont a i ni ng B os e l l i i da e a nd P l a c obr a nc h i da e M e m be r s of t he f a m i l y P l a t yhe dyl i da e w e r e not a va i l a bl e f or a na l ys i s a nd a r e t he onl y r e m a i ni ng m e m be r of t he s upe r f a m i l y P l a c obr a nc hoi de a W i t hi n t he P l a c obr a nc hi da e t w o m a j or c l a de s w i t h hi gh ( E l y s i a ) a nd m ode r a t e ( P l ak obr anc hus / T hur i di l l a ) pos t e r i or pr oba bi l i t y va l ue s w e r e i de nt i f i e d. B ot h t he m t D N A da t a a nd c om bi ne d a n a l ys i s i ndi c a t e d a s e pa r a t i on be t w e e n a P l ak obr anc hus / T hur i di l l a c l a de a nd t he r e m a i ni ng pl a c obr a nc hi ds ( F i gur e s 1. 2 a nd 1 9) W i t hi n t he P l ak obr anc hus / T hur i di l l a c l a de t he nu c l e a r da t a e nha nc e d t he s e pa r a t i on of P l ak obr anc hus f r om t he t hur i di l l i ds ( F i gu r e 1. 9 ) A l t hough r e l a t i ons hi ps a m ong t hur i di l l i d s pe c i e s w e r e not r e s ol ve d, t he r e w a s a c l os e a f f i ni t y a m ong T hur i di l l a undul a T bay e r i a nd T r at na A s s ugge s t e d by G os l i ne r ( 1995) T hur i di l l a bay e r i i s l i ke l y a c ol or va r i a nt o f T hur i di l l a r at na t hus t he r e t e nt i on of T hur i di l l a bay e r i a s t he s e ni or s ynonym T he di ve r ge nc e be t w e e n T hur i di l l a und ul a a nd T hur i di l l a bay e r i i s not ve r y l a r ge but t he t w o a r e c ons i s t e nt l y s e pa r a t e d i n a l l a na l ys e s T hur i di l l a hof f ae c ons i s t e nt l y gr oups w i t h T hur i di l l a c ar l s oni a nd s u ppor t s G os l i ne r 's ( 1995) s pe c i e s de s i gna t i on.

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24 W i t hi n t he ot he r m a j or c l a de r e s ol ut i on a t de e pe r node s w a s l a c ki ng or l ow e ve n w i t h t he a ddi t i on of t he H i s t one 3 da t a ( F i gu r e 1 9) I n bot h a na l ys e s ( m t D N A a nd c om bi ne d) a pol yt om y ( r e d l i ne ) w a s obs e r ve d w i t h s i gni f i c a nt r e s ol ut i on bot h a bove a nd be l ow t he pol yt om y I n a ddi t i on t o t he l a r ge r a nd m or e i nt e r i or po l yt om y w i t h i n t he e l ys i i ds t he r e w a s a not he r pol yt o m y a m ong E l y s i a or nat a a nd E l y s i a r uf e s c e ns ( bl ue l i ne ) O f t he node s l e a di ng t o t he bl ue a nd ye l l ow s ha de d c l a de s ( s e e F i gur e 1. 13) onl y t he ye l l ow c l a de ba s a l node i s hi ghl y s uppor t e d. T he bl ue c l a de a nd t he node j oi ni ng t he s e t w o c l a de s e xhi bi t l ow ppv s uppor t B ot h c l a de s r e pr e s e nt popul a t i on a nd s pe c i e s l e ve l di f f e r e nc e s I n t he bl ue c l a de t he pos i t i on of E l y s i a ni gr oc api t at a di f f e r s f r om t he m t D N A a na l ys i s i n t ha t i t gr oups w i t h s pe c i e s f r o m bot h t he A t l a nt i c a nd P a c i f i c B os e l l i a m ar c us i a ppe a r s t o ha ve a n a f f i ni t y f or t hi s gr oup a l t hough t he ppv i s l ow E l y s i a pr at e ns i s a l w a ys gr oups w i t h E s ubor nat a s ugge s t i ng a r e c e nt s e pa r a t i on be t w e e n t he s e t w o s pe c i e s E l y s i a c f at r ov i r i di s a ppe a r s t o be a s pe c i m e n of E l y s i a s e t oe ns i s a s t he i r di f f e r e nc e s a r e m i ni m a l I n t he ye l l ow c l a de t he r e i s a hi ghl y s uppor t e d br e a k be t w e e n t w o gr oups r e pr e s e nt i ng E l y s i a t r i s i nuat a a nd E l y s i a c f j apon i c a. T hi s i s a n i nt e r e s t i ng c l a de a s i t e nc om pa s s e s a non m onophyl e t i c E l y s i a or nat a E l y s i a s p. 10 une qui voc a l l y g r oups w i t h E l y s i a or nat a f r om F r e nc h P ol yne s i a s ugge s t i ng t ha t t he obs e r ve d e xt e r na l m or phol ogi c a l va r i a t i on i s s i m pl y popul a t i on l e ve l va r i a t i on. T he H i s t one 3 da t a pul l s E l y s i a c f j aponi c a out of a n a f f i ni t y f or E l y s i a or nat a f r om J a pa n a s e xhi bi t e d i n t he m t D N A phyl oge ny ( F i gur e 1. 4 ) T he pos i t i on of E l y s i a r uf e s c e ns i n bot h a na l ys e s i s s ur pr i s i ng, but s ugge s t s t ha t t hi s s pe c i e s i s a l s o a m e m be r o f a n E l y s i a or nat a c om pl e x. E l y s i a s p. 42 i s a l w a ys a l i gne d w i t h E l y s i a t r i s i nuat a but t he i de nt i t y of t hi s s pe c i e s i s unknow n a t t hi s t i m e T he w hi t e c l a de ( s e e F i gur e 1. 13 ) c ons i s t i ng of E l y s i a

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25 pat i na a nd E papi l l os a f o r m s a m ode r a t e l y s uppor t e d c l a de A l t hough t he r e i s s om e i ndi c a t i on of a n a f f i ni t y be t w e e n E be nne t t ae a nd popul a t i ons of E t uc a, t hi s r e l a t i ons hi p i s a s s oc i a t e d w i t h l ow ppv a nd i n s om e a na l ys e s E pus i l l a i s s i s t e r t o E t uc a T he s i l ve r c l a de ( s e e F i gur e 1 13) i s c om pos e d of ot he r m e m be r s of t he ge ne r a E l y s i a a nd a hi ghl y s uppor t e d gr oupi ng o f T r i dac hi e l l a a nd T r i dac hi a A n I L D t e s t i ndi c a t e d t ha t t he l e ngt h o f t r e e s f r om t he t hr e e ge ne s w e r e not s i gni f i c a nt l y he t e r oge ne ous ; t he r e f or e t he da t a w e r e c om bi ne d i nt o a s i ngl e m a xi m um pa r s i m ony a na l ys i s A he ur i s t i c s e a r c h yi e l de d s i x m os t pa r s i m oni ous t r e e s of l e ngt h 4161. A t ot a l of 5 30 pa r s i m ony i n f or m a t i ve a nd 7 3 uni nf or m a t i ve c ha r a c t e r s w e r e us e d i n t hi s r e c ons t r uc t i on. A c om pa r i s on t o one m i l l i o n r a ndom t r e e s i ndi c a t e d s i gni f i c a nt phyl oge ne t i c i nf or m a t i on ( g1 = 0 5719; H i l l i s & H ue l s e nbe c k, 1992) A s t r i c t c ons e ns us of t he s i x m os t pa r s i m oni ous t r e e s r e s ul t e d i n a t op ol ogy t ha t c ont a i ne d t he s a m e pol yt om y a s r e c ove r e d i n t he B a ye s i a n a na l ys i s M i nor di f f e r e nc e s oc c ur r e d i n t he pl a c e m e nt of t hr e e t a xa E l y s i e l l a pus i l l a E l y s i a b e nne t t ae a nd E l y s i a ni gr oc api t at a A s e c ond M P a na l ys i s w a s c onduc t e d on t he R Y c ode d 3 r d pos i t i ons of c ox 1 T h i s he ur i s t i c s e a r c h yi e l de d 12 m os t pa r s i m oni ous t r e e s f r om 464 pa r s i m ony i n f or m a t i ve a nd 76 pa r s i m ony uni nf o r m a t i ve c ha r a c t e r s A ga i n, a c om pa r i s on t o one m i l l i on r a ndom t r e e s i ndi c a t e d s i g ni f i c a nt phyl oge ne t i c i n f or m a t i o n w i t h t he e xc l us i on of s i l e nt t r a ns i t i ons a t 3 r d pos i t i ons of c ox 1 ( g1 = 0. 5160 ) T he s t r i c t c ons e ns us of t he 12 t r e e s r e c ove r e d pol yt om i e s a t t e r m i na l pos i t i ons of t he t r e e ( E l y s i a or nat a + E l y s i a r uf e s c e ns ; F i gur e 1. 11 ) A l l ot he r node s w e r e r e s ol ve d but t h e r e w a s l ow boot s t r a p s uppor t f or t he r e s ol ut i ons I n t hi s a na l ys i s onl y t he pos i t i on of E l y s i a ni gr oc api t at a w a s di f f e r e nt f r om w ha t w a s f ound i n t he B a ye s i a n a na l ys i s be s i de s t hos e c l a de s / t a xa i nvol ve d i n t he

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26 B a y e s i a n pol yt om y. T he num be r s o f una m bi guous c ha nge s a r e i ndi c a t e d i n F i gur e 1 12. T he br a nc he s i nvol ve d i n t he pol yt o m y a r e s hor t w i t h num be r s of c ha nge s r a ngi ng f r om 19 21 ( r e d l i ne s ) a nd 18 31 ( gr e e n l i ne s ) T he l ow num be r o f una m bi guous c ha nge s s ugge s t s e i t he r of t w o s i t ua t i ons : 1) i ns uf f i c i e nt nu m be r of c ha r a c t e r s a va i l a bl e or 2 ) s i m ul t a ne ous br a nc hi ng. B e c a us e of t he i na bi l i t y of M P t o f ul l y ut i l i z e i n f or m a t i on a t t hi s l e ve l a B a ye s i a n a ppr oa c h w a s us e d t o t e s t t he s e hypot he s e s T o t e s t i f t he i n di c a t i on of s i m ul t a ne ous br a nc hi ng w a s a r e s ul t of i ns uf f i c i e nt c ha r a c t e r s t o r e s ol ve t he pol yt om y a s ubs a m pl i ng of t a xa w a s c onduc t e d us i ng t he s hor t e s t br a nc he s i n r e s ol ve d c l a de s T he r e s ul t s o f t hi s a na l ys i s i ndi c a t e d no s i gni f i c a nt s t r uc t ur e i n t he r e gi on o f i nt e r e s t I n t hi s a na l ys i s t he pol yt om y i nvo l ve d P l ak obr anc hus oc e l l at us w hi c h ha d not be e n i m pl i c a t e d i n t he po l yt om y pr e vi ous l y. S i gni f i c a nt s t r uc t ur e w a s a ga i n de t e c t e d a t i nt e r i or node s a nd be l ow t he pol yt om y ( t r e e not s how n) A uni f or m c l oc k w a s e nf or c e d a nd a c l oc k l i ke m o de l of e vol ut i on c oul d not be r e j e c t e d f or t hi s l i m i t e d a na l ys i s ( L R = 17 64, df = 13, p < 0. 05) A l t hough t he hypot he s i s of i ns uf f i c i e nt phyl oge ne t i c c ha r a c t e r s c a nnot be e l i m i na t e d, t he s e c ond s e t of hypot he s e s us i ng t he l onge s t br a nc he s f r om r e s ol ve d c l a de s w a s t e s t e d. T he B a ye s i a n a na l ys i s of l i m i t e d t a xa w i t h l ong b r a nc he s yi e l de d no s i gni f i c a nt s uppor t f o r t he node s i n que s t i on ( F i gur e 1. 13) T he b r a nc h l e ngt hs a s s oc i a t e d w i t h t he s e node s a r e s m a l l c om pa r e d t o t hos e f o r t he ot he r br a nc he s w i t hi n t he t r e e c onf i r m i ng t he pr e vi ous hypot he s i s t e s t i ng r e ga r di ng pr e s e nc e of s i gni f i c a nt c ha r a c t e r s f or r e s ol ut i on of t he pol yt om y T he a ve r a ge l e ngt h of node s 1 5 ( 0 0428 + 0. 0113 r a nge = 0. 0273 0 0559) w hi c h c om p r i s e t he m a j or pol y t om y i n t he c om bi ne d phyl oge ny i s not s i gni f i c a nt l y di f f e r e nt f r om t he a ve r a ge l e ngt h of node s 6 8 ( 0. 0479 + 0 0120, r a nge =

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27 0. 0341 0. 0551 ) w hi c h ha ve l i ne a ge s i nvol ve d i n t he s e c ond pol yt om y a m ong t he t hur i di l l i ds F ul l y r e s ol ve d node s ( 9 14) d o ha ve a hi ghe r a ve r a ge l e ngt h ( 0 1616 + 0. 0664, r a nge = 0 0799 0 2551) T he r e l a t i ons hi ps de pi c t e d i n t hi s l i m i t e d t a xa a na l ys i s a r e ge ne r a l l y t he s a m e a s t ha t r e c ove r e d us i ng a l l t a xa e xc e pt f or T r i dac hi a c r i s pat a f r om t he F l or i da K e ys ( F K ) + E l y s i a s ubor nat a a nd P l a k obr anc hus oc e l l at us f r om G ua m ( G U ) + T hur i di l l a hof f ae T he t e r m i na l b r a nc he s i n T r i d ac hi a c l ar k i F K + E l y s i a s ubor nat a a r e t w o of t he l onge s t i n t hi s gr oup w i t h onl y t he t e r m i na l br a nc h l e a di ng t o E l y s i a s p. 42 be i ng l onge r I n t he c a s e of P l ak obr anc hus oc e l l at us G U + T hur i di l l a hof f ae t he t e r m i na l br a nc he s a r e t he l onge s t i n t h i s c l a de ( F i g ur e 1. 13 ) T he a ppl i c a t i on o f a m ol e c ul a r c l oc k t o t hi s s ubs a m pl i ng of t a xa w a s t e s t e d us i ng a uni f or m c l oc k s e t t i ng i n M r B a ye s t o de t e r m i ne i f t he r e l a t i ve r a t e s w e r e ho m oge nous a c r os s t a xa T he a ppl i c a t i on of a uni f or m c l oc k t o t he s e t a xa w a s r e j e c t e d ( L R = 37. 58, df = 16, p > 0. 01) i ndi c a t i ng he t e r oge ne ous r a t e s of e vol ut i on a m ong l i ne a ge s D I S C U S S I O N D i v e r ge nc e l e v e l s am ong t ax onom i c c at e gor i e s and w i t hi n s pe c i e s v ar i at i on A s i n pr e vi ous s t udi e s ( B a s s & K a r l 2006 ) a n a t t e m pt w a s m a de t o a s s e s s c ongr ue nc e a m ong di ve r ge nc e l e ve l s a nd c ur r e nt t a xonom y w i t hi n t he P l a c obr a nc hi da e T he a ppr oa c h us e d he r e i nvol ve d s e pa r a t e a na l ys e s of m i t oc ho ndr i a l D N A a nd nuc l e a r D N A W he n t he da t a w e r e c om bi ne d a nd 3 r d pos i t i ons of c ox 1 w e r e e xc l ude d a f t e r e vi de nc e of s a t ur a t i on, t he r a nge o f di ve r ge nc e s f or w i t hi n s pe c i e s w a s 0. 2 3. 0% ( a ve r a ge d T a bl e 1. 3 ) T he s e e s t i m a t e s of d i ve r ge nc e a r e n ot c om pa r a b l e t o t he e s t i m a t e s ba s e d on i ndi vi dua l ge ne s a l one be c a us e t he y a r e ge ne r a t e d f r om a m ode l a ve r a ge pr oc e s s a nd

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28 i nvol ve t he e xc l us i on of s i t e s T hi s m ode l a ve r a ge a ppr oa c h w a s t a ke n s o t ha t ove r a l l e s t i m a t e s of m i t oc hondr i a l D N A va r i a t i on c oul d b e de t e r m i ne d a nd c om pa r e d a m ong va r i ous t a xonom i c l e ve l s A l t hough a s t r i c t c l oc k l i ke m ode l of e vol ut i on doe s not f i t t he m i t oc hondr i a l or nuc l e a r ge ne s e que nc e s a n e xa m i na t i on of s e que nc e di ve r ge nc e w i t hi n t he s ur ve ye d t a xa i s s t i l l us e f ul a s a c he c k of a s s oc i a t i on be t w e e n t a xonom y a nd di ve r ge nc e F o r t he m i t oc hondr i a l D N A c ong r ue nc e a m ong t a xonom i c l e ve l s a nd e s t i m a t e s of di ve r ge nc e w a s s t r ong up t o t he f a m i l y l e ve l ( F i gu r e 1 2) F or H i s t one 3, t he di ve r ge nc e w i t hi n s pe c i e s r a nge d f r om 0. 6 2. 3% ( a ve r a ge d T a bl e 1. 4 ) a nd c ongr ue nc e a m ong t a xonom i c l e ve l s qui c kl y de g r a de d a bove t he s pe c i e s l e ve l r e f l e c t i ng t he l i m i t e d us e of H i s t one 3 a s a n i nd i c a t or o f t a xonom i c l e ve l T hi s pa t t e r n i s l i ke l y a r e s ul t o f c ons t r a i nt s on c ha nge s i n H i s t one 3 s e que nc e s F o r e xa m pl e w hi l e 3 r d pos i t i ons of H i s t one 3 e xhi bi t e d m i l d s a t ur a t i on ( F i gur e 1 1B ) l i t t l e t o no va r i a t i on w a s pr e s e nt i n f i r s t a nd s e c ond pos i t i ons W hi l e H 3 doe s not yi e l d a s t r ong c onc or da nc e be t w e e n t a xonom i c l e ve l a nd de gr e e of di ve r ge nc e t he m i t oc hondr i a l D N A doe s pr ovi de a good ya r ds t i c k f or a s s e s s i ng t a xonom y w i t hi n t he P l a c obr a nc hi da e T he l e ve l s of di ve r ge nc e a m ong t he ge ne r a a s r e c ogni z e d pr i or t o G os l i ne r ( 1995) a r e r e l a t i ve l y c ons i s t e nt i n t e r m s o f e qui va l e nt de gr e e s of di ve r ge nc e A n e xa m i na t i on of t he br a nc hi ng pa t t e r ns a nd c l a de s i n t he phyl oge ny, how e ve r doe s not s uppor t a l l o f t he ge ne r i c l e ve l c l a s s i f i c a t i ons T o i l l us t r a t e a c l os e e xa m i na t i on of t he s i l ve r c l a de ( F i gur e 1. 13 ) i s us e f ul T hi s c l a de c ont a i ns t hr e e di f f e r e nt ge ne r a E l y s i a, T r i dac hi e l l a a nd T r i dac hi a B e c a us e t he bl ue c l a de c ont a i ni ng E l y s i a t i m i da t he or i gi na l ge ne r i c de s c r i pt i on ( R i s s o, 1818) w oul d be de s i gna t e d a s t he E l y s i a ge ne r a t he r e qui r e m e nt of us i ng t he ba s a l ge nus i n t he r e m a i ni ng

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29 c l a de s i s now obs ol e t e T he t w o a va i l a bl e ge ne r a w i t hi n t he s i l ve r c l a de a r e T r i dac hi e l l a M c F a r l a nd, 1924 a nd T r i dac hi a D e s ha ye s 1857 I f t he ol de r of t he s e t w o ge ne r a i s a c c e pt a bl e ba s e d on nom e nc l a t ur a l r ul e s t he n a l l m e m be r s of t hi s c l a de w oul d c ha nge t o t he T r i dac hi a ge nus F or t he ye l l ow c l a de a ga i n t he ba s a l ge nus i s obs ol e t e a nd t he ol de s t ge ne r i c na m e T hal l e pus S w a i ns on, 1840 ( t y pe s pe c i e s T hal l e pus or nat us S w a i ns on, 1840 i s c ons i de r e d e qui va l e nt t o E l y s i a or nat a ) w oul d be t he ge nus f or t hi s c l a de i f t he na m e i s va l i d T he de s i gna t i on of ge n e r a f or t he r e m a i ni ng c l a de s ( w hi t e a nd gr e e n) a nd E l y s i e l l a pus i l l a i s unc l e a r a s onl y t he gr e e n c l a de i s w e l l s uppor t e d a nd a l l a r e pa r t o f t he pol yt om y. N e w ge ne r a m a y be ne e de d t o a c c om m oda t e t he s e gr oups P hy l oge ny of t he P l ac obr anc hi dae and as s oc i at e d f am i l i e s A l t hough t he ge ne s us e d he r e do not f ul l y r e s ol ve phyl oge ne t i c r e l a t i ons hi ps w i t hi n t he P l a c obr a nc hi da e t he r e a r e i nt e r e s t i ng f i ndi ngs t ha t m a y he l p t o de c i phe r s om e of t he t a xonom i c c onf us i on. T he t a xonom y doe s n ot a ppe a r t o r e f l e c t t he e vol ut i ona r y hi s t or y w i t hi n t he f a m i l y S a c ogl os s a ns how e ve r do f or m a m onophyl e t i c gr oup i n r e l a t i on t o S ys t e l l om m a t ophor a a nd A pl ys i om o r ph a ( V onne m a n e t a l 2005) a nd t he t a xa r e pr e s e nt i ng P l a c obr a nc hoi de a a nd L i m a pont i ode a f or m m onophyl e t i c g r oups ( J e ns e n, 1996; M i kke l s on, 1998) W i t hi n t he P l a c obr a nc hi da e t w o m onophyl e t i c gr oups a r e r e c ogni z e d r e pr e s e nt i ng P l ak obr anc hus + T hur i di l l a a nd t he r e m a i ni ng m e m be r s o f t he P l a c obr a nc hi da e ( G os l i ne r 1995 ) T he ge nus E l y s i a i s pa r a phyl e t i c but how be s t t o r e s ol ve t hi s i s s ue i s not c l e a r ba s e d on t he s e da t a I f t he c l a de s i l l us t r a t e d i n F i gur e 1 13 a r e va l i d, t he n t he ge ne r i c na m e s T hal l e pus S w a i n s on, 1840 a nd T r i dac hi a D e s ha ye s 1857 s houl d be r e s ur r e c t e d a nd ne w ge ne r i c na m e s f o r t he r e m a i ni ng c l a de s s houl d be de ve l ope d.

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30 E xt e r na l m o r phol ogy i s no t a good i ndi c a t or of t he de gr e e of di ve r ge nc e a m ong t a xa a nd i n s om e c a s e s i s pos i t i ve l y m i s l e a di ng a s t o s pe c i e s i de nt i f i c a t i on ( e g E l y s i a s e t oe ns i s a nd E l y s i a c f at r ov i r i di s ) B os e l l i a m ar c us i i s a c t ua l l y a m e m be r of t he P l a c obr a nc hi da e a nd t he r e f or e s houl d be r e na m e d E l y s i a m ar c us i T he m or phol ogi c a l s i m i l a r i t y t o m e m be r s of t he ge nus B os e l l i a i s l i ke l y a n e xa m pl e of c onve r ge nc e i n body f or m T he r e c e nt l y na m e d T r i dac hi a c l ar k i ( P i e r c e e t a l 2006) r e nde r s T r i dac hi a c r i s pat a a pa r a phyl e t i c gr oup. I f t hi s i s a va l i d s pe c i e s t he n t he popul a t i ons i n B e l i z e a nd U S V I s houl d be c ons i de r e d s pe c i e s I f t he D N A s e que nc e di ve r ge nc e f or T r i dac hi a c l ar k i i ndi c a t e s s pe c i f i c s t a t us t he n a l l t e r m i na l no de s e xc e pt f or E l y s i a c f at r ov i r i di s E l y s i a s p. 10 a nd E r uf e s c e ns f r om H a w a i i a r e s e pa r a t e s pe c i e s E l y s i a t uc a f r om t he F l or i da K e ys a nd t he B a ha m a s a r e di s t i nc t f r om E l y s i a t uc a f r om t he G ul f of M e xi c o a nd t he t w o s pe c i m e ns of E l y s i a pa pi l l os a f r om t he B a ha m a s a r e s e pa r a t e s pe c i e s W i t hi n t he t hur i di l l i ds T hur i di l l a bay e r i i s a va l i d s pe c i e s a nd T hur i di l l a r at na f r om G ua m a nd T r at na f r om t he P hi l i pp i ne s a r e va l i d s pe c i e s c ont r a r y t o t he f i ndi ngs of G os l i ne r ( 1995) I n a c c or da nc e w i t h t he a bove s t a t e m e nt s P l ak obr a nc hus oc e l l at us f r om H a w a i i a nd G ua m a r e s e pa r a t e s pe c i e s w hi c h ha s be e n s ugge s t e d by J e ns e n ( 1992) S pe c i m e ns de s i gna t e d a s E l y s i a t i m i da f r om t he F l or i da K e ys a nd t he B a ha m a s m a y r e pr e s e nt E l y s i a c or ni ge r a N ut t a l l 1989 a s i ndi c t e d by t he di ve r ge nc e be t w e e n t he M e di t e r r a ne a n a nd W e s t e r n A t l a nt i c s pe c i m e ns ( 2. 1% ) a nd f ol l ow i ng t he de s i gna t i on of s pe c i e s a s de s c r i be d a bove

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31 G e ne pe r f or m anc e i n phy l oge ne t i c r e c ons t r uc t i on A l t hough t he i ndi vi dua l ge ne m ode l s us e d t o e s t i m a t e t he r e l a t i ve r a t e s of e vol ut i on a m ong ge ne s a r e di f f e r e nt f r om t he s i ngl e m ode l us e d t o e s t i m a t e pe r c e nt s e que nc e di ve r ge nc e t he y a r e i m po r t a nt f o r a s s e s s i ng t he ut i l i t y of i ndi vi dua l ge ne s f or phyl oge ne t i c i nf e r e nc e ( F i gu r e 1 7A ) T he m i t oc h ondr i a l g e ne s e xhi bi t e d hi ghe r r e l a t i ve r a t e s of e vol ut i on t ha n H i s t one 3 pr ovi di ng i nde pe nde nt c or r obor a t i on of t he l i m i t e d us e of H i s t one 3 f or t he e xa m i na t i on o f di ve r ge nc e e s t i m a t e s T he hi ghl y a s ym m e t r i c a l i ns t a nt a ne ous r a t e m a t r i c e s of t he m i t oc hondr i a l ge ne s a l s o hi ghl i ght t he i s s ue of hom opl a s y a s s oc i a t e d w i t h t he obs e r ve d t r a ns i t i on bi a s A m ong t he t hr e e ge ne s t r a ns ve r s i on r a t e s a r e c om pa r a bl e ye t f e w e r i n num be r ; t he r e f o r e c ont r i but i ng t o t he l a c k of phyl oge ne t i c s i gna l a m ong s pe c i e s of pl a c obr a n c hi ds T he r a t i o of nons ynonym ous a nd s ynonym ous s ubs t i t ut i ons f or c ox 1 ( 0. 0038 ) a nd H i s t one 3 ( 0 0034) a r e l e s s t ha n one i ndi c a t i ng pur i f yi n g s e l e c t i on ( R a nd, 2001) T he l a c k of va r i a t i on of a m i no a c i d s ubs t i t ut i ons i n c ox 1 a nd H i s t one 3 a nd l ow dN / d S r a t i os s ugge s t t he l i m i t e d us e of t he s e ge ne s f or phyl oge ny r e c ons t r uc t i on. T he l a r ge p r o por t i on of i nva r i a nt s i t e s i n 1 s t a nd 2 n d pos i t i ons of c ox 1 a nd H 3 i ndi c a t e t he i r l ow pe r f o r m a nc e i n phyl oge ne t i c r e c ons t r uc t i on w i t hi n t hi s f a m i l y A l pha va l ue s w hi c h i ndi c a t e t he s ha pe of t he ga m m a di s t r i but i on, f o r i ndi vi dua l ge ne s c a n be us e d a s qua l i t y i ndi c a t or s of pe r f o r m a nc e i n phyl oge ne t i c r e c ons t r uc t i on ( L i n & D a nf or t h 2004 ) L i n & D a nf or t h ( 2004) i n a n e xt e ns i ve r e vi e w of i ns e c t s t udi e s us i ng m i t oc hondr i a l p r ot e i n c odi ng ge ne s f ound a c or r e l a t i on be t w e e n hi gh a l pha va l ue s a nd c ons i s t e nc y i ndi c e s s ugge s t i ng t ha t hi gh va l ue s yi e l d be t t e r pe r f or m a nc e i n phyl oge ny r e c ons t r uc t i on. F o r m i t oc hond r i a l ge ne s e s t i m a t e s of a l pha l e s s t ha n one

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32 yi e l d c ons i s t e nc y i ndi c e s r a ngi ng f r om 0. 1 0. 45 a nd a l pha e s t i m a t e s f r om 2 3 do not s i gni f i c a nt l y i m pr ove c ons i s t e nc y i n f i ndi ng t he c o r r e c t t r e e F or nuc l e a r e xons e s t i m a t e s of a l pha f r om 0 1 yi e l d c ons i s t e nc y i ndi c e s l e s s t ha n 0. 45 a nd onl y a t a l pha va l ue s a ppr oa c hi ng t w o a r e c ons i s t e nc y i ndi c e s gr e a t e r t ha n 0. 50 but ne ve r gr e a t e r t ha n 0. 65. I n t hi s s t udy, a l pha va l ue s e s t i m a t e d f or i ndi vi dua l ge ne s a r e l ow ( 16S % = 0 2856; c ox 1 % = 0 2982; H 3, % = 1. 6414 ) a nd f a l l i n t o t h e r e gi on of l ow c ons i s t e nc y i n phyl oge ne t i c r e c ons t r uc t i on. W he t he r t he s e s i m i l a r i t i e s t o m i t oc hond r i a l a nd nu c l e a r e vol ut i ona r y pa t t e r ns i n i ns e c t s a r e due t o ge ne r a l p r ope r t i e s of or ga ne l l ul a r a nd nuc l e a r D N A e vol ut i on o r due t o s i m i l a r i t i e s i n l i f e hi s t or y a s pe c t s of s a c ogl os s a ns a nd i ns e c t s c a nnot be de t e r m i ne d he r e T he r e a r e s om e s i m i l a r i t i e s i n l i f e hi s t or y a s pe c t s s uc h a s s hor t ge ne r a t i on t i m e s a nd r e por t e d f e e di ng s pe c i f i c i t y. T he c onc a t e na t e d da t a s e t w hi l e pr ovi di ng gr e a t e r r e s ol ut i on t o t he phyl oge ne t i c r e l a t i ons hi ps a m ong s pe c i e s ( F i gur e 1 9 ) di d not r e s ol ve t he de e pe r i nt e r na l phyl oge ny t hus pr om pt i ng t he que s t i on of w he t he r t hi s i s a ha r d or s of t pol yt o m y? T he r e s ul t s f r om t he B a ye s i a n hypot he s i s t e s t i ng de s c r i be d he r e i ndi c a t e d t ha t i ns uf f i c i e nt va r i a t i on e xi s t s t o r e s ol ve t he pol yt o m y de t e c t e d i n t hi s a na l ys i s F ur t he r a na l ys i s of nuc l e a r i nt r ons or nuc l e a r r i bos om a l ge ne s m a y de t e r m i ne br a nc hi ng pa t t e r ns a t t hi s l e ve l

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33 R E F E R E N C E S A L T E K A R G D W A R K A D A S S H U E L S E N B E C K J P & R O N Q U I S T F 2004. P a r a l l e l M e t r opol i s c oupl e d M a r ko v c ha i n M ont e C a r l o f or B a ye s i a n phyl oge ne t i c i nf e r e nc e B i oi nf or m at i c s 20: 407 415 B A B A K 1938. O pi s t hobr a nc hi a of K i i M i ddl e J a pa n. J our nal of t he D e par t m e nt of A gr i c ul t ur e K y us hu I m pe r i al U ni v e r s i t y 6: 1 19 B A B A K 1949. O pi s t hobr a nc hi a of S a ga m i B a y c ol l e c t e d by H i s M a j e s t y, t he E m pe r or of J a pa n. I w a na m i S ho t e n, T okyo. B A B A K 1955. O pi s t hoba nc hi a of S a ga m i B a y. S uppl e m e nt pp. 1 59 T okyo, T w a na m i S hot e n. B A B A K 1957. T he s pe c i e s of t he ge nus E l y s i a f r om J a pa n. P ubl i c at i ons of t he Se t o M a r i ne B i ol og i c al L abor at or y 6: 69 74. B A S S A L & K A R L S A 2006. M ol e c ul a r phyl oge ne t i c a na l ys i s of t he ge ne r a i n t he f a m i l y P l a kob r a nc hi da e ( M ol l us c a : O pi s t hobr a nc hi a : S a c ogl os s a ) R e c or ds of t he W e s t e r n A us t r al i an M us e um S uppl e m e nt 69: 61 68 B E R G H R S 1872. M al ac ol ogi s c he U nt e r s uc hunge n 1: 137 203 pl s 17 24

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42 S T O L I C Z K A F 1868 C r e t a c e ous f a una o f s out he r n I ndi a P a l a e ont ol ogi a I ndi c a be i ng f i gur e s a nd de s c r i pt i ons of t he or ga ni c r e m a i ns pr oc ur e d du r i ng t he pr ogr e s s of t he G e ol o gi c a l S oc i e t y of I ndi a M e m oi r s of t he G e ol ogi c al Sur v e y of I ndi a, V ol um e 2 7 10: 433. S W O F F O R D D L 1998. P A U P 4 0: P hy l oge ne t i c A nal y s i s U s i ng P ar s i m ony and O t he r M e t hods S i na ue r A s s oc i a t e s S unde r l a nd, M a s s a c hus e t t s T A Y L O R D L 1968 C hl or opl a s t s a s s ym bi ot i c o r ga ne l l e s i n t he di ge s t i ve gl a nd of E l y s i a v i r i di s ( G a s t r opoda : O pi s t hobr a nc hi a ) J our nal M ar i ne B i ol ogi c al A s s oc i at i on U ni t e d K i ngdom 48: 1 15. T H O L L E S S O N M 1999 P hyl oge ne t i c a na l ys i s of E ut hyne u r a ( G a s t r opoda ) by m e a ns of t he 16S r R N A ge ne : us e of a f a s t ge ne f or hi ghe r l e ve l phy l oge ni e s P r oc e e di ngs of t he R oy al Soc i e t y of L ondon B 266 : 75 83 T H O M P S O N T E 1973 S a c ogl os s a n ga s t r opod m ol l us ks f r om E a s t e r n A us t r a l i a P r oc e e di ngs of t he M al ac ol ogi c al Soc i e t y of L ondon 40: 239 2 51. T R I N C H E S E S 1891 D e s c r i z i one de l nuovo ge n e r e B os e l l i a M e m or i e de l l a R e gi a A c c ade m i a de l l e Sc i e nz e de l l I s t i t ut o d i B ol o gna 5: 773 778 V E R R I L L A E 1901. A ddi t i ons t o t he f a una of t h e B e r m uda s f r om t he Y a l e e xpe di t i on of 1901 w i t h no t e s on ot he r s pe c i e s T r ans ac t i ons of t he C onne c t i c ut A c ade m y of Sc i e nc e 11: 15 62

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43 V O N N E M A N N V S C H R O D L M K L U S S M A N N K O L B A & W A G E L E H 2005. R e c ons t r uc t i on o f t he phyl oge ny of t he O pi s t hobr a nc hi a ( M ol l us c a : G a s t r opoda ) by m e a ns of 18S a nd 28S r R N A ge ne s e que nc e s J our nal of M ol l us c an St udi e s 71: 113 125 W A L S H H E M E T Z G E R D A & H I G U C H I R 1991 C he l e x m e di um f o r s i m pl e e xt r a c t i on of D N A f o r P C R ba s e d t ypi ng f r om f or e ns i c m a t e r i a l B i oT e c hni que s 10: 506 513 W A U G H G D & C L A R K K B 1986. S e a s ona l a nd ge ogr a phi c va r i a t i on i n c hl or ophyl l l e ve l o f E l y s i a t uc a ( A s c ogl os s a : O pi s t hobr a nc hi a ) M ar i ne B i ol ogy 92: 483 487. W O E S E C R A C H E N B A C H L R O U V I E R E P & M A N D E L C O L 1991. A r c ha e a l phyl oge ny: r e e xa m i na t i on o f t he phy l oge ne t i c pos i t i on of A r c hae ogl obus f ul gi dus i n l i ght of c e r t a i n c om pos i t i on i nduc e d a r t i f a c t s Sy s t e m at i c and A pp l i e d M i c r obi ol ogy 14: 364 371

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44 T a bl e 1. 1: L i s t of s pe c i e s us e d i n t he phyl oge ne t i c a na l ys i s L e t t e r a bbr e vi a t i ons f or l oc a t i on a r e us e d i n f i gur e s f or c l a r i t y A c c e s s i on num be r a nd num be r of i ndi vi dua l s s c r e e ne d ( i n pa r e nt he s e s ) f or e a c h ha pl ot ype o f a gi ve n ge ne i s s how n. S i ngl e a c c e s s i on num be r s a c c om pa ni e d by m ul t i pl e i ndi vi dua l s i ndi c a t e s t ha t a l l i ndi vi dua l s s ha r e d t he s a m e ha pl ot ype T a x o n o m i c U n i t s L o c a t i o n 1 6 S C o x 1 H i s t o n e 3 C l a d e S a c o g l o s s a S u b c l a d e P l a c o b r a n c h a c e a S u p e r f a m i l y P l a c o b r a n c h o i d e a G r a y 1 8 4 0 F a m i l y B o s e l l i i d a e E v M a r c u s 1 9 8 2 B o s e l l i a m a r c u s i E v M a r c u s 1 9 7 2 B a h a m a s ( B A ) D Q 4 8 0 1 9 1 ( 1 ) D Q 4 7 1 2 5 4 ( 1 ) D Q 5 3 4 7 8 3 ( 1 ) B o s e l l i a m i m e t i c a T r i n c h e s e 1 8 9 1 B a h a m a s ( B A ) D Q 4 8 0 2 0 2 2 0 3 ( 2 ) D Q 4 7 1 2 1 2 2 1 5 ( 4 ) D Q 5 3 4 7 9 3 ( 1 ) F a m i l y P l a c o b r a n c h i d a e G r a y 1 8 4 0 E l y s i a c f a t r o v i r i d i s B a b a 1 9 5 5 J a p a n ( J P ) ; O k i n a w a D Q 4 8 0 1 6 4 ( 1 ) D Q 4 7 1 2 5 7 ( 1 ) D Q 5 3 4 7 6 4 ( 1 ) E l y s i a b e n n e t t a e T h o m p s o n 1 9 7 3 G u a m ( G U ) D Q 4 8 0 1 8 3 ( 2 ) D Q 4 7 1 2 1 6 2 1 7 ( 2 ) D Q 5 3 4 7 7 8 ( 3 ) E l y s i a c a n g u z u a M a r c u s 1 9 5 5 U S A : F l o r i d a D Q 4 8 0 1 9 6 ( 3 ) D Q 4 7 1 2 1 8 2 2 0 ( 3 ) D Q 5 3 4 7 8 7 ( 1 ) E l y s i a c h l o r o t i c a G o u l d 1 8 7 0 U S A : M a s s a c h u s e t t s D Q 4 8 0 2 0 0 ( 3 ) D Q 4 7 1 2 2 1 2 2 2 ( 3 ) D Q 5 3 4 7 9 1 ( 1 ) E l y s i a n i g r o c a p i t a t a B a b a 1 9 5 7 J a p a n ( J P ) : O k i n a w a D Q 4 8 0 1 7 5 ( 3 ) D Q 4 7 1 2 2 6 2 2 8 ( 3 ) D Q 5 3 4 7 7 1 ( 1 ) E l y s i a o b t u s a B a b a 1 9 3 8 J a p a n ( J P ) : O k i n a w a D Q 4 8 0 1 8 2 ( 1 ) D Q 4 7 1 2 5 9 ( 1 ) D Q 5 3 4 7 7 7 ( 1 ) E l y s i a o r n a t a S w a i n s o n 1 8 4 0 F r e n c h P o l y n e s i a ( F P ) ; P h i l i p p i n e s ( P H ) ; J a p a n ( J P ) D Q 4 8 0 1 7 7 1 8 1 ( 5 ) D Q 4 7 1 2 6 0 2 6 4 ( 5 ) D Q 5 3 4 7 7 3 7 7 6 ( 4 ) E l y s i a p a t i n a M a r c u s 1 9 8 0 U S A : F l o r i d a ( F K ) D Q 4 8 0 1 8 9 1 9 0 ( 2 ) D Q 4 7 1 2 2 9 2 3 0 ( 5 ) D Q 5 3 4 7 8 2 ( 5 ) E l y s i a p a p i l l o s a V e r r i l l 1 9 0 1 B a h a m a s ( B A ) D Q 4 8 0 1 8 7 1 8 8 ( 2 ) D Q 4 7 1 2 3 1 2 3 2 ( 2 ) D Q 5 3 4 7 8 0 7 8 1 ( 2 ) E l y s i a p r a t e n s i s O r t e a & E s p i n o s a 1 9 9 6 B a h a m a s ( B A ) D Q 4 8 0 1 6 2 ( 1 ) D Q 4 7 1 2 5 8 ( 1 ) D Q 5 3 4 7 6 2 ( 1 ) E l y s i a r u f e s c e n s P e a s e 1 8 7 1 G u a m ( G U ) ; H a w a i i ( H A ) D Q 4 8 0 1 7 1 1 7 2 ( 2 ) D Q 4 7 1 2 3 7 2 3 8 ( 2 ) D Q 5 3 4 7 6 8 ( 1 ) E l y s i a s e r c a M a r c u s 1 9 5 5 B a h a m a s ( B A ) D Q 4 8 0 1 9 2 ( 3 ) D Q 4 7 1 2 4 2 2 4 4 ( 3 ) D Q 5 3 4 7 8 4 ( 2 ) E l y s i a s e t o e n s i s H a m a t a n i 1 9 6 8 J a p a n ( J P ) : O k i n a w a D Q 4 8 0 1 6 3 ( 3 ) D Q 4 7 1 2 3 9 2 4 1 ( 3 ) D Q 5 3 4 7 6 3 ( 1 ) E l y s i a s u b o r n a t a V e r r i l l 1 9 0 1 U S A : F l o r i d a ( F K ) D Q 4 8 0 1 6 5 ( 9 ) D Q 4 7 1 2 8 3 ( 2 6 ) D Q 5 3 4 7 6 5 ( 1 ) E l y s i a t i m i d a R i s s o 1 8 1 8 B a h a m a s ( B A ) ; F r a n c e ( M e d ) ; U S A : F l o r i d a ( F K ) D Q 4 8 0 1 6 6 1 6 9 ( 6 ) D Q 4 7 1 2 4 5 2 4 8 ( 4 ) D Q 5 3 4 7 6 6 7 6 7 ( 2 ) E l y s i a t r i s i n u a t a B a b a 1 9 4 9 J a p a n ( J P ) : O k i n a w a D Q 4 8 0 1 7 4 ( 1 ) D Q 5 3 4 7 7 0 ( 2 ) E l y s i a t u c a M a r c u s & M a r c u s 1 9 6 7 B a h a m a s ( B A ) ; U S A : F l o r i d a ( F K ) T a r p o n S p r i n g s ( G O M ) D Q 4 8 0 1 8 4 8 6 ( 5 ) D Q 4 7 1 2 4 9 2 5 1 ( 3 ) D Q 5 3 4 7 7 9 ( 2 )

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45 T a bl e 1. 1: ( C ont i nue d) T a x o n o m i c U n i t s L o c a t i o n 1 6 S C o x 1 H i s t o n e 3 E l y s i a v i r i d i s M o n t a g u 1 8 0 4 P o r t u g a l D Q 4 8 0 1 9 5 ( 3 ) D Q 4 7 1 2 1 1 ( 3 ) D Q 5 3 4 7 8 6 ( 2 ) E l y s i a s p 1 0 G u a m ( G U ) D Q 4 8 0 1 7 0 ( 2 ) D Q 4 7 1 2 8 2 ( 1 ) E l y s i a s p 4 2 ( E l y s i a s p 2 o n f o r u m ) G u a m ( G U ) D Q 4 8 0 1 7 3 ( 1 ) D Q 4 7 1 2 5 6 ( 1 ) D Q 5 3 4 7 6 9 ( 1 ) E l y s i a c f j a p o n i c a E l i o t 1 9 1 3 G u a m D Q 4 8 0 1 7 6 ( 1 ) D Q 4 7 1 2 5 5 ( 1 ) D Q 5 3 4 7 7 2 ( 1 ) E l y s i e l l a p u s i l l a B e r g h 1 8 7 2 U S A : H a w a i i ( H A ) D Q 4 8 0 2 0 1 ( 2 ) D Q 4 7 1 2 3 3 2 3 6 ( 4 ) D Q 5 3 4 7 9 2 ( 3 ) E l y s i a c l a r k i U S A : F l o r i d a ( F K ) D Q 4 8 0 1 9 7 ( 1 ) D Q 4 7 1 2 2 5 ( 3 ) D Q 5 3 4 7 8 8 ( 1 ) T r i d a c h i a c r i s p a t a M r c h 1 8 6 3 B a h a m a s ( B A ) ; B e l i z e ( B E ) ; V i r g i n I s l a n d s ( U S V I ) D Q 4 8 0 1 9 8 1 9 9 ( 2 ) D Q 4 7 1 2 2 3 2 2 4 ( 7 ) D Q 5 3 4 7 8 9 7 9 0 ( 4 ) T r i d a c h i e l l a d i o m e d e a B e r g h 1 8 9 4 C o s t a R i c a D Q 4 8 0 1 9 3 1 9 4 ( 2 ) D Q 4 7 1 2 6 5 ( 1 ) D Q 5 3 4 7 8 5 ( 1 ) T h u r i d i l l a b a y e r i M a r c u s 1 9 6 5 G u a m ( G U ) D Q 4 8 0 2 0 7 ( 2 ) D Q 4 7 1 2 7 1 2 7 2 ( 2 ) D Q 5 3 4 7 9 7 ( 1 ) T h u r i d i l l a c a r l s o n i G o s l i n e r 1 9 9 5 U S A : H a w a i i ( H A ) D Q 4 8 0 2 1 4 ( 2 ) D Q 4 7 1 2 7 3 2 7 4 ( 2 ) D Q 5 3 4 8 0 4 ( 2 ) T h u r i d i l l a h o f f a e G o s l i n e r 1 9 9 5 G u a m ( G U ) D Q 4 8 0 2 1 3 ( 1 ) D Q 4 7 1 2 6 6 ( 1 ) D Q 5 3 4 8 0 3 ( 1 ) T h u r i d i l l a l i v i d a B a b a 1 9 5 5 G u a m ( G U ) D Q 4 8 0 2 1 1 ( 3 ) D Q 4 7 1 2 7 5 2 7 6 ( 2 ) D Q 5 3 4 8 0 1 ( 2 ) T h u r i d i l l a n e o n a G o s l i n e r 1 9 9 5 U S A : H a w a i i ( H A ) D Q 4 8 0 2 0 9 ( 2 ) D Q 4 7 1 2 8 0 2 8 1 ( 3 ) D Q 5 3 4 7 9 9 ( 2 ) T h u r i d i l l a r a t n a M a r c u s 1 9 6 5 G u a m ( G U ) ; P h i l i p p i n e s ( P H ) D Q 4 8 0 2 0 6 & 2 0 8 ( 3 ) D Q 4 7 1 2 7 7 2 7 9 ( 3 ) D Q 5 3 4 7 9 6 & 7 9 8 ( 2 ) T h u r i d i l l a u n d u l a G o s l i n e r 1 9 9 5 P h i l i p p i n e s ( P H ) D Q 4 8 0 2 1 0 ( 1 ) D Q 4 7 1 2 6 7 ( 1 ) D Q 5 3 4 8 0 0 ( 1 ) T h u r i d i l l a v a t a e R i s b e c 1 9 2 8 G u a m ( G U ) D Q 4 8 0 2 1 2 ( 1 ) D Q 4 7 1 2 6 8 ( 1 ) D Q 5 3 4 8 0 2 ( 1 ) P l a k o b r a n c h u s o c e l l a t u s v a n H a s s e l t 1 8 2 4 G u a m ( G U ) ; U S A : H a w a i i ( H A ) D Q 4 8 0 2 0 4 2 0 5 ( 3 ) D Q 4 7 1 2 6 9 2 7 0 ( 3 ) D Q 5 3 4 7 9 4 7 9 5 ( 3 ) S u p e r f a m i l y L i m a p o n t i o i d e a G r a y 1 8 4 7 F a m i l y L i m a p o n t i i d a e G r a y 1 8 4 7 C o s t a s i e l l a k u r o s h i m a e I c h i k a w a 1 9 9 3 G u a m D Q 4 8 0 2 1 5 ( 1 ) D Q 4 7 1 2 5 2 ( 1 ) D Q 5 3 4 8 0 5 ( 1 ) C o s t a s i e l l a o c e l l i f e r a S i m r o t h 1 8 9 5 B a h a m a s D Q 4 8 0 2 1 6 ( 1 ) D Q 4 7 1 2 5 3 ( 1 ) D Q 5 3 4 8 0 6 ( 1 ) S u b c l a d e O x y n o a c e a F a m i l y O x y n o i d a e S t o l i c z k a 1 8 6 8 O x y n o e a n t i l l a r u m M r c h 1 8 6 3 U S A : F l o r i d a D Q 4 8 0 2 1 7 ( 2 ) D Q 5 3 4 8 0 7 ( 2 ) F a m i l y V o l v a t e l l i d a e P i l s b r y 1 8 9 5 A s c o b u l l a f r a g i l i s J e f f r e y s 1 8 5 6 A Y 0 9 8 9 2 9 A Y 3 4 5 0 2 2

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46 T a bl e 1. 1: ( C ont i nue d) T a x o n o m i c U n i t s L o c a t i o n 1 6 S C o x 1 H i s t o n e 3 C l a d e A p l y s i o m o r p h a [ = A n a s p i d e a ] F a m i l y A p l y s i d a e L a m a r c k 1 8 0 9 A p l y s i a c a l i f o r n i c a C o o p e r 1 8 6 3 A Y 5 6 9 5 5 2 A Y 5 6 9 5 5 2 A Y 0 6 4 4 7 2 C l a d e S y s t e l l o m m a t o p h o r a [ = G y m n o m o r p h a ] F a m i l y O n c h i d i i d a e R a f i n e s q u e 1 8 1 5 O n c h i d e l l a c e l t i c a C u v i e r 1 8 1 7 A Y 3 4 5 0 4 8 A Y 3 4 5 0 4 8 O n c h i d i u m s p A F 0 3 3 7 0 6

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47 T a bl e 1. 2: M ode l s of e vol ut i on us e d i n e s t i m a t e s of di ve r ge nc e a t va r i ous t a xonom i c l e ve l s M t D N A i s t he m ode l f or c onc a t e na t e d 16S a nd c ox 1 da t a s e t s E s t i m a t e d ba s e f r e que nc i e s f or e a c h ge ne o r c onc a t e na t e d da t a s e t a r e i ndi c a t e d. T he s ha pe of t he ga m m a di s t r i but i on ( A l pha ) a nd pr op or t i on of i nva r i a nt s i t e s ( P i nva r ) a r e a l s o i ndi c a t e d f or t he va r i ous da t a s e t s N s t r e f e r s t o t he num be r of s ubs t i t ut i on t ype s unde r t he di f f e r e nt m ode l s T V M a nd T I M a r e t he T r a n s ve r s i ona l a nd T r a ns i t i ona l m ode l s of e vol ut i on r e s pe c t i ve l y. G T R i s e qui va l e nt t o t he G e ne r a l T i m e R e ve r s i bl e m ode l I a nd G r e f e r t o t he i nc or por a t i on o f t he i nva r i a nt s i t e s a nd ga m m a di s t r i but i on i nt o t he va r i ous m ode l s of e vo l ut i on. G e ne 16S ( T V M + I + G ) C ox 1 ( T I M + I + G ) m t D N A ( G T R + I + G ) H i s t one 3 ( G T R + I + G ) B a s e F r e que nc y A 0. 3434 0. 1959 0. 2542 0. 2080 C 0. 1252 0. 2303 0. 1730 0. 3474 G 0. 1551 0. 2451 0. 2079 0. 2651 T 0. 3763 0. 3287 0. 3648 0. 1795 A l pha 0. 2856 0. 2982 0. 3400 1. 6414 P i nva r 0. 1493 0. 4290 0. 4347 0. 6422 N s t 6 6 6 6

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48 T a bl e 1. 3: M a xi m um l i ke l i hood e s t i m a t e s of di ve r ge nc e ba s e d on m t D N A S om e e s t i m a t e s w e r e ba s e d on one c om pa r i s on, t he r e f or e no s t a nda r d de vi a t i o n or r a nge o f di ve r ge nc e s i s pr e s e nt e d. C om pa r i s on d + s t d R a nge W i t hi n S pe c i e s B os e l l i a m i m e t i c a 0. 0080 E l y s i a pat i na 0. 0027 E l y s i a papi l l os a 0. 0099 E l y s i a or nat a 0. 0153 + 0 0169 0. 0000 0. 0315 E l y s i a r uf e s c e ns 0. 0072 E l y s i a t i m i da 0. 0215 + 0 0163 0. 0013 0. 0361 E l y s i a t uc a 0. 0089 + 0 0049 0. 0054 0. 0123 P l ak obr anc hus oc e l l at us 0. 0304 T hur i di l l a r at na 0. 0154 T r i dac hi a c r i s pat a 0. 0156 + 0 0029 0. 0135 0. 0176 B e t w e e n G e ne r a E l y s i a/ E l y s i e l l a 0. 0999 + 0 0 217 0. 0607 0. 1536 E l y s i a/ P l ak obr anc hus 0. 0912 + 0 0190 0. 0615 0. 1570 E l y s i a/ T hur i di l l a 0. 1175 + 0 0242 0. 0509 0. 1740 E l y s i a/ T r i dac hi a 0. 1001 + 0 0197 0. 0499 0. 1560 E l y s i a/ T r i dac hi e l l a 0. 0881 + 0 0236 0. 0392 0. 1444 E l y s i e l l a/ P l ak obr anc hus 0. 0783 + 0 0098 0. 0713 0. 0852 E l y s i e l l a/ T hur i di l l a 0. 1039 + 0 0174 0. 0711 0. 1301 E l y s i e l l a/ T r i dac hi a 0. 0752 + 0 0049 0. 0723 0. 0809 E l y s i e l l a/ T r i dac hi e l l a 0. 0739 P l ak obr anc hus / T hur i di l l a 0. 0786 + 0 0106 0. 0570 0. 0954 P l ak obr a nc hus / T r i dac hi a 0. 0841 + 0 0052 0. 0757 0. 0919 P l ak obr anc hus / T r i dac hi e l l a 0. 0848 + 0 0042 0. 0818 0. 0878 T hur i di l l a/ T r i dac hi a 0. 1143 + 0 0190 0. 0785 0. 1444 T hur i di l l a/ T r i dac hi e l l a 0. 1102 + 0 0205 0. 0807 0. 1485 T r i dac hi a/ T r i dac hi e l l a 0. 062 9 + 0. 0035 0. 0599 0. 0667 B e t w e e n F a m i l i e s B os e l l i i da e / L i m a pont i i da e 0. 1449 + 0 0177 0. 1288 0. 1606 B os e l l i i da e / P l a c obr a nc hi da e 0. 0975 + 0 0177 0. 0656 0. 1445 B os e l l i i da e / V ol va t e l l i da e 0. 3013 + 0 0124 0. 2925 0. 3101 L i m a pont i i da e / P l a c obr a nc h i da e 0. 1936 + 0 0262 0. 1383 0. 2506 L i m a pont i i da e / V ol va t e l l i da e 0. 3672 + 0 0030 0. 3651 0. 3693 P l a c obr a nc hi da e / V ol va t e l l i da e 0. 3255 + 0 0378 0. 2576 0. 4042 B e t w e e n C l a de s S a c ogl os s a / A pl ys i om or pha 0. 3909 + 0 0411 0. 3217 0. 5196 S ys t e l l om m a t op hor a / O pi s t hobr a nc hi a 0. 4748 + 0 0462 0. 3761 0. 5768

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49 T a bl e 1. 4: M a xi m um l i ke l i hood e s t i m a t e s of di ve r ge nc e ba s e d on H i s t one 3. S om e e s t i m a t e s w e r e ba s e d on one c om pa r i s on, t he r e f or e no s t a nda r d de vi a t i on or r a nge o f di ve r ge nc e s i s pr e s e nt e d. C om pa r i s on d + s t d R a nge W i t hi n S pe c i e s E l y s i a or nat a 0. 0238 + 0 0119 0. 0031 0. 0347 E l y s i a papi l l os a 0. 0063 E l y s i a t i m i da 0. 0163 P l ak obr anc hus oc e l l at us 0. 0097 T r i dac hi a c r i s pat a 0. 0045 + 0 0020 0. 0033 0. 0067 T hur i di l l a r at na 0. 0097 B e t w e e n G e ne r a E l y s i a/ E l y s i e l l a 0. 1443 + 0 0403 0. 0847 0. 2367 E l y s i a/ P l ak obr anc hus 0. 1995 + 0 0440 0. 1369 0. 2959 E l y s i a/ T hur i di l l a 0. 1749 + 0 0546 0. 0834 0. 3133 E l y s i a/ T r i dac hi a 0. 2162 + 0 0350 0. 1483 0. 3018 E l y s i a/ T r i dac hi e l l a 0. 2298 + 0 0350 0. 1337 0. 3068 E l y s i e l l a/ P l ak obr anc hus 0. 1623 + 0 0046 0. 1590 0. 1656 E l y s i e l l a/ T hur i di l l a 0. 1014 + 0 0180 0. 0796 0. 1432 E l y s i e l l a/ T r i dac hi a 0. 2005 + 0 0078 0. 1955 0. 2096 E l y s i e l l a/ T r i dac hi e l l a 0. 2289 P l ak obr anc hus / T h ur i di l l a 0. 1383 + 0 0291 0. 1020 0. 2128 P l ak obr anc hus / T r i dac hi a 0. 2471 + 0 0067 0. 2370 0. 2557 P l ak obr anc hus / T r i dac hi e l l a 0. 2450 + 0 0028 0. 2430 0. 2469 T hur i di l l a/ T r i dac hi a 0. 2492 + 0 0208 0. 2100 0. 2925 T hur i di l l a/ T r i dac hi e l l a 0. 2494 + 0 0193 0. 2269 0. 2904 T r i dac hi a/ T r i dac hi e l l a 0. 1260 + 0 0074 0. 1211 0. 1345 B e t w e e n F a m i l i e s B os e l l i i da e / L i m a pont i i da e 0. 2222 + 0 0295 0. 2013 0. 2430 B os e l l i i da e / P l a c obr a nc hi da e 0. 2098 + 0 0358 0. 1357 0. 2780 L i m a pont i i da e / P l a c obr a nc hi da e 0. 2 701 + 0 0465 0. 1864 0. 3745 O xynoi da e / L i m a pont i i da e 0. 2550 + 0 0846 0. 1952 0. 3148 O xynoi da e / B os e l l i i da e 0. 3240 O xynoi da e / P l a c obr a nc hi da e 0. 3232 + 0 0503 0. 2537 0. 4662 B e t w e e n C l a de s S a c ogl os s a / A pl ys i om or pha 0. 2731 + 0 0565 0. 1618 0. 3808 S ys t e l l om m a t ophor a / O pi s t hobr a nc hi a 0. 2552 + 0 0356 0. 1899 0. 3309

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50 T a bl e 1. 5: B a ye s i a n pa r a m e t e r e s t i m a t e s f r o m t he G T R + I + G m ode l T he m ode l i s de r i ve d f r om t he c onc a t e na t e d m t D N A a nd nuc D N A da t a s e t B a s e f r e que nc i e s a r e e s t i m a t e d f or t he pa r t i t i o ns de f i ne d i n t he B a ye s i a n a na l ys i s P oi nt e s t i m a t e s a nd 95% c onf i de nc e i nt e r va l s a r e pr e s e nt e d f o r t he s ha pe of t he ga m m a di s t r i but i on ( A l pha ) a nd pr opo r t i on of i nva r i a nt s i t e s ( P i nva r ) R e l a t i ve r a t e i s t he r e po r t e d r a t e m ul t i pl i e r e s t i m a t e d by M r B a ye s G e ne B a s e F r e que nc i e s A l pha A C G T P oi nt E s t i m a t e 95% c onf i de nc e i nt e r va l 16S 0. 3436 0. 1205 0. 1658 0. 3702 0. 4741 0. 3094 0 7287 C ox 1 1s t 0. 2546 0. 2133 0. 2835 0. 2487 0. 3879 0. 1084 1. 3383 2nd 0. 1152 0. 2318 0. 2191 0. 4339 34. 1067 0. 2667 187. 5925 3r d 0. 3535 0. 0868 0. 1065 0. 4533 0. 8370 0. 6389 1. 0285 H 3 1s t 0. 2728 0. 2927 0. 3005 0. 1341 84. 5952 0. 5358 191. 9045 2nd 0. 2925 0. 2700 0. 2063 0. 2312 98. 0150 2. 7323 195. 5846 3r d 0. 1254 0. 4087 0. 2711 0. 1948 1. 8324 1. 1135 2. 8311

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51 T a bl e 1. 5: ( C ont i nue d) G e ne P i nva r R e l a t i ve R a t e P oi nt E s t i m a t e 95% c onf i de nc e i nt e r va l P oi nt E s t i m a t e 95% c onf i de nc e i nt e r va l 16S 0. 2850 0. 1347 0. 4045 0. 4410 0. 3645 0. 5158 C ox 1 1s t 0. 3097 0. 0164 0. 6631 0. 2264 0. 1557 0. 3373 2nd 0. 7933 0. 6062 0. 8944 0. 0199 0. 0108 0. 0391 3r d 0. 0089 0. 0003 0. 0269 5. 0152 4. 7703 5. 2551 H 3 1s t 0. 7197 0. 5480 0. 8391 0. 0485 0. 0252 0. 0781 2nd 0. 8732 0. 2895 0. 9915 0. 0093 0. 0007 0. 0508 3r d 0. 0945 0. 0280 0. 1701 0. 8442 0. 6792 1. 0449

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52 F i gur e 1. 1 : S a t ur a t i on a s i ndi c a t e d by t he non l i ne a r r e l a t i ons hi p be t w e e n unc or r e c t e d p di s t a nc e s a nd unc or r e c t e d p t r a ns ve r s i on di s t a nc e s f or 3 r d pos i t i ons o f A ) c o x 1 a nd B ) H i s t one 3. A 0 0 0 5 0 1 0 1 5 0 2 0 2 5 0 3 0 3 5 0 4 0 0 0 5 0 1 0 1 5 0 2 0 2 5 0 3 0 3 5 0 4 T r a n s v e r s i o n s u n c o r r e c t e d p B 0 0 0 5 0 1 0 1 5 0 2 0 2 5 0 3 0 0 0 5 0 1 0 1 5 0 2 0 2 5 0 3 3 r d p o s i t i o n s H i s t o n e 3 U n c o r r e c t e d p U n c o r r e c t e d p T r a n s v e r s i o n s u n c o r r e c t e d p 3 r d p o s i t i o n s c o x 1

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53 F i gur e 1. 2 : M a xi m um l i ke l i hood e s t i m a t e s of s e que nc e di ve r ge nc e ba s e d on m t D N A S t a nda r d de vi a t i ons f or m e a n e s t i m a t e s a r e i ndi c a t e d ( y e r r or ba r s ) T he x a xi s i s c a t e gor i c a l a nd r e pr e s e nt s 33 t a xonom i c c om pa r i s ons T h e s e c om pa r i s ons c or r e s pond t o t hos e pr e s e nt e d i n T a bl e 1 3 a nd a r e r a nke d by t a xonom i c l e ve l S e que nc e D i ve r ge nc e 0 1 0 0 1 0 2 0 3 0 4 0 5 0 6 T a xonom i c C om pa r i s on W i t hi n N om i na l S pe c i e s A m ong P l a c obr a nc hi da e G e ne r a A m ong S a c ogl os s a n F a m i l i e s A m ong O r de r s

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54 F i gur e 1. 3 : M a xi m um l i ke l i hood e s t i m a t e s of s e qu e nc e di ve r ge nc e ba s e d on H i s t one 3. S t a nda r d de vi a t i ons f or m e a n e s t i m a t e s a r e i ndi c a t e d ( y e r r o r ba r s ) T he x a xi s i s c a t e gor i c a l a nd r e pr e s e nt s t he 29 t a xonom i c c om pa r i s ons T he s e c om pa r i s ons c or r e s pond t o t hos e pr e s e nt e d i n T a bl e 1. 4 a nd a r e r a nke d by t a xonom i c l e ve l 0. 01 0. 09 0. 19 0. 29 0. 39 T a xonom i c C om pa r i s on W i t hi n N om i na l S pe c i e s A m ong P l a c obr a nc hi da e G e ne r a A m ong S a c ogl os s a n F a m i l i e s S e que nc e D i ve r ge nc e

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55 F i gur e 1. 4 : B a ye s i a n phyl ogr a m f or m t D N A P os t e r i or pr oba bi l i t y va l ue s a r e e xpr e s s e d a s pe r c e nt a ge s C ol or e d l i ne s a r e pol yt om i e s r e f e r e nc e d i n t e xt f or d i s c us s i on pur pos e s L oc a t i on a bbr e vi a t i ons a r e p r ovi de d i n T a bl e 1. 1 0. 1 s ubs t i t ut i ons / s i t e P l a ko b r a n ch u s o c el l a t u s G U P o cel l a t u s H A Th u r i d i l l a u n d u l a T. b a yer i T. r a t n a P H T. r a t n a G U Th u r i d i l l a n eo n a T. l i vi d a Th u r i d i l l a va t a e Th u r i d i l l a h o f f a e T. ca r l s o n i E l ys i a b en n et t a e B o s el l i a m a r cu s i E l ys i el l a p u s i l l a E l ys i a vi r i d i s E l ys i a ca n g u z u a E l ys i a s er ca E ch l o r o t i ca Tr i d a ch i el l a d i o m ed ea Tr i d a ch i a cr i s p a t a BE Tr i d a ch i a cl a r ki F K Tr i d a ch i a cr i s p a t a U S V I E l ys i a p r a t en s i s E s u b o r n a t a E l ys i a s et eo n s i s E cf a t r o vi r i d i s E l ys i a t i m i d a M ed E t i m i d a 2 B A E t i m i d a F K E t i m i d a 3 B A E l ys i a n i g r o ca p i t a t a E l ys i a cf j a p o n i ca E l ys i a o b t u s a E l ys i a o r n a t a P H E l ys i a s p 1 0 G U E o r n a t a F P E l ys i a r u f es cen s G U E r u f es cen s H A E l ys i a o r n a t a 9 J P E o r n a t a 7 J P E o r n a t a 8 J P E l ys i a s p 4 2 G U E l ys i a t r i s i n u a t a E l ys i a t u ca G O M E t u ca F K E t u ca B A E l ys i a p a p i l l o s a 6 B A E p a p i l l o s a 9 B A E l ys i a p a t i n a F K E p a t i n a G O M B o s el l i a m i m et i ca 1 B A B m i m et i ca 3 B A Co s t a s i el l a ku r o s h i m a e C. o cel l i f er a A s co b u l l a f r a g i l i s O x yn o e a n t i l l a r u m 1 0 0 1 0 0 1 0 0 1 0 0 8 2 9 4 1 0 0 9 2 9 5 9 5 1 0 0 9 9 9 5 1 0 0 8 9 1 0 0 1 0 0 1 0 0 7 5 8 2 8 7 7 3 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 7 0 9 6 9 9 7 9 7 1 1 0 0 1 0 0 1 0 0 1 0 0 9 2 1 0 0 1 0 0 1 0 0

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56 F i gur e 1. 5 : B a ye s i a n phyl ogr a m f or H i s t one 3 P o s t e r i or pr oba bi l i t y va l ue s a r e e xpr e s s e d a s pe r c e nt a ge s L oc a t i on a bbr e vi a t i ons a r e i ndi c a t e d i n T a bl e 1. 1 e xc e pt f or W A = W e s t e r n A t l a nt i c 0. 1 s ubs t i t ut i ons / s i t e Sy s t el l o mmat o p h o ra E l ys i a b en n et t a e E l ys i a p a t i n a E l ys i el l a p u s i l l a B o s el l i a m i m et i ca A p l ys i a ca l i f o r n i ca E l ys i a t u ca E l ys i a p a p i l l o s a E l ys i a c f. j a p o n i ca E l ys i a o b t u s a E l ys i a r u f es cen s E l ys i a o r n a t a P H E l ys i a o r n a t a F P E l ys i a s p 4 2 E l ys i a t r i s i n u a t a E l ys i a ca n g u z u a E l ys i a s er ca E l ys i a ch l o r o t i ca E l ys i a vi r i d i s Tr i d a ch i el l a d i o m ed ea Tr i d a ch i a cr i s p a t a BE Tr i d a ch i a cl a r ki F K Tr i d a ch i a cr i s p a t a U S V I O x yn o e a n t i l l a r u m Co s t a s i el l a ku r o s h i m a e Co s t a s i el l a o cel l i f er a Th u r i d i l l a h o f f a e P l a ko b r a n ch u s o c el l a t u s G U P l a ko b r a n ch u s o c el l a t u s H A Th u r i d i l l a ca r l s o n i Th u r i d i l l a r a t n a G U Th u r i d i l l a r a t n a G U Th u r i d i l l a b a yer i G U Th u r i d i l l a u n d u l a PH Th u r i d i l l a n eo n a H A Th u r i d i l l a l i vi d a G U Th u r i d i l l a va t a e G U E l ys i a n i g r o ca p i t a t a B o s el l i a m a r cu s i E l ys i a p r a t en s i s E l ys i a s u b o r n a t a E l ys i a t i m i d a W A E l ys i a t i m i d a M ed E l ys i a s et eo n s i s E l ys i a cf a t r o vi r i d i s E l ys i a o r n a t a J P 1 0 0 9 5 9 1 1 0 0 9 4 9 5 9 8 1 0 0 9 1 1 0 0 1 0 0 9 2 9 9 8 3 8 9 9 6 7 0 1 0 0 6 0 9 6 9 6 8 9 1 0 0 1 0 0 1 0 0 5 9 5 5 5 1 5 5 5 2

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57 F i gur e 1. 6 : P r opor t i on of nuc l e ot i de s A ) by ge ne f or a l l t hr e e ge ne s a nd B ) by pos i t i on f or t he pr ot e i n c odi ng ge ne s O nl y p r opor t i ons of A & T by pos i t i on a r e s how n f o r t he pr ot e i n c odi ng ge ne s P a r a m e t e r va l ue s w e r e ge ne r a t e d f r om G T R + I + G m ode l s e t t i ngs a ppl i e d t o ge ne onl y a nd ge ne by pos i t i on pa r t i t i on s i n t he B a ye s i a n a na l ys i s

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58 F i gur e 1. 7 : R e l a t i ve r a t e s of e vol ut i on A ) by ge ne a nd B ) by ge ne f or 16S a nd by pos i t i on f or t he pr ot e i n c odi ng ge ne s R e l a t i ve r a t e s w e r e d e t e r m i ne d unde r G T R + S S R ( S i t e S pe c i f i c R a t e ) m ode l s e t t i ngs a ppl i e d t o bot h ge ne onl y a nd ge ne by pos i t i on pa r t i t i on s

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59 F i gur e 1. 8 : R e l a t i ve r a t e s de r i ve d f r o m t he i ns t a nt a ne ous r a t e m a t r i x f or a l l ge ne s ge ne r a t e d f r om G T R + I + G by ge ne m ode l s e t t i ngs T he p r opor t i on of i nva r i a nt s i t e s a nd t he t ot a l num be r of nuc l e ot i de s ( by ge ne ) w e r e us e d t o t r a ns f or m t he r a t e m a t r i x i nt o num be r of s ubs t i t ut i ons pe r c a t e gor y.

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60 0. 1 s ubs t i t ut i ons / s i t e Sy s t el l o mmat o p h o ra A p l ys i a ca l i f o r n i ca B o s el l i a m i m et i ca E l ys i el l a p u s i l l a E l ys i a n i g r o ca p i t a t a B o s el l i a m a r cu s i E l ys i a p r a t en s i s E l ys i a s u b o r n a t a E l ys i a s et eo n s i s E l ys i a cf a t r o vi r i d i s E l ys i a t i m i d a W A E l ys i a t i m i d a M ed E l ys i a cf j a p o n i ca E l ys i a o b t u s a E l ys i a o r n a t a J P E l ys i a o r n a t a G U E l ys i a s p 1 0 G U E l ys i a o r n a t a F P E l ys i a r u f es cen s G U E l ys i a r u f es cen s H A E l ys i a s p 4 2 G U E l ys i a t r i s i n u a t a E l ys i a b en n e t t a e E l ys i a t u ca G O M E t u ca F K E t u ca B A E l ys i a p a t i n a E l ys i a p a p i l l o s a 6 B A E l ys i a p a p i l l o s a 9 B A E l ys i a ca n g u z u a E l ys i a s er ca E l ys i a ch l o r o t i ca E l ys i a vi r i d i s Tr i d a ch i el l a d i o m ed ea Tr i d a ch i a cr i s p a t a BE Tr i d a ch i a cl a r ki F K Tr i d a ch i a cr i s p a t a U S V I P l a ko b r a n ch u s o c el l a t u s G U P l a ko b r a n ch u s o c el l a t u s H A Th u r i d i l l a va t a e Th u r i d i l l a u n d u l a Th u r i d i l l a b a yer i Th u r i d i l l a r a t n a PH Th u r i d i l l a r a t n a G U Th u r i d i l l a n eo n a Th u r i d i l l a l i vi d a Th u r i d i l l a h o f f a e Th u r i d i l l a ca r l s o n i Co s t a s i el l a ku r o s h i m a e Co s t a s i el l a o cel l i f er a A s co b u l l a f r a g i l i s O x yn o e a n t i l l a r u m 9 5 9 9 8 7 9 7 8 5 9 8 9 7 7 2 7 4 8 7 6 1 9 8 7 2 6 6 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 F i gur e 1. 9 : B a ye s i a n phyl ogr a m o f G T R + I + G m od e l f or t he c om bi ne d m t D N A a nd nuc D N A da t a s e t s P os t e r i or pr oba bi l i t y va l ue s a r e e xpr e s s e d a s a pe r c e nt a ge C ol or e d l i ne s i ndi c a t e pol yt om i e s di s c us s e d i n t e x t a nd l oc a t i on a bbr e vi a t i ons a r e de t a i l e d i n T a bl e 1. 1 e xc e pt f or W A = W e s t e r n A t l a nt i c

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61 F i gur e 1. 10 : M a xi m um pa r s i m ony c l a dogr a m o f c onc a t e na t e d m t D N A a nd nuc D N A da t a s e t s C ons e ns u s of 12 t r e e s f ound du r i ng a he ur i s t i c s e a r c h w i t h 30 0 r a ndom s t e pw i s e a ddi t i on r e pl i c a t i ons B oot s t r a p va l ue s > 60 f r om 100 r e pl i c a t e s a r e i nd i c a t e d a bove t he br a nc he s L oc a t i on a bbr e vi a t i ons a r e de t a i l e d i n T a bl e 1. 1 e xc e pt f o r W A = W e s t e r n A t l a nt i c Sy s t el l o mmat o p h o ra E l ys i a b en n et t a e B o s el l i a cf m a r cu s i E l ys i a p r a t en s i s E l ys i a s u b o r n a t a E l ys i a s et eo n s i s E l ys i a cf a t r o vi r i d i s E l ys i a t i m i d a M ed E l ys i a t i m i d a B A + F K E l ys i a p a p i l l o s a 6 B A E l ys i a p a p i l l o s a 9 B A E l ys i a p a t i n a E l ys i a t r i s i n u a t a E l ys i a cf j a p o n i ca E l ys i a o b t u s a E l ys i a o r n a t a G U E l ys i a s p 1 0 G U E l ys i a o r n a t a F P E l ys i a r u f es cen s G U E r u f es cen s H A E l ys i a o r n a t a J P E l ys i a s p 4 2 G U E l ys i a n i g r o ca p i t a t a E l ys i el l a p u s i l l a E t u ca G O M E t u ca F K E t u ca B A E l ys i a ca n g u z u a E l ys i a s er ca E l ys i a ch l o r o t i ca E l ys i a vi r i d i s Tr i d a ch i el l a d i o m ed ea Tr i d a ch i a cl a r ki F K Tr i d a ch i a cr i s p a t a U S V I T. cr i s p a t a B E P l a ko b r a n ch u s o c el l a t u s G U P o cel l a t u s H A Th u r i d i l l a u n d u l a T. r a t n a G U T. r a t n a P H T. b a yer i T. n e o n a T. l i vi d a T. ca r l s o n i T. va t a e T. h o f f a e B o s el l i a m i m et i ca Co s t a s i el l a ku r o s h i m a e Co s t a s i el l a o cel l i f er a A s co b u l l a f r a g i l i s O x yn o e a n t i l l a r u m A p l ys i a ca l i f o r n i ca 8 3 9 2 9 3 1 0 0 7 4 9 9 9 0 1 0 0 1 0 0 1 0 0 9 4 6 7 8 8 1 0 0 9 0 1 0 0 1 0 0 9 3 6 7 9 0 7 5 1 0 0 1 0 0 1 0 0 1 0 0 8 5 6 8

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62 F i gur e 1. 11 : M a xi m um pa r s i m ony phyl ogr a m of c onc a t e na t e d m t D N A a nd nuc D N A da t a s e t s w i t h br a nc h l e ngt hs pr opor t i ona l t o una m bi guous c ha nge s N um be r s of c ha nge s a l ong br a nc he s a r e i ndi c a t e d. B r a nc he s t ha t w oul d c ol l a ps e i nt o t he pol yt om i e s i de nt i f i e d i n F i gur e 1. 9 a r e i nd i c a t e d us i ng t he s a m e c ol or s c he m e T he r e d l i ne s i ndi c a t e t he br a nc he s i nvol ve d i n t he l a r ge pol yt om y a m ong a l l e l ys i i ds gr e e n a nd bl ue l i ne s a r e t he t hur i di l l i d a nd E l y s i a or nat a pol yt om i e s r e s pe c t i ve l y. E l ys i a b en n et t a e B o s el l i a m a r cu s i E l ys i a p r a t en s i s E l ys i a s u b o r n a t a 4 3 E l ys i a s et eo n s i s E l ys i a cf a t r o vi r i d i s 4 4 3 0 E l ys i a t i m i d a M ed 2 0 4 1 3 9 2 7 E l ys i a p a p i l l o s a 4 5 E l ys i a p a t i n a 4 5 1 9 2 0 E l ys i a t r i s i n u a t a E l ys i a cf j a p o n i ca E l ys i a o b t u s a 1 3 E l ys i a r u f es cen s 1 9 8 E l ys i a o r n a t a J P 1 7 2 1 3 2 1 6 2 1 E l ys i a s p 4 2 E l ys i a n i g r o c a p i t a t a 3 0 2 6 1 9 E l ys i el l a p u s i l l a E l ys i a t u ca 4 5 2 3 2 4 E l ys i a ca n g u z u a E l ys i a s er ca E l ys i a ch l o r o t i ca E l ys i a vi r i d i s Tr i d a ch i el l a d i o m ed ea 4 7 Tr i d a ch i a cr i s p a t a 5 0 3 3 3 5 1 9 1 9 2 3 2 1 2 6 P l a ko b r a n ch u s o c el l a t u s 3 8 Th u r i d i l l a u n d u l a T. r a t n a G U T. r a t n a P H T. b a yer i 1 4 3 1 T. n eo n a T. l i vi d a 2 2 T. ca r l s o n i T. va t a e T. h o f f a e 2 5 3 1 1 8 2 7 2 1 3 5 B o s el l i a m i m et i ca 4 3 4 7 Co s t a s i el l a ku r o s h i m a e Co s t a s i el l a o cel l i f er a 4 8 6 1 A s co b u l l a f r a g i l i s O x yn o e a n t i l l a r u m 6 3 3 6 Sy s t el l o mmat o p h o ra A p l ys i a ca l i f o r n i ca 3 5 E l ys i a t i m i d a W A E l ys i a o r n a t a P H FP

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63 F i gur e 1. 12 : B a ye s i a n phyl ogr a m o f a s ubs a m pl e o f t a xa us e d t o t e s t l ong b r a nc h di vi s i on by m ul t i pl e s hor t br a nc he s P os t e r i or pr oba bi l i t y v a l ue s a r e e xpr e s s e d a s pe r c e nt a ge s N ode s ( a s i ndi c a t e d by c i r c l e d num be r s ) w i t h l ow ppv s uppor t a r e i ndi c a t e d by a r e d b ox T he pol yt om y not e d i n pr e vi ous a na l ys e s a r e i ndi c a t e d by r e d l i ne s 0. 1 s ubs t i t ut i ons / s i t e Sy s t el l o mmat o p h o ra A p l ys i a ca l i f o r n i ca B o s el l i a m i m et i ca E l ys i a s p 4 2 G U E l ys i el l a p u s i l l a E l ys i a s u b o r n a t a Tr i d a ch i a cl a r ki F K 9 3 5 1 E l ys i a p a p i l l o s a 9 B A E l ys i a b en n et t a e E l ys i a t u ca G O M 6 2 6 1 8 8 P l a ko b r a n ch u s o c el l a t u s G U Th u r i d i l l a h o f f a e 6 5 Th u r i d i l l a r a t n a PH Th u r i d i l l a l i vi d a 9 8 9 7 9 8 9 9 Co s t a s i el l a ku r o s h i m a e Co s t a s i el l a o cel l i f er a 1 0 0 1 0 0 A s co b u l l a f r a g i l i s O x yn o e a n t i l l a r u m 1 0 0 1 0 0 1 4 1 3 1 1 7 8 6 2 9 1 2 4 1 3 1 0 5

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64 F i gur e 1. 13 : P o r t i on o f B a ye s i a n phyl ogr a m ba s e d on t ot a l e vi de nc e ( F i gur e 1 9) C ol or e d boxe s a r e pr ovi de d f or e a s y r e f e r e nc e i n d i s c us s i on. P os t e r i or p r oba bi l i t y va l ue s e xpr e s s e d a s pe r c e nt a ge s N ode s w i t hout ppv i ndi c a t e d a l l ha ve a va l ue o f 100 L oc a t i on a bbr e vi a t i ons a r e de t a i l e d i n T a bl e 1 1 e xc e pt f or W A = W e s t e r n A t l a nt i c 0. 1 s ubs t i t ut i ons / s i t e E l ys i el l a p u s i l l a E l ys i a n i g r o ca p i t a t a B o s el l i a m a r cu s i E l ys i a p r a t en s i s E l ys i a s u b o r n a t a E l ys i a s et eo n s i s E l ys i a cf a t r o vi r i d i s E l ys i a t i m i d a B A + F K E l ys i a t i m i d a M ed E l ys i a cf j a p o n i ca E l ys i a o b t u s a E l ys i a o r n a t a J P E l ys i a o r n a t a G U E l ys i a s p 1 0 G U E l ys i a o r n a t a F P E l ys i a r u f es cen s G U E l ys i a r u f es cen s H A E l ys i a s p 4 2 G U E l ys i a t r i s i n u a t a E l ys i a b en n et t a e E l ys i a t u ca G O M E t u ca F K E t u ca B A E l ys i a p a t i n a E l ys i a p a p i l l o s a 6 B A E l ys i a p a p i l l o s a 9 B A E l ys i a ca n g u z u a E l ys i a s er ca E l ys i a ch l o r o t i ca E l ys i a vi r i d i s Tr i d a ch i el l a d i o m ed ea Tr i d a ch i a cr i s p a t a BE Tr i d a ch i a cl a r ki F K Tr i d a ch i a cr i s p a t a U S V I 9 9 7 2 7 4 8 7 6 1 9 8 7 2 6 6 T o a l l ot he r s

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65 C H A P T E R 2: E V I D E N C E O F I N C R E A S E D C L A D O G E N E S I S I N T H E F A M I L Y P L A C O B R A N C H I D A E I N T R O D U C T I O N W he t he r i nt r i ns i c f a c t or s ha ve a c c e l e r a t e d c l a doge ne s i s ha s l ong be e n a f oc us of s t udi e s i n e vol ut i ona r y bi ol ogy I gno r i ng t he r ol e of c om pe t i t i on i n e c ol ogi c a l di ve r s i f i c a t i on, bi ol og i s t s ha ve a t t e m pt e d t o i de nt i f y c a us a l r e l a t i ons hi ps be t w e e n f or m a nd s pe c i a t i on. T he c onc e pt of a n e vol ut i ona r y no ve l t y a s de f i ne d by M a yr ( 1963) i s a ny ne w l y a c qui r e d s t r uc t ur e o r p r ope r t y t ha t pe r m i t s t he pe r f o r m a nc e of a ne w f unc t i on, w hi c h i n t ur n w i l l ope n a ne w a da pt i ve z one I f t he s e e vol ut i ona r y nove l t i e s a s de f i ne d by M a yr p r om ot e di ve r s i f i c a t i on t he n t h e y a r e t ypi c a l l y r e f e r r e d t o a s ke y i nnova t i ons ( S l ow i ns ki & G uye r 1993 ) M os t a na l ys e s of ke y i nnova t i ons ha ve f oc us e d on hi ghe r t a xonom i c l e ve l s t ha n s pe c i e s or on m a c r oe vol ut i on ( S t r e e l m a n & K a r l 1997; H unt e r 1998 ) E xa m pl e s of ke y i nnova t i ons i nc l u de t he m ol a r c us ps of m a m m a l s ( J e r nva l l H unt e r & F o r t e l i us 1996 ) ne c t a r s pur s i n c ol um bi ne s ( H odge s & A r nol d 1995) l oc om o t or m odul e s i n bi r ds ( G a t e s y & D i a l 1996) a nd s ym bi os i s i n f or a m i ni f e r a ( N or r i s 1996) O t he r r e s e a r c he r s ha ve l ooke d f o r c or r e l a t i ons be t w e e n i nt r i ns i c a nd/ or e xt r i ns i c f a c t or s a nd c l a doge ne s i s ( P a r a di s 2005; F i s he r B l om be r g & O w e ns 2003 ) T he s e m e t hods di f f e r m e t hodol ogi c a l l y f r om t hos e a dvoc a t e d by S l ow i ns ki & G uye r ( 1993 )

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66 w hi c h us e a s i s t e r gr oup a s a s t a nda r d r e s ul t i ng i n a n e xa m i na t i on of r e l a t i ve num be r s of t a xa i ns t e a d of a bs ol ut e num be r s o f t a xa P a r a di s ( 2005) t a ke s a m or e t r a di t i ona l s t a t i s t i c a l a ppr oa c h of a na l yz i ng s e ve r a l t r a i t s s i m u l t a ne ous l y i n a m ode l f r a m e w or k a nd t he n us i ng l i ke l i hood r a t i o t e s t s t o a s s e s s t he s i gni f i c a nc e of t he i ndi vi dua l t r a i t 's e f f e c t on di ve r s i f i c a t i on r a t e s T hi s c o r r e l a t i ve a ppr oa c h i nc or por a t e s t he phyl oge ny, t r a i t s o f r e c e nt s pe c i e s a nd t he e s t i m a t i on o f a nc e s t r a l c ha r a c t e r s t a t e s e i t he r by pa r s i m ony or m a xi m um l i ke l i hood ( M L ) m e t hods f r om e i t he r c o nt i nuous or di s c r e t e c ha r a c t e r s T he t ype of c ha r a c t e r a nd m i s s i ng s t a t e s f or t e r m i na l O T U s w i l l l i m i t t he c hoi c e of m e t hod f o r e s t i m a t i on of a nc e s t r a l s t a t e s a s M L m e t hods do n ot a l l ow f o r m i s s i ng c ha r a c t e r t ype s M os t s t udi e s us e c ont i nuous c ha r a c t e r s s uc h a s body s i z e or t w o s t a t e di s c r e t e c ha r a c t e r s s uc h a s pr e s e nc e / a bs e nc e of a n e c ol ogi c a l c ha r a c t e r i s t i c T he a ppl i c a t i on of i nde pe nde nt c ont r a s t s i n a c o m pa r a t i ve f r a m e w or k ha s be e n us e d t o s t udy c or r e l a t i ons be t w e e n t r a i t s i n a phyl oge ne t i c c ont e xt ( F e l s e ns t e i n, 1985) how e ve r m os t a na l ys i s pr ogr a m s r e qui r e e i t he r bot h t r a i t s t o be c ont i nuous or a t l e a s t one t r a i t t o be c ont i nuous A l l m e t hods a s s um e a f ul l y bi f u r c a t i ng t r e e a nd no m i s s i ng da t a f or t e r m i na l O T U s O pi s t hobr a nc hs a r e a hi ghl y s pe c i os e gr oup o f ga s t r opods w i t h 5000 6000 na m e d s pe c i e s ( W ge l e & K l us s m a n K ol b, 2005) T he hi s t or y of t a xonom i c s t udy of t he opi s t hobr a nc hs i s a l ong one w i t h o r i gi na l de s c r i pt i ons da t i ng t o t he s e ve nt e e nt h c e nt ur y ( e g. Sc y l l ae a pe l agi c a L i nna e us 1758) W hi l e pa s t r e s e a r c he r s ha ve be e n qui t e f r e ne t i c i n t he de s c r i pt i ons of s pe c i e s r e l a t i ve l y l i t t l e a t t e nt i on ha s be e n pa i d t o ge ne r a l l i f e hi s t or y pa t t e r ns s uc h a s l a r va l de ve l opm e nt r e p r od uc t i ve be ha vi or or f ood c hoi c e N ot a bl e e xc e pt i ons t o t hi s l a c k of i nf o r m a t i on e xi s t s uc h a s A pl y s i a c al i f or ni c a

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67 ( A nge l oni B r a dbur y & B ur t on 2003 ; K r i e gs t e i n, C a s t e l l uc c i & K a nde l 1974) M e m be r s of t he or de r S a c ogl os s a i nc l ude t he s ol a r pow e r e d s e a s l ugs ( R um pho, S um m e r & M a nha r t 2000) s uc h a s E l y s i a ( = T r i dac hi a) c r i s pat a M r c h, 1863. T he o r de r S a c ogl os s a c ons i s t s of ni ne f a m i l i e s w i t h a s f e w a s t w o t o a s m a ny a s 106 de s c r i be d s pe c i e s pe r f a m i l y ( T a bl e 2. 1; J e ns e n, 199 7) T he f a m i l i e s L i m a pont i i da e G r a y, 1847 a nd P l a c obr a nc hi da e G r a y, 1840 dom i na t e i n t e r m s o f s pe c i e s r i c hne s s w i t h 89 a nd 106 s pe c i e s r e s pe c t i ve l y ( J e ns e n, 1997) N um e r ous a ut hor s ha ve s ugge s t e d a n a da pt i ve r a di a t i on w i t hi n t he S a c ogl os s a a s s oc i a t e d w i t h hos t pl a nt s ( C l a r k & B us a c c a 197 8; J e ns e n, 1997) T o s uppor t t hi s hypot he s i s of a da pt i ve r a di a t i on, e xa m i na t i on o f f a m i l y l e ve l phyl oge ni e s i s a us e f ul a r e a of i nve s t i ga t i on, a s i t c a n c l a r i f y w he t he r t he r e por t e d e xi s t e nc e of l a r ge num be r s of s pe c i e s i s a n a r t i f a c t of t a xonom i c c onf us i on o r r e f l e c t s t r ue c l a doge ni c e ve nt s ( S l ow i ns ki & G uye r 1993 ) I s t he s pe c i e s r i c hne s s obs e r ve d w i t hi n f a m i l i e s a s s oc i a t e d w i t h a ke y i nnova t i on t ha t ha s i nc r e a s e d s pe c i a t i on r a t e ? H e r e t he f oc us i s on a s ubs e t of s pe c i e s w i t hi n t he P l a c obr a nc hi da e t o de t e r m i ne i f a c ha nge i n t he r a t e of c l a doge ne s i s ha s oc c ur r e d. I n a ddi t i on t o t he e xa m i na t i on of r a t e of c l a doge ne s i s l i f e hi s t or y t r a i t s s uc h a s l a r va l de ve l opm e nt k l e pt opl a s t y a nd f ood c hoi c e a r e e xa m i ne d a s pot e n t i a l c a us e s of c ha nge s i n r a t e us i ng r e c ons t r uc t i on o f a nc e s t r a l c h a r a c t e r s t a t e s M A T E R I A L S A N D M E T H O D S A t ot a l of 24 de s c r i be d s pe c i e s f r om P l a c obr a nc hi d a e t w o s pe c i e s f r om B os e l l i i da e a nd t w o s pe c i e s f r om a s i ngl e ge nus i n L i m a pont i i da e w e r e us e d i n t hi s

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68 a na l ys i s ( T a bl e 2. 2) T he a na l ys i s w a s l i m i t e d t o a n i nt e r m e di a t e num be r of s pe c i e s f or t he f ol l ow i ng r e a s ons F i r s t i nc l us i on of a l l s e que nc e d s a m pl e s r e s ul t e d i n a l a r ge pol yt om y de e p w i t hi n t he phyl oge ny T hi s i s a s of t pol yt om y r e s ul t i ng f r om t he l a c k of i nf or m a t i ve c ha r a c t e r s a t t hi s l e ve l ( C ha pt e r 1) T hr ough t r i a l a nd e r r or I di s c ove r e d t ha t r e m ova l of popul a t i on l e ve l s a m pl e s a nd s pe c i e s t ha t c ons i s t e nt l y m ove d a r ound t he t r e e i n pr e vi ous a na l ys i s r e s ul t e d i n be t t e r r e s ol ut i on of t he phyl o ge ny. S e c ond, a n a t t e m pt w a s m a de t o m a xi m i z e t he nu m be r o f s pe c i e s f or w hi c h da t a on va r i ous c ha r a c t e r t r a i t s a r e a va i l a bl e f r om t he l i t e r a t ur e ( T a bl e 2 3) T ot a l c e l l D N A w a s i s ol a t e d f r om a s m a l l por t i on of t he a nt e r i or e nd of t he a ni m a l s ubj e c t e d t o a non boi l i ng c he l e x m e t hod ( W a l s h, M e t z ge r & H i guc hi 1991) a nd us e d i n s ubs e que nt pol ym e r a s e c ha i n r e a c t i on ( P C R ) a m pl i f i c a t i ons o f t hr e e ge ne s A l l t r e a t e d s a m pl e s w e r e di l ut e d w i t h 1X T E ( 10 m M T r i s 1 m M E D T A ; pH 7. 5 ) a nd s t or e d a t 20 C S e gm e nt s o f t w o m i t oc hondr i a l ge ne s ( ~ 700 bp o f c yt oc hr om e c oxi da s e s ubuni t I a nd ~ 450 bp o f t he l a r ge s ubuni t R N A ) a nd one nu c l e a r ge ne ( ~ 380 bp of H i s t one 3) w e r e P C R a m pl i f i e d w i t h pr i m e r pa i r s r e s pe c t i ve l y, L C O 1490 5 G G T C A A C A A A T C A T A A A G A T A T T G G 3 a nd H C O 2198 5 T A A A C T T C A G G G T G A C C A A A A A A T C A 3 ( F ol m e r e t a l 1994) 16 S s a r 5 C G C C T G T T T A T C A A A A A C A T 3 a nd 16s a 5 C T C C G G T T T G A A C T C A G A T C 3 ( K e s s i ng e t a l 1989 ) a nd H 3F 5 A T G G C T C G T A C C A A G C A G A C V G C 3 a nd H 3R 5 A T A T C C T T R G G C A T R A T R G T G A C 3 ( C ol ga n, P onde r & E ggl e r 2000) A m pl i f i c a t i on r e a c t i ons ( 25 o r 50 L ) c ons i s t e d of 1X buf f e r ( E nz ypol L T D D e nve r C O ) 1 5 uni t s of E nz ypol P l us 2000 pol ym e r a s e ( E nz ypol L T D D e nve r C O ) 0 2 m M e a c h dN T P s 3. 0 m M M gC l 2 ( c ox 1 a nd 16S ) o r

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69 1. 5 m M M gC l 2 ( H 3) 0 5 M o f e a c h pr i m e r 1. 0 M B e t a i ne 0. 12 g/ L of bovi ne s e r um a l bum e n, a nd 2 0 4. 0 L of t e m pl a t e T he c yc l i ng c ondi t i ons f or t he c ox 1 a nd 16S pr i m e r s c ons i s t e d of 1 m i n. a t 95 C f ol l ow e d by 3 5 45 c yc l e s of 30 s e c a t 95 C 45 s e c a t 48 C a nd 1 m i n a t 72 C w i t h a f i na l e xt e ns i on of 3 m i n. a t 72 C C yc l i ng c ondi t i ons f or t he H 3 pr i m e r s c ons i s t e d of 1 c yc l e of 4 m i n a t 95 C 1 m i n. a t 50 C a nd 1 m i n a t 72 C f ol l ow e d by 35 c yc l e s of 45 s e c a t 95 C 30 s e c a t 52 C a nd 45 s e c a t 7 2 C a nd a f i na l e xt e ns i on of 3 m i n a t 72 C A t e m pl a t e f r e e r e a c t i on w a s i nc l ude d f or t he de t e c t i on of c ont a m i na t i on. A m pl i c ons w e r e pur i f i e d us i ng s t e r i l e na nopur e w a t e r a nd 30, 000 M W M i l l i por e f i l t e r s ( M i l l i po r e I nc B e df or d, M A ) or a Q I A qui c k P C R pur i f i c a t i on ki t ( Q i a ge n, I nc V a l e nc i a C A ) T he m a s s of t he a m pl i c ons w a s de t e r m i ne d by c om pa r i ng e t hi di um br om i de s t a i ni ng i nt e ns i t y o f 2 0 5 0 L o f e a c h pu r i f i e d r e a c t i on r e l a t i ve t o a s t a nda r d m a s s D N A l a dde r ( I nvi t r oge n L i f e T e c hnol ogi e s C a r l s ba d, C A ) C yc l e s e que nc i ng r e a c t i ons ( A m e r s ha m E T T e r m i na t or K i t A m e r s ha m B i os c i e nc e s C or p. B i s c a t a w a y, N J ) w e r e c onduc t e d w i t h a ppr oxi m a t e l y 100 ng of pur i f i e d P C R pr oduc t a c c or di ng t o m a nuf a c t ur e r 's s pe c i f i c a t i ons a nd f l uor e s c e nt l y l a b e l e d pr oduc t s w e r e s i z e s or t e d a nd vi s ua l i z e d us i ng a n A B I 310 G e ne t i c A na l yz e r ( A p pl i e d B i os ys t e m s I nc F os t e r C i t y C A ) T he s e que nc e s f r om bot h s t r a nds of t he a m pl i c on w e r e c om pa r e d a nd e di t e d ( w he n ne e de d) us i ng S e que nc he r ( v4 1; G e ne C ode s C or p A nn A r bor M I ) T he 16 S g e ne r e gi on f r a gm e nt s w e r e a l i gne d t o A pl ys i om or pha s e c onda r y s t r uc t ur e us i ng S e a vi e w ( G a ul t i e r G ouy & G a ut i e r 1996 ) a nd hype r va r i a bl e r e gi ons w he r e no one a l i gnm e nt a ppe a r e d s upe r i or ( i e m i ni m i z e d c ha nge s ) t o a not he r w e r e e xc l ude d f r om f ur t he r

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70 a na l ys e s T he ope n r e a di ng f r a m e s f or t he c ox 1 a nd H 3 ge ne s w e r e us e d t o a i d i n p r ope r a l i gnm e nt A B a ye s i a n f r a m e w or k w a s us e d t o a s s e s s r e l a t i ons hi ps a m ong t he s pe c i e s of i nt e r e s t ( M r B a ye s v3. 1. 2 ; H ue l s e nbe c k & R onqui s t 2001, R onqui s t & H ue l s e nbe c k, 2003) P r i or t o r unni ng M r B a ye s t he be s t f i t m od e l w a s e s t i m a t e d us i ng M r M ode l t e s t ( v2. 2; N yl a nde r 2004 ) w hi c h us e s A ka i ke I nf o r m a t i on C r i t e r i a a nd a n a bbr e vi a t e d s e t o f pot e nt i a l m ode l s t o t e s t i n c om pa r i s on t o M ode l t e s t ( v3. 7 ; P os a da & C r a nda l l 1998 ) A l l B a ye s i a n a na l ys e s w e r e r un i n a n M P I e nvi r on m e nt ( A l t e ka r e t a l 2004 ) us i ng t he R e s e a r c h C om put i ng C or e F a c i l i t y ( R C C F ) a t t he U ni ve r s i t y of S ou t h F l o r i da T he da t a w e r e di vi de d i nt o 7 pa r t i t i ons : put a t i ve 1 s t 2 n d a nd 3 r d c odon pos i t i ons of c ox 1 a l l pos i t i ons of 16S e xc e pt f o r hype r va r i a bl e r e gi ons a nd put a t i ve 1 s t 2 n d a nd 3 r d c odon pos i t i ons of H i s t one 3. I n a l l B a ye s i a n s e a r c he s t w o r uns of 1, 000 000 ge ne r a t i ons w e r e c onduc t e d s i m ul t a ne ous l y a nd s a m pl e d e ve r y 1, 00 0 ge ne r a t i ons T o a s s e s s c on ve r ge nc e of t he M C M C s a m pl i ng r uns t he a ve r a ge s t a nda r d de vi a t i on of t he s pl i t f r e que nc i e s of t he t w o r uns w a s i ns pe c t e d a nd i f gr e a t e r t ha n 0 01 a n a ddi t i ona l one m i l l i on ge ne r a t i ons w e r e r un ( R onqui s t H ue l s e nbe c k & va n de r M a r k, 2006) T hi s pr oc e s s w a s r e pe a t e d unt i l t he a ve r a ge s t a nda r d de vi a t i on of t he s pl i t f r e que nc i e s of t he t w o r uns w a s l e s s t ha n 0. 01. T o de t e r m i ne t he bur ni n num be r t he pa r a m e t e r s of a l l i ndi vi dua l r uns w e r e s um m a r i z e d a nd t he i ni t i a l r uns be l ow t he a s ym pt o t e w e r e di s c a r de d. I n ge ne r a l onl y t he l a s t 500 s a m pl e s of ge ne r a t i ons f r om bot h r uns w e r e us e d t o de t e r m i ne pa r a m e t e r a nd pos t e r i or pr oba bi l i t y va l ue s I n a ddi t i on t o a s s e s s i ng c onve r ge nc e dur i ng t he a na l ys i s t he c ha i n s w a p i nf or m a t i on f or e a c h i ndi vi dua l r un w a s e xa m i n e d a nd i f t he pr opo r t i on o f

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71 s uc c e s s f ul s t a t e e xc ha nge s be t w e e n c ha i n s w a s be t w e e n 10 a nd 70% t he n c onve r ge nc e w i t hi n t he i ndi v i dua l r uns w a s a s s um e d ( R onqui s t e t a l 2006) M ode l pa r a m e t e r s pr opor t i on o f i nva r i a nt s i t e s ga m m a di s t r i but i on a nd nuc l e ot i de s ubs t i t ut i on r a t e s w e r e e s t i m a t e d i nde pe nde nt l y f or e a c h da t a s e t us i ng M r B a ye s va l ue s of f our c ha i ns a nd 0. 1 f or t he c ha i n t e m pe r a t ur e pa r a m e t e r M ul t i pl e r un s s t a r t i ng f r om r a ndom t r e e s w e r e c onduc t e d t o ve r i f y c onve r ge nc e L e ve l s of s uppor t f o r n ode s w e r e c ons i de r e d hi gh i f t he pos t e r i or pr oba bi l i t y va l ue ( p pv) w a s > 95, m ode r a t e i f be t w e e n 80 94 a nd l ow i f < 79 A n a s s e s s m e nt of c ha r a c t e r e vol ut i on of l i f e hi s t or y t r a i t s l a r va l de ve l opm e nt de gr e e of kl e pt opl a s t y a nd f ood c hoi c e w a s c ond uc t e d us i ng M a c C l a de ( v4. 08; M a ddi s on & M a ddi s on, 2003) C ha r a c t e r s w e r e c ode d a s di s c r e t e s t a t e s a nd t r e a t e d a s unor de r e d ( T a bl e 2. 3 ) A nc e s t r a l s t a t e s w e r e de t e r m i ne d us i ng pa r s i m ony m e t hods i m pl e m e nt e d i n M a c C l a de A l t hough l i ke l i hood r a t i o t e s t s of m a x i m um l i ke l i h ood va l ue s of t r e e s ge ne r a t e d unde r c l oc k a nd non c l oc k a s s um pt i ons a r e t he m o s t c om m on m e t hod t o t e s t f o r a m ol e c ul a r c l oc k, p r obl e m s a r e a s s oc i a t e d w i t h t hi s m e t hod. T he L R T t e s t s f o r a g l oba l uni f or m c l oc k; t he r e f o r e de vi a t i ons f r om t hi s g l ob a l c l oc k t ha t m a y oc c ur on a ny br a nc h or i n a ny c l a de c a n c a us e t he r e j e c t i on of a c l oc k. A n a l t e r na t i ve opt i on i s t o us e nonpa r a m e t r i c r a t e s m oot hi ng ( N P R S ) t o ge ne r a t e a n ul t r a m e t r i c t r e e ( S a nde r s on, 1997 ) a nd a n a xi s de pe nde nt on t i m e B e c a us e f os s i l da t a a r e none xi s t e nt f or t he s e s of t bodi e d t a xa t i m e i s a s m oot he d r a t e of c ha nge a l ong br a n c he s T he s m oot hi ng of r a t e i nvol ve s t he e s t i m a t i on of a l oc a l r a t e f or e a c h br a nc h a nd m i ni m i z a t i on of t he di f f e r e nc e be t w e e n l oc a l r a t e e s t i m a t e s a nd t he i m m e di a t e de s c e nda nt 's l oc a l r a t e T he B a ye s i a n ge ne r a t e d

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72 c ons e ns u s t r e e w i t h m e a n b r a nc h l e ngt hs w a s t r a ns f or m e d us i ng N P R S i nt o a n ul t r a m e t r i c t r e e A s I w a s onl y i nt e r e s t e d i n t he nu m be r of l i ne a ge s w i t hi n t he P l a c obr a nc hi da e t he m os t r e c e nt c om m on a nc e s t or B os e l l i a m i m e t i c a w a s a s s um e d t he m os t ba s a l node T he num be r of l i ne a ge s t hr ough t i m e pl ot w a s c ons t r uc t e d us i ng l og t r a ns f or m e d e s t i m a t e s of t he num be r o f l i ne a ge s obs e r ve d i n t he ul t r a m e t r i c t r e e ( N e e B a r r ow c l ough & H a r ve y, 1996) T o t e s t i f t he nu m be r of l i ne a ge s t hr ough t i m e w a s s i gni f i c a nt l y di f f e r e nt f r om r a ndom a r uns t e s t w a s c onduc t e d i n S P S S ( v12 0. 2 A pa c he S of t w a r e F ounda t i on I l l i noi s ) R E S U L T S A t ot a l of 1448 nuc l e ot i de s ( 16S : 535 nt a l i gne d, c ox 1 : 630 n t H 3: 321 nt ) f r om 28 s p e c i e s w e r e us e d i n t he a na l ys i s T w o r e gi ons c om pr i s i ng a t ot a l of 46 pos i t i ons of t he 16S a l i gnm e nt w e r e hi ghl y va r i a bl e a nd e xc l ude d f r om t he a na l ys i s C os t as i e l l a oc e l l i f e r a w a s de s i gna t e d a s t he out gr oup a s t hi s w a s t he c l os e s t s i s t e r gr oup t o t he B o s e l l i i da e a nd P l a c obr a nc hi da e i n a l a r ge r a na l ys i s ( C ha pt e r 1) T he be s t f i t m ode l a s c hos e n by A I C i n M r M ode l t e s t w a s G T R + I f o r t h e 16S s e que nc e s a nd G T R + I + G f or t he pr ot e i n c odi ng r e gi ons B a s e f r e que nc i e s ga m m a di s t r i but i on s ha pe a nd pr opo r t i on o f i nva r i a nt s i t e s w e r e e s t i m a t e d by M r B a ye s f or e a c h pa r t i t i on o f t he c onc a t e na t e d da t a s e t T he r e s ul t i ng c ons e ns us phyl ogr a m i s r e s ol ve d a t a l l node s e xc e pt f or E l y s i a ni gr oc api t at a a nd B os e l l i a m ar c us i w hi c h f o r m e d a pol yt om y a t t he ba s e of t he c l a de c om pr i s i ng E l y s i a t i m i da a nd ot he r s ( F i gur e 2. 1 ) T he m a j or i t y of node s s how e d hi gh pos t e r i or pr oba bi l i t y va l ue s ( ppv) T he r e m a i ni ng node s e xhi bi t e d l ow s uppor t T he s e

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73 f i ndi ngs a r e c ons i s t e nt w i t h t he l a r ge r phyl oge ne t i c a na l ys i s i nc l udi ng a l l a va i l a bl e O T U s T he E l y s i a pat i na c l a de w a s i nvol ve d i n t h e m a j or pol yt o m y de t e c t e d pr e vi ous l y a nd r e f l e c t s t he l a c k o f phyl oge ne t i c a l l y i nf or m a t i ve c ha r a c t e r s a t t hi s l e ve l F o r f ur t he r a na l ys e s i t i s a s s um e d t ha t t hi s i s t he c or r e c t phyl o ge ny. F or t he pur pos e of t r a c i ng c ha r a c t e r e vol ut i on, I a s s um e d t ha t t he r e w a s a bi f ur c a t i on a t t he E l y s i a ni gr oc api t at a/ B os e l l i a m ar c us i node pl a c i ng B m a r c us i ba s a l i n t hi s gr oup. C har ac t e r t r ac i ng L a r va l de ve l opm e nt a l t ype w a s c ode d a s di s c r e t e unor de r e d c ha r a c t e r s w i t h t hr e e s t a t e s ; pl a nkt ot r ophi c l e c i t hot r oph i c a nd di r e c t N o pol a r i t y i n t he e vol ut i on of de ve l opm e nt a l t ype w a s a s s um e d a s pr e vi ous s t udi e s ha ve s how n l a r va l de ve l opm e nt t o be qui t e l a bi l e i n e vol ut i on ( H a r t 2000 S c hul t z e t a l 2000 ) O f t he 28 s pe c i e s i nvol ve d i n t he a na l ys i s t he t e r m i na l s t a t e s f or onl y 15 w e r e know n i ndi c a t e d by boxe s on F i gu r e 2. 2. T he m os t pa r s i m oni ous r e c ons t r uc t i on ( M P R ) of l a r va l de ve l opm e nt on t he B a ye s i a n phyl oge ny r e s ul t e d i n 18 M P R s of s e ve n s t e ps ( F i gur e 2. 2 ) O ve r a l l t he r e c ons t r uc t i on s ugge s t s t w o pa r a l l e l c ha nge s f r om pl a nkt ot r ophi c t o l e c i t hot r ophi c m ode s a nd one pa r a l l e l c ha nge f r om pl a nkt ot r ophi c t o di r e c t or l e c i t hot r ophi c de ve l opm e nt T he l a t t e r c ha nge i s i ndi c a t e d i n bot h t he B os e l l i a m ar c us i c l a de a nd i n t he s pe c i e s E l y s i a c hl or ot i c a. I n t h r e e t a xa B os e l l i a m ar c us i E l y s i a t i m i da, a nd E c hl or ot i c a t he t e r m i na l s t a t e i s pol ym or phi c a nd 1 & 2 1 & 2 or 0 & 2 r e s pe c t i ve l y ( T a bl e 2 3) T he c l a s s i f i c a t i on f or l e ve l of kl e pt opl a s t y f ol l ow s t ha t of C l a r k ( 199 2 ) L e ve l s w e r e c ode d a s di s c r e t e unor de r e d c ha r a c t e r s w i t h s i x s t a t e s ; L e ve l 1, 2 3 4 5 a nd 6. L e ve l 1 o r ga ni s m s do not r e t a i n c hl or opl a s t s w i t h pl a s t i ds di ge s t e d i m m e di a t e l y a f t e r

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74 pha goc yt os i s L e ve l 2 a nd 3 or ga ni s m s r e t a i n pl a s t i ds f or a f e w hou r s or up t o 24 hour s r e s pe c t i ve l y, but ne i t he r pr oduc e s phot os ynt ha t e L e ve l 4 o r ga ni s m s pr oduc e phot os ynt ha t e i n t he f i e l d, bu t c e a s e pr oduc t i on a f t e r a f e w hour s i n t he l a b a nd di ge s t t he pl a s t i ds L e ve l 5 or ga ni s m s pr oduc e pho t os ynt ha t e f or l onge r t h a n 24 hou r s i n a da r k e nvi r onm e nt but f unc t i on c e a s e s a f t e r a w e e k of s t a r va t i on. L e ve l 6 or ga ni s m s e xhi bi t l ong t e r m f unc t i ona l r e t e nt i on w i t h phot os ynt ha t e pr oduc t i on f o r gr e a t e r t ha n 1 w e e k a f t e r s t a r va t i on. O f t he 28 s pe c i e s i nvol ve d i n t he a na l ys i s t he t e r m i na l s t a t e s f or onl y 10 s pe c i e s w e r e know n. T he M P R of de g r e e of kl e pt opl a s t y on t he B a ye s i a n phyl oge ny r e s ul t e d i n 8 M P R s of t hr e e s t e ps ( F i gu r e 2 3) O n l y one c l a de i ndi c a t e d a n e qui voc a l s t a t e f or t he a nc e s t r a l s t a t e a nd or t e r m i na l node I n t he E l y s i a pat i na c l a de t he a nc e s t r a l s t a t e w a s r e c ons t r uc t e d a s e i t he r L e ve l 2 5 or 6 a n d t he s e a r e t he m os t pa r s i m oni ous s t a t e s f or t he t w o unknow ns i n t hi s g r oup, E pat i n a a nd E be nne t t ae B e c a us e of t he l a r ge num be r of t ype s of a l ga e c ons um e d by t he s pe c i e s of i nt e r e s t t he f a m i l y o f e a c h t ype o f a l ga e w a s us e d i ns t e a d of ge ne r a ( T a bl e 2 3) T he f a m i l i e s w e r e c ode d a s di s c r e t e uno r de r e d c ha r a c t e r s w i t h e i ght s t a t e s C l a s s i f i c a t i on of a l ga l s pe c i e s t o f a m i l y w a s ba s e d on L a m & Z e c hm a n ( 2006) f o r t he s ubor de r s B r yops i di ne a e a nd H a l i m e di ne a e a nd G r a ha m & W i l c ox ( 2000) f or a l l ot he r s T he s e a gr a s s s t a t e r e pr e s e nt s t w o f a m i l i e s ( T a bl e 2. 3) but I ha ve us e d s e a gr a s s a s t he c a t e gor y he r e T he M P R of f ood c hoi c e on t he B a ye s i a n phyl oge ny r e s ul t e d i n 378 M P R s of 19 s t e ps ( F i gur e 2. 4)

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75 L i ne age s t hr ough t i m e T he B a ye s i a n phyl oge ny e xc l udi ng t he L i m a pont i i da e w a s t r a ns f or m e d i nt o a n ul t r a m e t r i c t r e e us i ng N P R S w i t h B os e l l i a m i m e t i c a a s t he ba s a l node T he num be r o f l i ne a ge s t hr ough t i m e ( L T T ) w a s l og t r a ns f or m e d a nd pl ot t e d a ga i ns t t he s m oot he d r a t e us e d a s a t i m e a xi s ( F i gu r e 2. 5 ) I f t he num be r of l i ne a ge s ha s i nc r e a s e d a t a c ons t a nt r a t e ( bi r t h r a t e = de a t h r a t e ) t he n a s t r a i ght l i ne i n t he s e m i l oga r i t hm i c L T T pl ot i s e xpe c t e d w he r e a s i f e xpone nt i a l gr ow t h i s oc c ur r i ng a c onve x s ha pe t o t he l i ne i s e xpe c t e d ( N e e e t a l 1996 ) T he s ha pe of t he l i ne he r e i s c onve x, e s pe c i a l l y i n t he r e gi on t o t he l e f t of t he f i r s t r e d l i ne ( F i gur e 2 5) i ndi c a t i ng w he n t he put a t i ve i nc r e a s e i n s pe c i a t i on r a t e be ga n C a l c ul a t i on of t he ga m m a ( ) s t a t i s t i c ( P ybus & H a r ve y, 2000 ) ge ne r a t e s a t e s t s t a t i s t i c f or t he nul l m ode l of c ons t a nt r a t e s w hi c h c a n be r e j e c t e d i f < 1. 645 T he s t a t i s t i c f or t he ul t r a m e t r i c t r e e s how n i n F i gu r e 2. 5 r e j e c t e d t he c ons t a nt r a t e s m ode l ( = 3 601, P = 0 0002) ; a nd P ybus & H a r ve y ( 2000 ) not e t ha t t hi s r e j e c t i on o f c ons t a nt r a t e s oc c ur s onl y i f s pe c i a t i on r a t e ha s de c r e a s e d ove r t i m e T h e pa t t e r n of br a nc hi ng e xpe c t e d w he n < 0 i s one w i t h m a ny node s c l os e t o t he r oo t of t h e t r e e a nd l ong t e r m i na l br a nc he s a s obs e r ve d i n t he phyl oge ny ( F i gu r e 2. 5 ) A r uns t e s t i ndi c a t e d t ha t t he num be r of l i ne a ge s t hr ough t i m e e xhi bi t e d a s i gni f i c a nt de pa r t ur e f r o m r a ndom ne s s ( Z = 4. 581 P 2 t a i l e d t e s t = 0. 000) D I S C U S S I O N F our l i ne s of e vi de nc e i ndi c a t e t he pr e s e nc e of a n e a r l y r a di a t i on w i t hi n t he P l a c obr a nc hi da e F i r s t t he c a l c ul a t e d s t a t i s t i c f o r t he P l a c obr a nc hi da e r e j e c t s t he nul l

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76 m ode l of c ons t a nt r a t e s of s pe c i a t i on a nd e xt i nc t i o n t hr oughout t i m e a nd a m ong l i ne a ge s S e c ond, t he c o nve x s ha pe of t he L T T pl ot i ndi c a t e s t ha t s pe c i a t i on r a t e s ha ve de c r e a s e d ove r t i m e w hi c h i s a ne c e s s a r y r e qui r e m e nt of a n e a r l y a nd r a pi d r a di a t i on T hi r d t he pr e ponde r a nc e of node s l oc a t e d t ow a r ds t he r oot p r ovi de s ge ne r a l e vi de nc e of a de c r e a s e i n s p e c i a t i on r a t e ove r t i m e F or e xa m pl e i f > 0 a nd s pe c i a t i on or e xt i nc t i on r a t e s a r e i nc r e a s i ng ove r t i m e t he n t he i nt e r na l node s of a p hyl oge ny w i l l be c l os e r t o t he t i ps t ha n e xpe c t e d unde r a c ons t a nt bi r t h a nd de a t h nu l l hyp ot he s i s C onve r s e l y, i f < 0 a nd s pe c i a t i on r a t e ha ve de c r e a s e d ove r t i m e t he n t he i nt e r na l node s w i l l be c l os e r t o t he r oot t ha n e xpe c t e d unde r a c ons t a nt r a t e s m ode l ( P ybus & H a r ve y, 2000) B e c a us e of t he a ppa r e nt de c r e a s e i n s pe c i a t i on a s i ndi c a t e d by f e w t e r m i na l node s i n t he phyl oge ny a nd t he va l ue of t he s t a t i s t i c ( P ybus & H a r ve y 2000 ) t he c ha nge i n s pe c i a t i on r a t e oc c ur r e d e a r l y i n t he e vol ut i on o f t he f a m i l y P l a c obr a nc hi da e A m or e a pp r opr i a t e t e s t f or t hi s phyl oge ny w oul d be t he M ont e C a r l o C ons t a nt R a t e s t e s t w hi c h a c c ount s f or m i s s i ng t a xa i n t he phyl oge ny ( P ybus & H a r ve y, 2000) ho w e ve r a ne c e s s a r y pr e r e qui s i t e of t hi s t e s t i s know l e dge of t he t ot a l num be r of s pe c i e s T he f our t h l i ne of e vi de nc e s i s pr ovi de d by a c om pa r i s on of t he t w o m a j or c l a de s de pi c t e d i n F i gur e 2 1, P l ak obr anc hus / T hur i di l l a a nd E l y s i a. T he r e l a t i ve r a t e of c l a doge ne s i s i s s i gni f i c a nt l y gr e a t e r w i t hi n t he m a j or E l y s i a c l a de ( P = 0 03) w hi c h m a y be t he ba s i s f or t he c onve x s ha pe of t he L T T pl ot A l t hough, a l l T hur i di l l a s pp. w e r e not i nc l u de d i n t he a na l ys i s t he ge nus i s s m a l l e r i n t e r m s of num be r o f s pe c i e s ( n = 16; G os l i ne r 1995) w he n c om pa r e d t o E l y s i a ( n= 76 90; J e ns e n, 1997) T he r e l a t i ve i nc r e a s e i n c l a doge ne s i s w he n c om pa r i ng t he P l ak obr anc hus / T hur i di l l a a nd E l y s i a c l a de s pr ovi de s f ur t he r s uppor t f or

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77 a n ove r a l l c ha nge i n c l a doge ne s i s O ne c a ve a t s houl d be m e nt i one d he r e M a ny uns a m pl e d s pe c i e s e xi s t w i t hi n t hi s f a m i l y; he r e on l y 24 a r e i nc l ude d, bu t a s m a ny a s 106 s pe c i e s a r e r e por t e d w i t hi n t he f a m i l y P l a c obr a nc h i da e ( J e ns e n, 19 97) A phyl oge ny of a l l e xt a nt s pe c i e s c oul d a f f e c t c onc l us i ons r e ga r di n g c l a doge ne s i s i n t ha t s pe c i a t i on r a t e s m a y a ppe a r t o be c ons t a nt ove r t i m e W ha t f a c t or s c oul d c ont r i but e t o a n i nc r e a s e i n c l a doge ne s i s w i t hi n t he P l a c obr a nc hi da e ? H e r e I ha ve e xa m i ne d t he e vol ut i on of t hr e e l i f e hi s t or y c ha r a c t e r i s t i c s : de gr e e of kl e pt opl a s t y, l a r va l de ve l opm e nt a l m ode a nd f ood c hoi c e T he s e l i f e hi s t or y c ha r a c t e r i s t i c s w e r e e xa m i ne d b e c a us e of t he di ve r s i t y of l a r va l de ve l opm e nt a l f or m s i n t he f a m i l y, t he pr e va l e nc e of e xc e l l e nt kl e pt opl a s t s know n f r om t hi s f a m i l y a nd t he di ve r s i t y of a l ga e f ood t ype s T he de gr e e of k l e pt opl a s t y doe s not a ppe a r t o be c ont r i but i ng t o t hi s i nc r e a s e a s w a s i ni t i a l l y s us pe c t e d, a s t he a nc e s t r a l node s f or bot h t he P l ak obr anc hus / T hur i di l l a a nd E l y s i a c l a de s e xhi bi t L e ve l 6 kl e pt opl a s t y a s t he a nc e s t r a l s t a t e T hi s r e c ons t r uc t i on m a y be bi a s e d be c a us e of t he a bs e nc e of i nf or m a t i on on m a ny o f t he t e r m i na l node s A s w i t h a l l l i f e hi s t or y c ha r a c t e r i s t i c s e xa m i ne d he r e t he t e r m i na l c ha r a c t e r s t a t e s f or m a ny t a xa a r e unknow n or pol ym or phi c w hi c h, i n t ur n, i m pa c t s t he m os t pa r s i m oni ous r e c o ns t r uc t i on of a nc e s t r a l s t a t e s by i nc r e a s i ng t he pot e nt i a l s t a t e s a nd e qui voc a l s t a t e s of a nc e s t r a l br a nc he s ( M a ddi s on & M a ddi s on, 2003) N one t he l e s s t he r e c ons t r uc t i on s ugge s t s t ha t kl e pt opl a s t y oc c ur r e d e a r l i e r i n t he c l a doge ne s i s of t he s a c ogl os s a ns ( e g. C os t as i e l l a oc e l l i f e r a i s a L e ve l 6 kl e pt opl a s t ) or t ha t kl e pt opl a s t y e vol ve d i nde pe nde nt l y i n t he t w o f a m i l i e s L i m a pont i i da e a nd P l a c obr a nc hi da e A m or e r e l e v a nt e xa m i na t i on of t he e f f e c t of

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78 kl e pt opl a s t y on s pe c i a t i on r a t e s w oul d i nvol ve t he i nc l us i on of a l l s a c ogl os s a n f a m i l i e s ; how e ve r da t a a r e not a va i l a bl e a t t hi s t i m e t o c ond uc t s uc h a n a na l ys i s I n t e r m s o f l a r va l de ve l opm e nt a l m ode c ha r a c t e r t r a c i ng s ugge s t s t ha t l a r va l de ve l opm e nt a l m ode i s pl a s t i c a nd t ha t ga i n o r l os s of s t a t e s m a y oc c ur i nd e pe nde nt l y of phyl oge ne t i c c ons t r a i nt s ( H a r t 2000) T hi s c onc l us i on i s s uppor t e d by t he pol ym or phi c s t a t e s of num e r ous t a xa B os e l l i a m ar c us i E l y s i a t i m i da a nd E c hl or ot i c a, a nd t he pr e di c t e d s t a t e c ha nge s f r om pl a nkt ot r ophi c t o di r e c t a nd pa r a l l e l s t a t e c ha nge s f r om pl a nkt ot r oph i c t o l e c i t hot r ophi c ( F i gur e 2 2) M or e s t udi e s of l a r va l de ve l opm e nt a l m ode i n t he r e m a i ni ng t a xa w i l l be i m pe r a t i ve t o a m or e a c c ur a t e r e c ons t r uc t i on of a n c e s t r a l s t a t e s F ood c hoi c e i n m e m be r s of t he f a m i l y P l a c obr a nc h i da e a ppe a r s t o be t he m os t c om pl i c a t e d i n t e r m s o f t he m os t pa r s i m oni ous r e c ons t r uc t i on ( > 300 M P R s ) di ve r s i t y a nd s t a t e c ha nge s T he m os t pa r s i m o ni ous r e c ons t r uc t i on s ugge s t s t ha t t he m os t r e c e nt c om m on a nc e s t or ( M R C A ) of t he m e m be r s of t he P l a c obr a nc hi da e f e d on U dot e a c e a e ( F i gur e 2 4) a s s ugge s t e d by J e ns e n ( 1997) T he M R C A of t he E l y s i a c l a de ( e xc l udi ng t he E l y s i a pat i na c l a de ) i s p r e di c t e d t o ha ve f e d on C odi a c e a e w i t h s ubs e que nt s hi f t s t o B r yops i da c e a e a nd ot he r f a m i l i e s i n t he r e m a i ni ng c l a de s A t e nt a t i ve r e c ons t r uc t i on of di e t c hoi c e i n t he f a m i l y s ugge s t s a U dot e a c e a e > C odi a c e a e > B r yops i da c e a e H a l i m e da c e a e P ol yphys a c e a e C a ul e r pa c e a e C l a d ophor a c e a e a nd V a uc he r i a c e a e pa t hw a y w i t h m ul t i pl e hos t s w i t c hi ng a nd a dopt i o n of uni que f ood s our c e s M e m be r s of t he P l a c obr a nc hi da e ge ne r a l l y f e e d on gr e e n a l ga e but f ood pr e f e r e nc e i s a di f f i c ul t de t e r m i na t i on i n s a c ogl os s a ns a s m os t r e por t s a r e ba s e d on obs e r va t i ons a nd not f ood c hoi c e e xpe r i m e nt s ( but s e e J e ns e n, 1983) O t he r s ha ve s t a t e d

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79 t ha t publ i s he d da t a on f ood p r e f e r e nc e i s i nc or r e c t ba s e d on c ur r e nt l a b e xpe r i m e nt s i nve s t i ga t i ng f ood c hoi c e i n s e l e c t e l ys i i ds ( S P i e r c e pe r s c om m ) F ur t he r c om pl i c a t i ng t he i s s ue of f ood pr e f e r e nc e i s t he l a c k of s t udi e s i nvol vi ng a t e m po r a l c om pone nt w hi c h ha s be e n i de nt i f i e d f o r a t l e a s t o ne s pe c i e s E l y s i a c f f ur v ac auda ( B r a ndl e y, 1984) A s s um i ng t ha t t he da t a a na l yz e d he r e a c c ur a t e l y r e f l e c t s f ood c hoi c e i n m e m be r s of t he P l a c obr a nc hi da e pr e l i m i na r y f i ndi ngs i ndi c a t e t ha t hos t s w i t c hi ng m a y s i gni f i c a nt l y a f f e c t s pe c i a t i on r a t e s T he s w i t c h f r om U dot e a c e a e t o C odi a c e a e a s a f ood c hoi c e by s l ugs c oul d ha ve ope ne d up m or e pot e nt i a l f ood c hoi c e s f o r t he s l ugs or i t m a y be t ha t pl a s t i c i t y i n f ood c hoi c e i s c om m on i n s om e c l a de s ( F i gur e 2 4) T r ow b r i dge & T odd ( 2001 ) de m ons t r a t e d hos t pl a nt s w i t c hi ng i n E l y s i a v i r i di s a nd t ha t c ha nge s i n hos t c oul d l e a d t o i nc r e a s e s i n de ve l opm e nt a l r a t e s a nd/ or m a xi m um s i z e of s l ugs H os t s w i t c hi ng a ppe a r s t o be be ne f i c i a l a nd m a y i nc r e a s e t he pot e nt i a l f or popul a t i on di f f e r e nt i a t i on a nd pot e nt i a l l y s pe c i a t i on. H os t s w i t c hi ng ha s be e n s ugge s t e d a s t he c a us e of s ym pa t r i c s pe c i a t i on i n s om e t e r r e s t r i a l p hyt opha gous i ns e c t s ( B e r l oc he r 1998 a nd r e f e r e nc e s t he r e i n) T he i nc r e a s e i n s pe c i a t i on r a t e w i t hi n t he P l a c obr a nc hi da e c oul d be a s s oc i a t e d w i t h t he s hi f t i n di e t a w a y f r om t he U dot e a c e a e t o C odi a c e a e a nd s ubs e que nt c ha nge s i n hos t s a m ong de r i ve d l i ne a g e s T he phy l oge ne t i c r e c ons t r uc t i on yi e l ds i nt e r e s t i ng pa t t e r ns r e l a t e d t o s pe c i a l i s t a nd ge ne r a l i s t s i f t he f ood c hoi c e o f t he i nc l ude d s pe c i e s a r e a c c ur a t e W i t hi n t he E l y s i a c anguz ua c l a de e xc l udi ng E l y s i a c hl or ot i c a t he be s t kl e pt opl a s t s f e e d on t he l a r ge s t n um be r of f a m i l i e s ( n = 8 ) t he r e f or e e xhi bi t i ng m or e of a ge ne r a l i s t s t r a t e gy i n f ood c hoi c e T h i s f i ndi ng s ugge s t s t ha t a hi gh de gr e e of kl e pt opl a s t y ( de m ons t r a t e d t h r ough

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80 e xpe r i m e nt a l s t udi e s ) e na bl e s t he ut i l i z a t i on o f m u l t i pl e di ve r s e a l ga l f a m i l i e s o r t ha t t he us e of m ul t i pl e a l ga l f a m i l i e s i nc r e a s e s t he pot e nt i a l f or hi gh f unc t i oni ng kl e pt opl a s t s A l t hough t he kl e pt opl a s t y c ha r a c t e r t r a c i ng i ndi c a t e s t ha t a l l m e m be r s o f t he o t he r de r i ve d c l a de s a r e L e ve l 6 kl e pt opl a s t s e xpe r i m e n t a l da t a f or onl y one s pe c i e s E l y s i a t i m i da a r e a va i l a bl e F ur t he r s t udi e s m a y i ndi c a t e t ha t t he de g r e e of kl e pt opl a s t y va r i e s w i t hi n t he s e t a xa ; t he r e f o r e c onc l us i ons r e ga r di ng a l i nk be t w e e n kl e pt opl a s t y a nd ge ne r a l i s t f e e di ng s t r a t e gy a r e pu r e l y s pe c ul a t i ve T he de r i ve d E l y s i a c l a de s a l l s ha r e C odi a c e a e a s t he f ood c hoi c e f or t he m os t r e c e nt c om m on a nc e s t or a nd t he s e t w o c l a de s e xhi bi t a l a r ge num be r o f s pe c i a l i s t s on di f f e r e nt f a m i l i e s of a l ga e C odi um s p. a s a f ood c hoi c e m a y e nha nc e hos t s w i t c hi ng a nd s ubs e que nt s pe c i a l i z a t i on i n f ood c hoi c e i n t he s e l i ne a ge s W i t hi n t he B os e l l i a m ar c us i c l a de t he c ha r a c t e r t r a c i ng unc ove r s t he hi ghe s t num be r of s pe c i a l i s t s on di f f e r e nt f a m i l i e s of a l ga e F or e xa m pl e E l y s i a t i m i da s pe c i a l i z e s on A c e t abul ar i a ( f a m i l y P o l yphys a c e a e ) E s ubor nat a s pe c i a l i z e s on C aul e r pa s pp. ( f a m i l y C a ul e r pa c e a e ) E s e t oe ns i s on C odi um s pp. ( f a m i l y C odi a c e a e ) a nd B os e l l i a m ar c us i on H al i m e da ( f a m i l y H a l i m e da c e a e ) F ood pr e f e r e nc e f or t he r e m a i ni ng m e m be r s of t hi s c l a de i s unknow n T he s i s t e r c l a de ( E l y s i a t r i s i nuat a ) a l s o c ont a i ns s pe c i a l i s t s on e i t he r B r yops i da c e a e or C o di a c e a e s ugge s t i ng a ge ne r a l t r e nd t ow a r ds s pe c i a l i s t he r bi vor e s i n m or e de r i ve d l i ne a ge s w i t hi n t he P l a c obr a nc hi da e I n t hi s a na l ys i s of a s ubs e t of s pe c i e s of t he f a m i l y P l a c obr a nc hi da e e vi de nc e of a n e a r l y r a di a t i on a nd de c r e a s e i n s pe c i a t i on ove r t i m e w a s di s c ove r e d. T hi s f i ndi ng i s s uppor t e d by t he va l ue of t he s t a t i s t i c t he l oc a t i o n of node s w i t hi n t he phyl oge ny a nd t he s ha pe of t he L T T pl ot A nc e s t r a l c ha r a c t e r s t a t e r e c ons t r uc t i ons s ugge s t t ha t f ood

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81 c hoi c e a nd s ubs e que nt hos t s w i t c hi ng ha ve pl a ye d i m por t a nt r o l e s i n t he c ha nge i n c l a doge ne s i s w i t hi n t he f a m i l y P l a c obr a nc hi da e L a r va l de ve l opm e nt doe s not a ppe a r t o ha ve pl a ye d a n i m por t a nt r ol e i n s pe c i a t i on r a t e w i t hi n t he f a m i l y P l a c obr a nc hi da e a s i t a ppe a r s t o be a l a bi l e c ha r a c t e r how e ve r f ur t he r i nf or m a t i on on l a r va l de ve l opm e nt f o r i ndi vi dua l s pe c i e s i s ne c e s s a r y. K l e pt opl a s t y a ppe a r s t o ha ve e vol ve d e a r l i e r i n t he s a c ogl os s a ns a s e vi de nc e d by t he a ppe a r a nc e of t hi s t r a i t i n m e m be r s of t he L i m a pont i i da e F u r t he r m or e a nc e s t r a l c ha r a c t e r s t a t e r e c ons t r uc t i on s ugge s t s t ha t t he a nc e s t or of a l l t h r e e f a m i l i e s B os e l l i i da e P l a c obr a nc hi da e a nd L i m a pont i i da e w a s a h i gh f unc t i oni ng kl e pt opl a s t ( i e L e ve l 6) ; t h e r e f or e kl e pt opl a s t y m a y ha ve pl a ye d a n i m por t a nt r o l e i n t he e a r l i e r di ve r s i f i c a t i on of t he O r de r S a c ogl os s a

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82 R E F E R E N C E S A L T E K A R G D W A R K A D A S S H U E L S E N B E C K J P & R O N Q U I S T F 2004. P a r a l l e l M e t r opol i s c oupl e d M a r kov c ha i n M ont e C a r l o f or B a ye s i a n phyl oge ne t i c i nf e r e nc e B i oi nf or m at i c s 20: 407 415 A N G E L O N I L B R A D B U R Y J W & B U R T O N R S 2003 M ul t i pl e m a t i ng pa t e r ni t y, a nd body s i z e i n a s i m ul t a ne ous he r m a p hr odi t e A pl y s i a c al i f or ni c a B e hav i or al E c ol ogy 14: 554 560. B E R L O C H E R S H 1998 C a n s ym pa t r i c s pe c i a t i on vi a hos t or ha bi t a t s hi f t be pr ove n f r om phyl oge ne t i c a nd bi oge ogr a phi c e vi de nc e ? I n: E ndl e s s F or m s : Spe c i e s and Spe c i at i on ( D J H ow a r d & S H B e r l oc he r e ds ) 9 9 113. O x f or d U ni ve r s i t y P r e s s L ondon. B E R T S C H H & S M I T H A A 1973 O bs e r va t i o ns on t hr e e opi s t hobr a nc hs ( M ol l us c a : G a s t r opoda ) of t he L a P a z a r e a B a j a C a l i f or ni a M e xi c o. Sout hw e s t e r n N at ur al i s t 18: 165 176. B R A N D L E Y B 1984. A s pe c t s of t he e c ol ogy a n d phys i ol ogy of E l y s i a c f f ur v ac auda ( M ol l us c a : S a c og l os s a ) B ul l e t i n of M a r i ne Sc i e nc e 34: 201 219.

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83 C L A R K K B 1992. P l a nt l i ke a ni m a l s a nd a ni m a l l i ke pl a nt s : s ym bi ot i c c oe vol ut i on of a s c ogl os s a n ( = s a c ogl os s a n) m ol l us ks t he i r a l ga l pr e y, a nd a l ga l pl a s t i ds I n: A l gae and Sy m bi os i s : P l ant s A n i m al s F ungi V i r us e s I nt e r ac t i ons E x pl or e d ( W R e i s s e r e d. ) 515 530. B i opr e s s L t d. B r i s t ol C L A R K K B & B U S A C C A M 1978 F e e di ng s pe c i f i c i t y a nd c hl or opl a s t r e t e nt i on i n f our t r opi c a l A s c ogl os s a w i t h a di s c us s i on of t he e xt e nt of c hl or opl a s t s ym bi os i s a nd t he e vol ut i on of t he o r de r J our nal o f M ol l us c an St udi e s 44: 272 282 C L A R K K B & J E N S E N K R 1981 A c om pa r i s on of e gg s i z e c a ps ul e s i z e a nd de ve l opm e nt pa t t e r ns i n t he or de r A s c ogl os s a ( S a c ogl os s a ) ( M ol l us c a : O pi s t hobr a nc hi a ) I nt e r nat i onal J our nal of I nv e r t e br at e R e pr oduc t i on 3: 57 64 C L A R K K B J E N S E N K R & S T I R T S H M 1 990. S ur ve y f or f unc t i ona l kl e pt opl a s t y a m ong W e s t A t l a nt i c A s c ogl os s a ( = S a c ogl os s a ) ( M ol l us c a : O pi s t hobr a nc hi a ) V e l i ge r 33: 339 45 C O L G A N D J P O N D E R W F & E G G L E R P E 2000 G a s t r opod e vol ut i ona r y r a t e s a nd P hy l oge ne t i c r e l a t i ons hi ps a s s e s s e d us i ng pa r t i a l 28S r D N A a nd hi s t one H 3 s e que nc e s Z ool ogi c a Sc r i pt a, 29: 29 6 3. F E L S E N S T E I N J 1985. P hyl oge ni e s a nd t he c o m pa r a t i ve m e t hod. A m e r i c an N at ur al i s t 1 25: 1 15. F I S H E R D O B L O M B E R G S P & O W E N S I P F 2003. E xt r i ns i c ve r s us i nt r i ns i c f a c t or s i n t he de c l i ne a nd e xt i nc t i on o f A u s t r a l i a n m a r s upi a l s P r oc e e di ngs of t he R oy al Soc i e t y of L ondon, B 270: 180 1 1808.

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87 M A R I N A & R O S J 1993. U l t r a s t r uc t ur a l a nd e c ol ogi c a l a s pe c t s of t he de ve l opm e nt of c hl or op l a s t r e t e nt i on i n t he s a c ogl os s a n ga s t r opod E l y s i a t i m i da M al ac ol ogi c al Soc i e t y of L ondon 59: 95 104 M A R I N A & R O S J 2004. C he m i c a l de f e ns e s i n s a c ogl os s a n opi s t hobr a nc hs : t a xonom i c t r e nds a nd e vol ut i ve i m pl i c a t i ons Sc i e n t i a M ar i na, 68( S uppl 1 ) : 227 241. M A Y R E 1 963. P opu l at i ons s pe c i e s and e v ol ut i on. H a r va r d U ni ve r s i t y P r e s s C a m br i dge M a s s a c hu s e t t s M I L E S C M & C L A R K K B 2002 C om pa r i s on of bi oc he m i c a l c om pos i t i on a nd de ve l opm e nt a l m ode i n t w o popul a t i ons o f C o s t as i e l l a [ O pi s t hobr a nc hi a : A s c ogl os s a ( = S a c ogl os s a ) ] J our nal of M ol l us c an St udi e s 68 : 101 109 N E E S B A R R A C L O U G H T G & H A R V E Y P H 1996. T e m por a l c ha nge s i n bi odi ve r s i t y: de t e c t i ng pa t t e r ns a nd i de nt i f yi ng c a us e s I n: B i odi ve r s i t y: A B i ol ogy of N um be r s a nd D i f f e r e nc e ( K J G a s t on, e d) 230 25 2. B l a c kw e l l S c i e nc e L ondon. N O R R I S R D 1996. S y m bi os i s a s a n e vol ut i ona r y i nn ova t i on i n t he r a di a t i on of P a l e oc e ne pl a nkt i c f or a m i ni f e r a P al e obi ol ogy 22: 461 480 N Y L A N D E R J A A 2004 M r M ode l t e s t v2. 2. P r ogr a m di s t r i but e d by t he a ut hor E vol ut i ona r y B i ol ogy C e nt r e U pps a l a U ni ve r s i t y. P A R A D I S E 2005. S t a t i s t i c a l a na l ys i s of di ve r s i f i c a t i on w i t h s pe c i e s t r a i t s E v ol ut i on 59: 1 12

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88 P I E R C E S K C U R T I S N E M A S S E Y S E B A S S A L K A R L S A & F I N N E Y C M 2006. A m or phol og i c a l a nd m ol e c ul a r c om pa r i s on be t w e e n E l y s i a c r i s pat a a nd a ne w s pe c i e s of kl e pt opl a s t i c s a c ogl os s a n s e a s l ug ( G a s t r opoda : O pi s t hobr a nc hi a ) f r om t he F l o r i da K e ys U S A M ol l us c an R e s e ar c h 26: 23 38. P O S A D A D & C R A N D A L L K A 1998 M O D E L T E S T : t e s t i ng t he m ode l o f D N A s ubs t i t ut i on. B i o i nf or m at i c s 14: 817 818. P Y B U S O G & H A R V E Y P H 2000. T e s t i ng m a c r oe vol ut i ona r y m ode l s us i ng i nc om pl e t e m ol e c ul a r phyl oge ni e s P r oc e e di ngs of t he R oy al Soc i e t y of L ondon, B 267: 2267 2272. R O N Q U I S T F & H U E L S E N B E C K J P 2003 M R B A Y E S 3: B a ye s i a n phyl oge ne t i c i nf e r e nc e unde r m i xe d m ode l s B i oi n f or m at i c s 19: 1572 1574. R O N Q U I S T F H U E L S E N B E C K J P & V A N D E R M A R K P 2006. M r B a ye s 3. 1 M a nua l A va i l a bl e on l i ne a t h t t p: / / m r ba ye s c s i t f s u. e du/ w i ki / i nde x. php/ M a nua l R U M P H O M E S U M M E R E J & M A N H A R T J R 2000. S o l a r pow e r e d s e a s l ugs M ol l us c / a l ga l c h l or opl a s t s ym bi os i s P l ant P hy s i ol ogy 123: 29 38 S A N D E R S O N M J 1997. A nonpa r a m e t r i c a ppr oa c h t o e s t i m a t i ng di ve r ge nc e t i m e s i n t he a bs e nc e of r a t e c ons t a nc y. M ol e c ul ar B i ol ogy and E v ol ut i on 14: 1218 1231. S C H U L T Z S R R I C E S R S I M O N J L & K A R L S A 2000 E vol ut i on of poe c i l ogony a nd t he bi oge ogr a phy of N or t h A m e r i c a n popul a t i ons of t he pol yc ha e t e St r e bl os pi o E v ol ut i on 54: 1247 1259

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89 S L O W I N S K I J B & G U Y E R C 1993. T e s t i ng w he t he r c e r t a i n t r a i t s ha ve c a us e d a m pl i f i e d di ve r s i f i c a t i on: a n i m pr ove d m e t hod ba s e d on a m ode l of r a ndom s pe c i a t i on a nd e xt i nc t i on. A m e r i c an N at ur al i s t 14 2: 1019 1024 S T R E E L M A N J T & S A K A R L 1997 R e c ons t r uc t i ng l a br oi d e vol ut i on w i t h s i ngl e c opy nuc l e a r D N A P r oc e e di ngs of t he R oy al Soc i e t y of L ondon, B 264 : 1011 1020. T H O M P S O N T E 1976 B i o l ogy of t he O pi s t hob r anc h M ol l us c s V ol I T he R a y S oc i e t y, L ond on. T R E N C H R K 1969 C hl or opl a s t s a s f unc t i ona l e ndos ym bi ont s i n t he m ol l us k T r i dac hi a c r i s pat a ( B e r gh) ( O pi s t hobr a nc hi a S a c ogl os s a ) N at ur e 222: 1071 1072 T R O W B R I D G E C D & T O D D C D 2001 H os t pl a nt c ha nge i n m a r i ne s pe c i a l i s t he r bi vor e s : s a c ogl os s a n s e a s l ugs on i nt r oduc e d m a c r oa l ga e E c ol ogi c al M onogr aphs 71: 219 243. W A L S H H E M E T Z G E R D A & H I G U C H I R 1991 C he l e x m e di um f o r s i m p l e e xt r a c t i on of D N A f o r P C R ba s e d t ypi ng f r om f or e ns i c m a t e r i a l B i oT e c hni que s 10: 506 513 W G E L E H & K L U S S M A N K O L B A 2005 O pi s t hobr a nc hi a ( M ol l us c a G a s t r opoda ) m o r e t ha n j us t s l i m y s l ugs S he l l r e d uc t i on a nd i t s i m pl i c a t i ons on de f e ns e a nd f o r a gi ng. F r ont i e r s i n Z ool ogy 2: D O I : 10. 11 86/ 1742 9994 2 3

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90 W E S T H H H A R R I G A N J F & P I E R C E S K 1984. H ybr i di z a t i on o f t w o popul a t i ons of a m a r i ne opi s t hobr a nc h w i t h di f f e r e nt de ve l opm e nt a l pa t t e r ns V e l i ge r 23 : 199 206. W I L L I A M S S I & W A L K E R D I 1999 M e s ohe r bi vor e m a c r oa l ga l i nt e r a c t i ons : f e e di ng e c ol ogy o f s a c ogl os s a n s e a s l ugs ( M ol l us c a O pi s t hobr a nc hi a ) a nd t he i r e f f e c t s on t he i r f ood a l ga e O c e anogr aphy an d M ar i ne B i o l ogy A nnual R e v i e w 37: 87 128.

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91 T a bl e 2. 1: S a c ogl os s a n f a m i l i e s ge ne r a a nd num b e r of s pe c i e s c ur r e nt l y r e c ogni z e d. F a m i l y G e nus # of S pe c i e s O xynoi da e R obur ne l l a, L obi ge r O x y noe 11 12 J ul i i da e J ul i a, B e r t he l i ni a 17 20 V ol va t e l l i da e A s c obul l a, V ol v at e l l a 20 26 B os e l l i i da e B os e l l i a 5 P l a t yhe dyl i da e P l at y he dy l e G as c oi gne l l a 2 P l a c obr a nc hi da e P l ak obr anc hus T hur i di l l a, E l y s i a 92 106 P ol ybr a nc hi i da e Sohge ni a, C y e r c e M our gona, P ol y br anc hi a, C al i phy l l a 24 28 H e r m a e i da e H e r m ae ops i s H e r m ae a, A pl y s i ops i s 19 25 L i m a pont i i da e St i l i ge r P l ac i da C al l i opae a O l e a, A l de r i a, A l de r i ops i s E r c ol ani a, L i m apont i a, C os t as i e l l a 54 89

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92 T a bl e 2. 2: T a xonom i c l i s t o f s pe c i e s us e d i n t he p hyl oge ne t i c a na l ys i s T he a c c e s s i on num be r f or e a c h s e que nc e of t he m t D N A a nd H i s t one 3 ge ne s i s i ndi c a t e d. L oc a t i on i s not t he r a nge o f t he s p e c i e s but r a t he r w he r e t h e i ndi vi dua l w a s c ol l e c t e d. N A i nd i c a t e s t ha t t he s e que nc e w a s not a va i l a bl e f or a na l ys i s T a xonom i c U ni t s L oc a t i on 16S C ox 1 H i s t one 3 C l a de S a c ogl os s a S ubc l a de P l a c obr a nc ha c e a S upe r f a m i l y P l a c obr a nc hoi de a G r a y 1 840 F a m i l y B os e l l i i da e E v. M a r c us 1982 B os e l l i a m ar c us i E v M a r c us 1972 B a ha m a s D Q 480191 D Q 471254 D Q 534783 B os e l l i a m i m e t i c a T r i nc he s e 1891 B a ha m a s D Q 480202 D Q 471212 D Q 534793 F a m i l y P l a c obr a nc hi da e G r a y 184 0 E l y s i a be nne t t ae T hom ps on, 1973 G ua m D Q 480183 D Q 471216 D Q 534778 E l y s i a c anguz ua M a r c us 1955 U S A : F l or i da D Q 480196 D Q 471219 D Q 534787 E l y s i a c hl or ot i c a G oul d 1870 U S A : M a s s a c hu s e t t s D Q 480200 D Q 471222 D Q 534791 E l y s i a ni gr oc api t at a B a ba 1957 J a pa n: O ki na w a D Q 480175 D Q 471226 D Q 534771 E l y s i a obt us a B a ba 1938 J a pa n: O ki na w a D Q 480182 D Q 471259 D Q 534777 E l y s i a or nat a S w a i ns on, 1840 J a pa n D Q 480181 D Q 471264 D Q 534776 E l y s i a pat i na M a r c us 19 80 U S A : F l or i da D Q 480189 D Q 471229 D Q 534782 E l y s i a pr at e ns i s O r t e a & E s pi nos a 1996 B a ha m a s D Q 480162 D Q 471258 D Q 534762 E l y s i a r uf e s c e ns P e a s e 1871 G ua m D Q 480171 D Q 471237 D Q 534768 E l y s i a s e r c a M a r c us 1955 B a ha m a s D Q 480192 D Q 47 1243 D Q 534784 E l y s i a s e t oe ns i s H a m a t a ni 1968 J a pa n: O ki na w a D Q 480163 D Q 471239 D Q 534763 E l y s i a s ubor nat a V e r r i l l 1901 U S A : F l or i da D Q 480165 D Q 471283 D Q 534765 E l y s i a t i m i da R i s s o, 1818 F r a nc e D Q 480169 D Q 471248 D Q 534767 E l y s i a t r i s i nuat a B a ba 1949 J a pa n: O ki na w a D Q 480174 N A D Q 534770 E l y s i a t uc a M a r c us & M a r c us 1 967 U S A : F l or i da D Q 480184 D Q 471249 D Q 534779 E l y s i a v i r i di s M ont a gu, 1804 P or t uga l D Q 480195 D Q 471211 D Q 534786

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93 T a bl e 2. 2: ( C ont i nue d) T a xonom i c U ni t s L oc a t i on 16S C ox 1 H i s t one 3 E l y s i a pus i l l a B e r gh 1872 U S A : H a w a i i D Q 480201 D Q 471236 D Q 534792 E l y s i a c r i s pat a M r c h, 1863 B e l i z e D Q 480199 D Q 471223 D Q 534790 E l y s i a di om e de a B e r gh 1894 C os t a R i c a D Q 480193 D Q 471 265 D Q 534785 T hur i di l l a bay e r i M a r c us 1965 G ua m D Q 480207 D Q 471271 D Q 534797 T hur i di l l a c ar l s oni G os l i ne r 1995 U S A : H a w a i i D Q 480214 D Q 471274 D Q 534804 T hur i di l l a undul a G os l i ne r 1995 P hi l i ppi ne s D Q 480210 D Q 471267 D Q 534800 T hur i di l l a v at ae R i s be c 1928 G ua m D Q 480212 D Q 471268 D Q 534802 P l ak obr anc hus oc e l l at us va n H a s s e l t 1824 U S A : H a w a i i D Q 480205 D Q 471270 D Q 534795 S upe r f a m i l y L i m a pont i oi de a G r a y, 1847 F a m i l y L i m a pont i i da e G r a y, 1847 C os t as i e l l a k ur os hi m ae I c hi ka w a 1993 G ua m D Q 480215 D Q 471252 D Q 534805 C os t as i e l l a oc e l l i f e r a S i m r ot h, 1895 B a ha m a s D Q 480216 D Q 471253 D Q 534806

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94 T a bl e 2. 3: C ha r a c t e r m a t r i x f o r s pe c i e s us e d i n t he a nc e s t r a l s t a t e r e c ons t r uc t i ons f or t hr e e l i f e h i s t or y t r a i t s L a r va l m ode : 0 = pl a nkt ot r ophi c 1 = l e c i t hot r ophi c 2 = d i r e c t o r e n c a ps ul a t e d. K l e pt opl a s t y: 0 = L e ve l 1, 1 = L e ve l 2 4 = L e ve l 5 5 = L e ve l 6. S our c e s f or l a r va l de ve l opm e nt : 1 M i l e s & C l a r k ( 2002) ; 2 J e ns e n & C l a r k ( 1983) ; 3 C l a r k & J e ns e n ( 1981) ; 4 W e s t e t a l ( 1984) ; 5 P i e r c e e t a l ( 2006) ; 6 M a r i n & R os ( 199 3) ; 7 J e ns e n ( 1992) ; 8 T hom ps on ( 1976 ) S our c e s f or kl e pt opl a s t y: 1 C l a r k e t a l ( 1990) ; 2 R um pho e t a l ( 2000) ; 3 T r e nc h ( 19 69) ; 4 M a r i n & R os ( 2004 ) ; 5 C l a r k & B us a c c a ( 1 978) ; 6 H i nde & S m i t h ( 1974) ; 7 I r e l a nd & S c he ue r ( 1979) S our c e s f o r f ood c hoi c e : A l l w e r e t a ke n f r om W i l l i a m s & W a l ke r ( 1999) e xc e pt E l y s i a c r i s pat a ( P i e r c e e t a l 2006 ) E s e t oe ns i s ( H a m a t a ni 1968) E t r i s i nuat a ( J e ns e n, 1985) E di om e de a ( B e r t s c h & S m i t h, 1973) a nd C os t as i e l l a oc e l l i f e r a ( M i l e s & C l a r k, 2 002) S pe c i e s L a r va l M ode K l e pt opl a s t y F ood C hoi c e ( F a m i l y ) C os t as i e l l a k ur o s hi m ae ? ? U dot e a c e a e C os t as i e l l a oc e l l i f e r a 2 1 5 1 U dot e a c e a e B os e l l i a m ar c us i 1, 2 2 ? H a l i m e da c e a e B os e l l i a m i m e t i c a 0 3 5 1 H a l i m e da c e a e E l y s i a be nne t t ae ? ? U dot e a c e a e E l y s i a c anguz ua 0 2 ? B r yops i da c e a e C odi a c e a e E l y s i a c hl or ot i c a 0, 2 4 5 2 V a uc he r i a c e a e E l y s i a c r i s pat a 1 5 5 1 H a l i m e da c e a e U dot e a c e a e E l y s i a di om e de a ? 5 3 P ha e ophyc e a e F l or i de ophyc e a e E l y s i a ni gr oc ap i t at a ? ? ? E l y s i a obt us a ? ? B r yops i da c e a e E l y s i a or nat a 0 3 ? B r yops i da c e a e E l y s i a pat i na 0 2 ? U dot e a c e a e E l y s i a pr at e ns i s ? ? ? E l y s i a pus i l l a ? ? H a l i m e da c e a e C odi a c e a e E l y s i a r uf e s c e ns ? ? B r yops i da c e a e E l y s i a s e r c a 0 3 0 1 C ym odoc e a c e a e H ydr oc h a r i t a c e a e

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95 T a bl e 2. 3: ( C ont i nue d) S pe c i e s L a r va l M ode K l e pt opl a s t y F ood C hoi c e ( F a m i l y ) E l y s i a s e t oe ns i s ? ? C odi a c e a e E l y s i a s ubor nat a 2 3 ? C a ul e r pa c e a e E l y s i a t i m i da 1, 2 6 5 4 P ol yphys a c e a e E l y s i a t r i s i nuat a 0 7 ? C odi a c e a e E l y s i a t uc a 1 3 4 5 H a l i m e da c e a e C a ul e r pa c e a e U dot e a c e a e E l y s i a v i r i di s 0 8 5 6 B r yops i da c e a e C odi a c e a e C l a dophor a c e a e P l ak obr anc hus oc e l l at us 0 7 5 7 U dot e a c e a e T hur i di l l a bay e r i ? ? ? T hur i di l l a c ar l s oni ? ? ? T hur i di l l a undul a ? ? ? T hur i di l l a v at ae ? ? ?

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95 F i gur e 2. 1 : B a ye s i a n phyl ogr a m ba s e d on c onc a t e n a t e d m t D N A a nd nuc D N A da t a s e t s P os t e r i or pr oba bi l i t y va l ue s a r e p r e s e nt e d a s pe r c e nt a ge s 0 1 s ubs t i t ut i ons / s i t e C os t as i e l l a oc e l l i f e r a B os e l l i a m i m e t i c a E l y s i a ni gr oc api t at a B os e l l i a m ar c us i E l y s i a t i m i da E l y s i a s e t oe ns i s E l y s i a pr at e ns i s E l y s i a s ubor nat a E l y s i a t r i s i nuat a E l y s i a obt us a E l y s i a r uf e s c e ns E l y s i a or nat a E l y s i a c anguz ua E l y s i a s e r c a E l y s i a c hl or ot i c a E l y s i a v i r i di s E l y s i a di om e de a E l y s i a c r i s pat a E l y s i a pat i na E l y s i a pus i l l a E l y s i a be nne t t ae E l y s i a t uc a P l ak obr anc hus oc e l l at us T hur i di l l a c ar l s oni T hur i di l l a v at ae T hur i di l l a bay e r i T hur i di l l a undul a C os t as i e l l a k ur o s hi m ae 1 00 100 100 100 100 100 100 100 100 100 100 100 100 100 96 99 64 75 72 98 97 55 69 72

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96 F i gur e 2. 2 : M os t pa r s i m oni ous r e c ons t r uc t i on o f l a r va l de ve l opm e nt on t he B a ye s i a n phyl oge ny. E i ght e e n M P R s c ons i s t i ng of s e ve n s t e ps w e r e f ound. P r e di c t e d s hi f t s f r om pl a nkt ot r ophi c t o e i t he r di r e c t or l e c i t hot r ophi c a r e i ndi c a t e d by a r r ow s C ol or e d boxe s i ndi c a t e know n s t a t e s f or t a xa I f n o box t he n t he t e r m i na l s t a t e w a s unknow n. E l y s i a ni gr oc api t at a P l a nkt ot r ophi c L e c i t hot r ophi c D i r e c t P ol ym or phi c C os t as i e l l a oc e l l i f e r a B os e l l i a m i m e t i c a B os e l l i a m ar c us i E l y s i a t i m i da E l y s i a s e t oe ns i s E l y s i a pr at e ns i s E l y s i a s ub or nat a E l y s i a t r i s i nuat a E l y s i a obt us a E l y s i a r uf e s c e ns E l y s i a or nat a E l y s i a c anguz ua E l y s i a s e r c a E l y s i a c hl or ot i c a E l y s i a v i r i di s E l y s i a di om e de a E l y s i a c r i s pat a E l y s i a pat i na E l y s i a pus i l l a E l y s i a be nne t t ae E l y s i a t uc a P l ak obr a nc hus oc e l l at us T hur i di l l a c ar l s oni T hur i di l l a v at ae T hur i di l l a bay e r i T hur i di l l a undul a C os t as i e l l a k ur o s hi m ae P l a nkt ot r ophi c T o D i r e c t P l a nkt ot r ophi c T o L e c i t hot r ophi c

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97 F i gur e 2. 3 : M os t pa r s i m oni ous r e c ons t r uc t i on o f l e ve l of kl e pt opl a s t y on t he B a ye s i a n phyl oge ny. E i ght M P R s c ons i s t i ng of t hr e e s t e ps w e r e f ound. P r e di c t e d s hi f t s f r om L e ve l 6 t o e i t he r 1, 2 or 5 a r e i ndi c a t e d by t he a r r o w s C ol or e d boxe s i ndi c a t e know n s t a t e s f or t a xa I f no box, t he n t he t e r m i na l s t a t e w a s unknow n. C os t as i e l l a oc e l l i f e r a B os e l l i a m i m e t i c a E l y s i a ni gr oc api t at a B os e l l i a m ar c us i E l y s i a t i m i da E l y s i a s e t oe ns i s E l y s i a pr at e ns i s E l y s i a s ubor nat a E l y s i a t r i s i nuat a E l y s i a obt us a E l y s i a r uf e s c e ns E l y s i a or nat a E l y s i a c anguz ua E l y s i a s e r c a E l y s i a c hl or ot i c a E l y s i a v i r i di s E l y s i a di om e de a E l y s i a c r i s pat a E l y s i a pat i na E l y s i a pus i l l a E l y s i a be nne t t ae E l y s i a t uc a P l ak obr anc hus oc e l l at us T hur i di l l a c ar l s oni T hur i di l l a v at ae T hur i di l l a bay e r i T hur i di l l a undul a C os t as i e l l a k ur o s hi m ae L e ve l 1 L e ve l 2 L e ve l 5 L e ve l 6 6 t o 1 6 t o 2 6 t o 5

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98 F i gur e 2. 4 : M os t pa r s i m oni ous r e c ons t r uc t i on o f f o od c hoi c e on t he B a ye s i a n phyl oge ny. 378 M P R s c ons i s t i ng of 19 s t e ps w e r e f ound D ou bl e ve r t i c a l l i ne s i ndi c a t e p r e di c t e d s hi f t s f r om C odi a c e a e t o d i f f e r e nt hos t f a m i l i e s A s t e r i s ks i ndi c a t e unknow n t e r m i na l s t a t e s f or a gi ve n s pe c i e s C os t as i e l l a oc e l l i f e r a B os e l l i a m i m e t i c a E l y s i a ni gr oc api t at a* B os e l l i a m ar c us i E l y s i a t i m i da E l y s i a s e t oe ns i s E l y s i a pr at e ns i s E l y s i a s ubor nat a E l y s i a t r i s i nuat a E l y s i a obt us a E l y s i a r uf e s c e ns E l y s i a or nat a E l y s i a c anguz ua E l y s i a s e r c a E l y s i a c hl or ot i c a E l y s i a v i r i di s E l y s i a di om e de a E l y s i a c r i s pat a E l y s i a pat i na E l y s i a pus i l l a E l y s i a be nne t t ae E l y s i a t uc a P l ak obr anc hus o c e l l at us T hur i di l l a c ar l s oni T hur i di l l a v at ae T hur i di l l a bay e r i T hur i di l l a undul a* C os t as i e l l a k ur o s hi m ae U dot e a c e a e t o C odi a c e a e

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99 F i gur e 2. 5 : N P R S t r a ns f or m e d u l t r a m e t r i c t r e e w i t h a s c a l e ba r pr opo r t i ona l t o s m oot he d r a t e of s ubs t i t ut i on B e l ow t he t r e e i s t he s e m i l og a r i t hm i c l i ne a ge s t hr ough t i m e pl ot w i t h B os e l l i a m i m e t i c a a s t he ba s a l node T he r e d l i ne s on bot h t he t r e e a nd t he pl ot i ndi c a t e t he r e gi on m os t c onve x i n s ha pe 0 0 0 1 0 3 0 4 0 5 0 6 0 2 0 8 0 9 1 0 0 7

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100 C H A P T E R 3: C O M P A R A T I V E P O P U L A T I O N G E N E T I C S T R U C T U R E A M O N G T H R E E S P E C I E S O F P L A C O B R A N C H I D S I N T R O D U C T I O N P opul a t i on ge ne t i c t he or y pr e di c t s t ha t hi gh m i g r a t i on r a t e s a m ong ge ogr a phi c l oc a t i ons w i l l hom oge ni z e popul a t i ons ; t he r e by, de c r e a s i ng l e ve l s of or e l i m i na t i ng popul a t i on s ubdi vi s i on. S pe c i e s w i t h pl a nkt oni c l a r va a nd, t he r e f or e put a t i ve l y hi gh di s pe r s a l pot e nt i a l s houl d ne c e s s a r i l y e xhi bi t l ow l e ve l s of popul a t i on s t r uc t u r e a s i ndi c a t e d by i ndi r e c t e s t i m a t e s s uc h a s F S T E xc e pt i ons t o t hi s pa r a di g m a r e num e r ous c a us i ng s om e a ut hor s t o s ugge s t t ha t pos s e s s i on of a pl a nkt oni c l a r va l s t a ge m a y not be a n a da pt a t i on f or ge ne f l ow ( H e dge c oc k, 1986 ) I ns t e a d of pot e nt i a l f or l o ng di s t a nc e di s pe r s a l t he a bi l i t y o f a l a r va t o s e t t l e a nd pe r s i s t i s a r gua b l y t he m os t i m por t a nt c om pone nt f or hom oge ni z i ng ge ne t i c pool s be t w e e n popul a t i ons ( B ha ud, 1998) O t he r f a c t or s s uc h a s t i m e i n pl a nkt on ( H e l l be r g, 1996) a nd c ur r e nt pa t t e r ns ( A r ndt & S m i t h, 1998) a r e a l s o i nf l ue nt i a l i n s t r uc t u r i ng popul a t i on s K yl e & B oul di ng ( 2000 ) f ound c ont r a di c t or y r e s ul t s a m ong p l a nkt oni c a nd di r e c t de ve l opi ng ga s t r opods w i t h one pl a nkt oni c de ve l ope r e xhi bi t i ng hom oge ni z e d pop ul a t i ons a c r os s l a r ge s pa t i a l s c a l e s a nd a not he r of t he pl a nkt oni c de ve l ope r s e xhi bi t i ng s i g ni f i c a nt pop ul a t i on s t r uc t u r e T odd, L a m be r t & T hor pe ( 1998) e xa m i ne d popul a t i on ge ne t i c s t r uc t ur e i n t w o s ym pa t r i c s pe c i e s of nudi br a nc hs a nd f ound t ha t w hi l e pl a nkt ot r ophi c s pe c i e s c onf or m e d t o

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101 e xpe c t a t i ons of no popul a t i on s t r uc t ur e t he l e c i t hot r ophi c s pe c i e s di d not I n ge ne r a l num e r ous e xa m pl e s a r e pr e s e nt i n t he l i t e r a t ur e i nd i c a t i ng t ha t t ype o f l a r va l de ve l opm e nt i s not t he p r i m a r y de t e r m i na nt o f popul a t i on s t r uc t ur i ng i n t he m a r i ne e nvi r onm e nt O t he r f a c t or s s uc h a s popul a t i on s pe c i f i c pr oc e s s e s a nd ot he r l i f e hi s t or y t r a i t s m a y a l s o be i m por t a nt i n popul a t i on s t r uc t ur i ng A va r i e t y of l a r va l l i f e h i s t or i e s i s know n f o r m e m be r s of t he s a c ogl os s a n f a m i l y P l a c obr a nc hi da e G r a y, 1840 r a ngi ng f r om be nt hi c e nc a ps ul a t e d t o hi ghl y va gi l e pl a nkt oni c de ve l opm e nt I n t e r m s of f e e di ng p r e f e r e nc e s s om e s pe c i e s of P l a c obr a nc hi da e s uc h a s E l y s i a s ubor nat a a r e be l i e ve d t o f e e d s ol e l y on C aul e r pa s pp. ( C l a r k, B us a c c a & S t i r t s 1979; C l a r k, 1984; J e ns e n, 1993) o r e xhi bi t a s t r ong pr e f e r e nc e f or a pa r t i c ul a r t ype of a l ga s uc h a s E t uc a f o r H a l i m e da s pp. ( J e ns e n, 1983) T he s e obs e r va t i ons m a y be a r e s ul t o f our l i m i t e d know l e dge of f ood c hoi c e but m a y a l s o r e f l e c t m or phol og i c a l c ons t r a i nt s i n f e e di ng s t r uc t u r e s ( J e ns e n, 1993) G e ne r a l i s t t ype f e e de r s e xi s t s uc h a s E l y s i a ( = T r i dac hi a) c r i s pat a, w hi c h ha s be e n r e por t e d t o f e e d on m ul t i pl e t ype s of a l ga e i nc l udi ng, but not ne c e s s a r i l y l i m i t e d t o, B r y ops i s s p. P e ni c i l l us s p. a nd H al i m e da s p. ( C ur t i s e t a l 2004) C onc om i t a nt w i t h t he de gr e e of f e e di ng s pe c i a l i z a t i on i s a phys i ol ogi c a l l i nk be t w e e n s pe c i e s a nd t he i r f ood s our c e s a s e xe m pl i f i e d by t he i r us e of c he m i c a l s ( kl e pt oc he m i s t r y; M a r i n & R os 2004) a nd c hl or op l a s t s e xt r a c t e d f r om t he i r f ood s our c e ( kl e pt opl a s t y; W a ugh & C l a r k, 1986) T a yl o r ( 19 68) pr ovi de d da t a i ndi c a t i ng a s ym bi ot i c r e l a t i ons hi p be t w e e n t he s l ugs a nd a l ga e a nd f u r t he r r e s e a r c h i ndi c a t e d t ha t w hi l e f e e di ng on t he i r p r e f e r r e d f ood s our c e s pe c i e s m a y e xt r a c t a ddi t i ona l e ne r gy by

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102 c om m a nde e r i ng a nd pr ol ongi ng phot os ynt he t i c a c t i vi t y of t he c hl or op l a s t s ( G r e e ne & M us c a t i ne 1972; P i e r c e B i r on & R um pho 1996; R um pho, S um m e r & M a nha r t 2000) T he a bi l i t y t o r e t a i n a nd s ubs e que nt l y m a i nt a i n c hl or opl a s t s va r i e s c a us i ng C l a r k ( 1992 ) t o de ve l op a c l a s s i f i c a t i on s c he m e ba s e d on di f f e r e nt t ype s of c h l o r opl a s t r e t e nt i on a nd us a ge L e ve l 1 or ga ni s m s do no t r e t a i n c hl or opl a s t s w i t h pl a s t i ds di ge s t e d i m m e di a t e l y a f t e r pha goc yt os i s L e ve l 2 a nd 3 o r ga ni s m s r e t a i n pl a s t i ds f or a f e w hou r s or up t o 24 hour s r e s pe c t i ve l y, bu t ne i t he r pr oduc e s phot os ynt ha t e L e ve l 4 o r ga ni s m s pr oduc e phot os ynt ha t e i n t he f i e l d, bu t c e a s e pr oduc t i on a f t e r a f e w hour s i n t he l a b a nd di ge s t t he pl a s t i ds L e ve l 5 or ga ni s m s pr oduc e pho t os ynt ha t e f or l onge r t ha n 24 hou r s i n a da r k e nvi r onm e nt but f unc t i on c e a s e s a f t e r a w e e k of s t a r va t i on. L e ve l 6 or ga ni s m s e xhi bi t l ong t e r m f unc t i ona l r e t e nt i on w i t h phot os ynt ha t e pr oduc t i on f o r gr e a t e r t ha n 1 w e e k a f t e r s t a r va t i on. H e r e I e xa m i ne t he l oc a l popul a t i on s t r uc t u r e of t h r e e s pe c i e s of P l a c obr a nc hi da e E l y s i a s ubor nat a, E l y s i a t uc a a n d E l y s i a c r i s pat a w hi c h e xhi bi t va r i ous l i f e hi s t or y s t r a t e gi e s I n t hi s s t udy, I w i l l e xa m i ne t he i nf l ue nc e of l a r va l de ve l opm e nt t ype ( l e c i t hot r oph i c vs d i r e c t de ve l o pm e nt ) f e e di ng pr e f e r e nc e ( s pe c i a l i s t vs ge ne r a l i s t ) a nd de gr e e o f kl e pt opl a s t y on popul a t i on s ubdi vi s i on a s i ndi c a t e d by ge ne t i c s e que nc e s of a f r a gm e nt o f t he c yt oc h r om e c oxi da s e s ubuni t 1 ge ne ( c ox 1) L e c i t hot r ophi c a nd di r e c t de ve l opm e nt s houl d yi e l d di f f e r e nc e s i n popul a t i on s t r uc t ur e be c a us e l e c i t hot r ophi c de ve l opm e nt i nvol ve s a de l a y i n t i m e t o m e t a m o r phos i s a nd di s pe r s a l pot e nt i a l H ow f e e di ng p r e f e r e nc e a nd d e gr e e of kl e pt opl a s t y w oul d a f f e c t

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103 popul a t i on s ubdi vi s i on i s unc l e a r I ni t i a l l y, I a s s um e d t ha t s pe c i a l i s t ve r s us ge ne r a l i s t s t r a t e gi e s a nd de gr e e of kl e pt opl a s t y w oul d not ha ve a n a f f e c t on popul a t i on s t r uc t ur i ng. M A T E R I A L S A N D M E T H O D S S a m pl e s w e r e c ol l e c t e d f r om f ou r br oa d s c a l e l oc a t i ons c or r e s pondi ng t o t he nor t he r n po r t i on o f t he r a nge of E l y s i a c r i s pat a ; F l or i da K e ys ( F L K ) B a ha m a s ( B A ) B e l i z e ( B E ) a nd U ni t e d S t a t e s V i r gi n I s l a nds ( U S V I ) T w o s i t e s i n t he F l or i da K e ys w e r e s a m pl e d: a c a na l on S uga r l oa f K e y ( n = 5 ) a nd a b or r ow pi t on G r a s s y K e y ( n = 20 ) O ne s i t e e a c h w a s s a m pl e d i n B e l i z e ( n = 7 ) a nd t he U S V I ( n = 6) T h r e e s i t e s i n t he B a ha m a s w e r e s a m pl e d: S pa ni s h C a y ( n = 5) C ha nne l C a y ( n = 4) a nd B i m i ni ( n = 2 ) A t ot a l o f 546 nt w a s us e d t o de f i ne c ox 1 ha pl ot ype s w i t hi n t hi s s pe c i e s F or E l y s i a t uc a, s a m pl e s f r om t h r e e br oa d s c a l e l oc a t i ons w e r e c ol l e c t e d: w e s t c oa s t of F l or i da ( G O M ) F l or i da K e ys ( F L K ) a nd B a ha m a s ( B A ) T w o l oc a t i ons w i t hi n t he F l or i da K e ys ( F L K ) a bor r ow pi t on G r a s s y K e y ( n = 3 ) a nd a r e e f r e f e r r e d t o a s W e s t e r n D r y R oc ks ( n = 10 ) w e r e s a m pl e d. T he B a ha m a s ( B A ) s a m pl e s i t e s w e r e l oc a t e d a t S pa ni s h C a y ( n = 17) a nd S t oc ki n g I s l a n d, E xu m a ( n = 2) T he G ul f of M e xi c o ( G O M ) s a m pl e s i t e i s l oc a t e d a t T a r pon S pr i ngs F l or i da ( n = 5) A t o t a l of 585 nt w a s us e d t o de f i ne c ox 1 ha pl ot ype s w i t hi n t h i s s pe c i e s L a s t l y, E l y s i a s ubor nat a i ndi vi dua l s f r om t w o b r oa d s c a l e l oc a t i ons w e r e a s s a ye d: F l or i da K e ys ( F L K ) a nd e a s t c oa s t of F l or i da ( I R L ) T h r e e l oc a t i ons i n F l or i da w e r e s a m pl e d: a c a na l on P l a nt a t i on K e y ( n = 16) a bor r ow pi t on G r a s s y K e y ( n = 19) a nd a

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104 s i t e w i t hi n t he I ndi a n R i ve r L a goon s ys t e m ( n = 20 ) A t ot a l of 537 nt w a s us e d t o de f i ne c ox 1 ha pl ot ype s A l l i ndi vi dua l s w e r e a ne s t he t i z e d w i t h M gC l 2 a nd s t or e d i n 95% E t O H S a m pl e s w e r e c ol l e c t e d be t w e e n 2000 a nd 2005 T ot a l c e l l D N A w a s i s ol a t e d f r om a s m a l l por t i on of t he a nt e r i or e nd of t he a ni m a l a nd t he t i s s ue s ubj e c t e d t o a non boi l i ng c he l e x e xt r a c t i on m e t hod ( W a l s h, M e t z ge r & H i guc hi 19 91) A n a l i quot of e a c h c he l e x t r e a t e d s a m pl e w a s di l ut e d w i t h 1X T E ( 10 m M T r i s 1 m M E D T A ; pH 7. 5 ) or na nopur e w a t e r pr i or t o us e i n t he pol ym e r a s e c ha i n r e a c t i on ( P C R ) a nd t he n s t or e d a t 20 C f or s ubs e que nt a m pl i f i c a t i ons I ni t i a l l y, por t i ons o f t he c ox 1 m i t oc hondr i a l ge ne w e r e P C R a m pl i f i e d w i t h F ol m e r e t a l 's ( 1994 ) p r i m e r s L C O 1490 a nd H C O 2198 ( T a bl e 3. 1) S pe c i e s s pe c i f i c pr i m e r s w e r e t he n de s i gne d f r om t he a ppr oxi m a t e l y 700bp f r a gm e nt ( T a bl e 3 1) A m pl i f i c a t i on r e a c t i ons ( 25 or 50 L ) c ons i s t e d of 1X buf f e r ( E nz ypol L T D D e nve r C O ) 1. 5 uni t s o f E nz ypol P l us 2000 pol ym e r a s e ( E nz ypol L T D D e nve r C O ) 0 2 m M e a c h dN T P s 3 0 m M M gC l 2 0. 5 M o f e a c h pr i m e r 1 0 M B e t a i ne 0. 12 g/ L o f bovi ne s e r um a l bum e n, a nd 0. 25 1 L o f t e m pl a t e T he c yc l i ng c ondi t i ons f or t he pr i m e r pa i r s c ons i s t e d of 1 m i n. a t 95 C f ol l ow e d by 35 45 c yc l e s of 30 s e c a t 95 C 45 s e c a t 48 54 C a nd 1 m i n. a t 72 C w i t h a f i na l e xt e ns i on of 3 m i n. a t 72 C A t e m pl a t e f r e e r e a c t i on w a s i nc l ude d f or t he de t e c t i on o f c ont a m i na t i on. T w o ot he r ge ne s l a r ge s ubuni t R N A ( 16S ) a nd H i s t one 3, w e r e a l s o a m pl i f i e d f r om E l y s i a c r i s pat a a nd E l y s i a s ubor nat a i ndi vi d ua l s i de nt i f i e d a s pos s e s s i ng ba s a l ha p l ot ype s i n t he c ox 1 a na l ys i s P r i m e r pa i r s 16 S s a r ( 5 C G C C T G T T T A T C A A A

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105 A A C A T 3 ) a nd 16s a ( 5 C T C C G G T T T G A A C T C A G A T C 3 ) ( K e s s i ng e t a l 1989 ) a nd H 3F ( 5 A T G G C T C G T A C C A A G C A G A C V G C 3 ) a nd H 3R ( 5 A T A T C C T T R G G C A T R A T R G T G A C 3 ) ( C ol ga n, P ond e r & E gg l e r 2000) w e r e us e d t o a m pl i f y ~ 450 bp of t he 16S ge ne a nd ~ 380 bp o f H i s t one 3. A m pl i f i c a t i on r e a c t i ons ( 25 or 50 L ) c ons i s t e d of 1X buf f e r ( E nz ypol L T D D e nve r C O ) 1. 5 uni t s of E nz ypol P l us 2000 pol ym e r a s e ( E nz ypol L T D D e nve r C O ) 0 2 m M e a c h dN T P s 3. 0 m M M gC l 2 ( 16S ) o r 1 5 m M M gC l 2 ( H 3) 0 5 M of e a c h p r i m e r 1 0 M B e t a i ne 0. 12 g/ L o f bovi ne s e r um a l bum e n, a nd 2. 0 4. 0 L of t e m pl a t e T he c yc l i ng c ondi t i ons f o r t he 16 S pr i m e r s c ons i s t e d of 1 m i n. a t 95 C f ol l ow e d by 3 5 45 c yc l e s of 30 s e c a t 95 C 45 s e c a t 48 C a nd 1 m i n a t 72 C w i t h a f i na l e xt e ns i on of 3 m i n. a t 72 C C yc l i ng c ondi t i ons f or t he H 3 pr i m e r s c ons i s t e d of 1 c yc l e of 4 m i n a t 95 C 1 m i n. a t 50 C a nd 1 m i n a t 72 C f ol l ow e d by 35 c yc l e s of 45 s e c a t 95 C 30 s e c a t 52 C a nd 45 s e c a t 72 C a nd a f i na l e xt e ns i on of 3 m i n a t 72 C A t e m pl a t e f r e e r e a c t i on w a s i nc l ude d f or t he de t e c t i on of c ont a m i na t i on. A m pl i c ons w e r e pur i f i e d us i ng a Q I A qui c k P C R p ur i f i c a t i on ki t ( Q i a ge n, I nc V a l e nc i a C A ) T he m a s s of t he a m pl i c ons w a s de t e r m i ne d by c om pa r i ng e t hi di um br om i de s t a i ni ng i nt e ns i t y o f 2 0 5 0 L o f e a c h pu r i f i e d r e a c t i on r e l a t i ve t o a s t a nda r d m a s s D N A l a dde r ( I nvi t r oge n L i f e T e c hnol ogi e s C a r l s ba d, C A ) C yc l e s e que nc i ng r e a c t i ons a nd s i z e s or t i ng of t h e D N A w e r e c onduc t e d w i t h a ppr oxi m a t e l y 50 ng / ul o f pur i f i e d P C R p r oduc t by pe r s onne l a t M a c r oge n, I nc ( S e oul K o r e a ) T he s e que nc e s f r om bot h s t r a nds of t he a m pl i c on w e r e c om pa r e d a nd e di t e d ( w he n ne e de d) us i ng

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106 S e que nc he r ( v4. 1; G e ne C ode s C or p. A nn A r bo r M I ) T he ope n r e a di ng f r a m e f or t he c ox 1 ge ne w a s us e d t o a i d i n pr ope r a l i gnm e nt N e i ghbor j oi ni ng ( N J ) t r e e s w e r e ge ne r a t e d f or e a c h s pe c i e s a nd t he i r a s s oc i a t e d ha pl ot ype s T w o a ppr oa c he s w e r e t a ke n t o e xa m i ne t he i nf l ue nc e o f di s t a nc e m e t r i c a n d i nc l us i on of a n out g r oup. F i r s t unc or r e c t e d p di s t a nc e s f or a l l pos i t i ons w e r e c a l c ul a t e d w i t h P A U P ( v4. 0b10; S w of f or d, 1998) a nd a ne i g hbor j oi ni ng a na l ys i s w a s c onduc t e d. E s t i m a t e s of w i t hi n s pe c i e s ha pl ot ype di ve r ge nc e w e r e e s t i m a t e d us i ng unc or r e c t e d p di s t a nc e s be c a u s e m ul t i pl e uns e e n c ha nge s i n nuc l e ot i de pos i t i ons ( m ul t i pl e hi t s ) s houl d not be a n i s s ue w i t hi n s pe c i e s a s t he s e s e qu e nc e s s houl d be c l os e l y r e l a t e d ( m a xi m um p di s t a nc e < 0. 1) a nd f ol l ow a m ol e c ul a r c l oc k; t he r e f or e unc or r e c t e d p di s t a nc e s s houl d be e qua l t o t he a c t ua l di s t a nc e a m ong ha pl ot ype s a nd not bi a s t he t r e e t opol ogy ( R z he t s ky & S i t ni kova 1996) S e c ond, s i s t e r s pe c i e s a s i ndi c a t e d by a f a m i l y l e ve l phyl oge ny f or t he P l a c obr a nc hi da e w e r e us e d a s out gr oups ( C ha pt e r 1) a nd ha p l ot ype di ve r ge nc e w a s ge ne r a t e d us i ng a m a xi m um l i ke l i hood e s t i m a t or F or E l y s i a t uc a, t he s i s t e r s pe c i e s w a s uni de nt i f i e d i n t he f a m i l y l e ve l phyl oge ny; t he r e f o r e t w o pos s i bl e c a ndi da t e s w e r e us e d, E l y s i a be nne t t ae a nd E l y s i a ( = E l y s i e l l a) pus i l l a F or E l y s i a c r i s pat a t he s i s t e r s pe c i e s E l y s i a ( = T r i dac hi e l l a) di om e de a a nd f or E l y s i a s ubor nat a, t he s i s t e r s pe c i e s E l y s i a pr at e ns i s w e r e de s i gna t e d a s out gr oups A l t houg h s a t ur a t i on of 3 r d pos i t i ons i s not a n i s s ue w i t hi n s pe c i e s t he us e of a n out g r oup f or r oo t i ng pur pos e s ne c e s s i t a t e s t he e xc l us i on of 3 r d pos i t i ons M a xi m um l i ke l i hood ( M L ) di s t a nc e s ba s e d on 1 s t a nd 2 n d pos i t i ons w e r e e s t i m a t e d f r om a be s t f i t m ode l o f e vol ut i on a s s e l e c t e d i n M ode l t e s t us i ng A ka i ke i nf or m a t i on c r i t e r i a ( v3. 7; P os a da & C r a nd a l l 1998) E s t i m a t e s of di ve r ge nc e

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107 w e r e ge ne r a t e d us i ng a m a xi m um l i ke l i hood e s t i m a t or w i t h P A U P ( v4 0b10; S w of f o r d, 1998) T he s e M L di s t a nc e s w e r e t he n us e d t o ge n e r a t e t he N e i ghbor J oi ni ng t r e e S uppor t f or a l l node s w a s de t e r m i ne d us i ng 1000 b oot s t r a ps E s t i m a t e s of ha pl ot ype ( h ) a nd nuc l e ot i de ( ) di ve r s i t i e s w e r e ge ne r a t e d us i ng N e i 's ( 1987) e qua t i ons 8. 4 a nd 10 5 a s i m p l e m e nt e d i n A r l e qui n ( v3 0; E xc of f i e r L a va l & S c hne i de r 2005 ) T o de t e r m i ne how t he m ol e c ul a r va r i a t i on w a s pa r t i t i one d a m ong l oc a t i ons a n A na l ys i s of M ol e c ul a r V a r i a nc e ( A M O V A ) w a s pe r f or m e d us i ng A r l e qui n ( v3. 0; E xc of f i e r e t a l 2005) F or t he A M O V A a n a l ys e s a m a t r i x of unc or r e c t e d p di s t a nc e s be t w e e n ha pl ot ype s w a s us e d w i t h 10, 00 0 pe r m ut a t i ons t o a s s e s s s i gni f i c a nc e of t he a s s oc i a t e d P va l ue E xa c t t e s t s of popul a t i o n di f f e r e nt i a t i on ba s e d on ha pl ot ype f r e que nc i e s ( R a ym ond & R ous s e t 1995) w e r e a l s o c onduc t e d us i ng A r l e qui n ( v3. 0; E xc of f i e r e t a l 2005) F or t he e xa c t t e s t s of d i f f e r e nt i a t i on, de f a ul t pa r a m e t e r s ( 10 000 s t e ps i n t he M a r kov C ha i n a nd 1000 de m e m or i z a t i on s t e ps ) w e r e us e d. I ni t i a l l y a l l s a m pl e l oc a t i ons w e r e t r e a t e d a s popul a t i ons i n t he pa i r w i s e c om pa r i s ons of S T O t he r pos s i bl e gr oupi ngs f or s t r uc t u r e a na l ys e s w e r e de t e r m i ne d ba s e d e i t he r on non s i gni f i c a nt di f f e r e nc e a m ong s a m pl e s or r e l a t i ons hi ps a m ong ha pl ot ype s a s i ndi c a t e d by N J a na l ys e s F u's F S t e s t w a s us e d t o a s s e s s de pa r t ur e s f r om s e l e c t i ve ne ut r a l i t y ( F u, 1997) M i s m a t c h di s t r i but i ons ba s e d on a s udde n e xpa ns i on m ode l a s i m pl e m e nt e d i n A r l e qui n w e r e c onduc t e d i f t he F s t e s t r e j e c t e d s e l e c t i ve ne ut r a l i t y ( S l a t ki n & H uds on, 19 91; R oge r s & H a r pe ndi ng, 1992; E xc of f i e r 2004)

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108 R E S U L T S E l y s i a t uc a S e ve nt e e n ha pl ot ype s w e r e de f i ne d by 36 pol ym o r phi c s i t e s c ons i s t i ng of 32 t r a ns i t i ons a n d f our t r a ns ve r s i ons A c c e s s i on num be r s f or E l y s i a t uc a ha pl ot ype s a r e D Q 781352 781365 ( E T U 2 = D Q 471249, E T U 8 = D Q 471250, E T U 17 = D Q 471251) T he m a j or i t y of ha pl ot ype s w e r e r e s t r i c t e d t o pa r t i c ul a r l oc a t i ons ( T a bl e 3. 2) T he onl y e xc e pt i ons t o t hi s t r e nd w e r e E T U 6 a nd E T U 13 d e t e c t e d i n i ndi vi dua l s f r om bot h t he F l or i da K e ys a nd t he B a ha m a s O ve r a l l e s t i m a t e s of ha pl ot ype a nd nuc l e ot i de di ve r s i t y w e r e 0. 8919 + 0. 0332 a nd 0 0121 + 0 0065, r e s pe c t i ve l y, a nd a l l s a m pl e d s i t e s e xhi bi t e d hi gh ha pl ot ype a nd l ow nuc l e ot i de di ve r s i t i e s ( T a b l e 3. 3) T he G O M s a m pl e s i t e e xhi bi t e d t he hi ghe s t ha pl ot ype di ve r s i t y f ol l ow e d by t he B a ha m a s a nd t he F l o r i da K e ys s a m pl e s N one of t he G O M ha pl ot ype s w a s obs e r ve d i n t he F l or i da K e ys o r B a ha m a s A N e i ghbor J oi ni ng a na l ys i s ba s e d on unc or r e c t e d p di s t a nc e s r e s ul t e d i n t w o m a j or c l a de s a m ong t he obs e r ve d ha pl ot ype s ( F i gu r e 3. 1A ) C l a de 1 c ons i s t e d of G ul f o f M e xi c o ha pl ot ype s a nd c l a de 2 w a s c om pos e d of h a pl ot ype s f r om t he F l or i da K e ys a nd t he B a ha m a s U nc or r e c t e d p d i s t a n c e s r e s ul t e d i n s ha l l ow ove r a l l ha pl ot ype di ve r ge nc e a m ong t he 17 ha pl ot ype s w i t h a ve r a ge d = 0. 0190 + 0. 0123 ( T a bl e 3 4) W i t hi n c l a de 1 t he a ve r a ge di ve r ge nc e a m ong a l l ha pl ot ype s w a s 0. 0044 + 0 0015 a nd s l i ght l y hi ghe r w i t hi n c l a de 2. F or t he de t e r m i n a t i on o f ha pl ot ype di ve r ge nc e i n r e l a t i on t o t he out gr oups E l y s i a be nne t t ae a nd E l y s i a pus i l l a t he be s t f i t m ode l un de r A I C w a s a T I M + I m ode l w i t h s i x s ubs t i t ut i on t ype s T hi s m ode l w a s ba s e d on 1 s t a n d 2 n d pos i t i ons onl y. N uc l e ot i de

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109 f r e que nc i e s w e r e e s t i m a t e d a s A = 0. 1926 C = 0 2120, G = 0 2472 a nd T = 0 3482. T he pr opor t i on o f i nva r i a nt s i t e s w a s e s t i m a t e d a s 0. 8568. R a t e va r i a t i on f ol l ow e d a c ont i nuous ga m m a di s t r i but i on e qua l ove r a l l s i t e s T he a ve r a ge di ve r ge nc e a m ong a l l E l y s i a t uc a ha pl ot ype s obs e r ve d w a s l ow e r t ha n t h e obs e r ve d di ve r ge nc e s us i ng a l l pos i t i ons a nd unc or r e c t e d p di s t a nc e s ( T a bl e 3. 4) T he N J a na l ys i s ba s e d on M L di s t a nc e s r e c ove r e d t he s a m e w e l l s uppor t e d t opol ogy a s t ha t obs e r ve d w i t h unc or r e c t e d p di s t a nc e s a nd no ou t gr oups T he onl y di f f e r e nc e s w e r e i n t he r e l a t i ons hi ps a m ong ha pl ot ype s w i t hi n t he i ndi vi dua l c l a de s W i t h i n t h e c l a de s i de nt i f i e d i n t he N J a na l ys i s t he a ve r a ge di ve r ge nc e w a s 0. 0008 + 0. 0013 ( G O M ) a nd 0. 0017 + 0 0023 ( F L K & B A ) T he a ve r a ge di ve r ge n c e e s t i m a t e be t w e e n t he t w o c l a de s w a s 6 t o 13 t i m e s g r e a t e r t ha n t he di ve r ge nc e obs e r ve d w i t hi n c l a de s C om pa r e d t o i nt e r c l a de di ve r ge nc e s w i t hi n E l y s i a t uc a t he di ve r ge nc e t o t he out gr oups E l y s i a be nne t t ae a nd E l y s i e l l a pus i l l a w a s 5 t o 6 t i m e s gr e a t e r T o de t e r m i ne i f s a m pl i ng l oc a t i ons a c t ua l l y r e p r e s e nt popul a t i ons t he di s t r i but i on of ha pl ot ype s by l oc a t i on ( T a bl e 3. 2 ) w a s e xa m i ne d us i ng A M O V A a nd a N e i ghbor J oi ni ng ne t w or k ba s e d on unc or r e c t e d p di s t a nc e s F or t he A M O V A t he s a m pl e s f r om di f f e r e nt s i t e s w i t hi n bot h t he F l or i da K e ys a nd t he B a ha m a s w e r e not e xa m i ne d s e pa r a t e l y due t o s m a l l s a m pl e s i z e s f or s om e s i t e s w i t hi n t he s e l oc a t i ons ; t he r e f or e t hr e e br oa d s c a l e l oc a t i ons w e r e us e d, G O M F L K a nd B A T he ove r a l l # S T w a s e qua l t o 0 669 ( P < 0. 0001 ) B ot h t he c om pa r i s on of popul a t i on pa i r w i s e # S T a nd t he e xa c t t e s t s of di f f e r e nt i a t i on ba s e d on ha pl ot ype f r e que nc i e s r e s ul t e d i n s i gni f i c a nt di f f e r e nc e s a m ong l oc a t i ons A s e c ond A M O V A w a s c onduc t e d ba s e d on t he g r oupi ngs obs e r ve d i n bot h

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110 N e i gh bor J oi ni ng t r e e s ( F i gur e 3 1A ) pl a c i ng F L K w i t h B A ve r s us G O M T he r e s ul t i ng # S T w a s l a r ge r a t 0. 785 ( P < 0 0001) pa r t i t i oni ng m or e va r i a t i on a m ong t he popu l a t i ons t ha n w i t hi n. A s i n t he pr e vi ous A M O V A bot h t he popul a t i on pa i r w i s e # S T a nd t he e xa c t t e s t s of di f f e r e nt i a t i on i ndi c a t e d s i gni f i c a nt di f f e r e nt i a t i on a m ong t he s e t w o gr oups F S t e s t s of s e l e c t i ve ne ut r a l i t y f a i l e d t o r e j e c t t he n ul l hypot he s i s of s e l e c t i ve ne ut r a l i t y i n bot h t he F L K ( P = 0 204) a nd B A ( P = 0. 519) s a m pl e F or t he G O M s a m pl e t he F S t e s t w a s s i gni f i c a nt ( P = 0. 009 ) i ndi c a t i ng t h a t s e l e c t i on m a y be oc c ur r i ng or t ha t a r e c e nt e xpa ns i on of t he popu l a t i on ha d oc c ur r e d, h ow e ve r t he s udde n e xpa ns i on m ode l f a i l e d t o c onve r ge s ugge s t i ng t ha t t he s a m pl e s i z e ( n = 5) i s t oo s m a l l t o m ode l E l y s i a c r i s pat a T w e nt y f i ve ha pl ot ype s w e r e de f i ne d by 78 pol ym or phi c s i t e s c ons i s t i ng of 68 t r a ns i t i ons a nd 14 t r a ns ve r s i ons A c c e s s i on num be r s f or E l y s i a c r i s pat a ha pl ot ype s a r e D Q 781377 781398 ( E C R 3 = D Q 471225, E C R 11 = D Q 471223, E C R 22 = D Q 4712 24) N one of t he 25 ha pl ot ype s w a s s ha r e d be t w e e n br o a d s c a l e l oc a t i ons ( T a bl e 3. 2 ) O ve r a l l e s t i m a t e s of ha pl ot ype a nd nuc l e ot i de di ve r s i t y w e r e 0. 9345 + 0 0237 a nd 0 0395 + 0. 0197, r e s pe c t i ve l y ( T a bl e 3. 3) T he B a ha m a s ( B A ) e xhi bi t e d t he hi ghe s t ha pl o t ype a nd nuc l e ot i de di ve r s i t y w i t h 60 pol ym o r phi c s i t e s obs e r ve d ( T a bl e 3 3) T he ove r a l l e s t i m a t e of popul a t i on s t r uc t u r e # S T = 0 788, w a s s i gni f i c a nt w i t h a p r oba bi l i t y of obs e r vi ng a gr e a t e r va l ue a t r a ndom e qua l t o z e r o. A l l popul a t i on pa i r w i s e # S T c om pa r i s ons r e s ul t e d i n s i gni f i c a nt di f f e r e nc e s be t w e e n popul a t i ons ( a l l P va l ue s < 0. 007) A c c or di ng t o t he e xa c t t e s t s of popu l a t i on di f f e r e nt i a t i on how e ve r t he B a ha m a s

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111 s a m pl e w a s not s i gni f i c a nt l y di f f e r e nt f r om U S V I ( P = 0 07) but w a s s i gni f i c a nt l y di f f e r e nt f r om B e l i z e a t P = 0 01. A l l ot he r c om pa r i s ons r e s ul t e d i n P va l ue s < 0 006. A l t hough t he ove r a l l e s t i m a t e of # S T w a s s i gni f i c a nt t he l a r ge num be r of pa i r w i s e di f f e r e nc e s ( 22. 47 + 10 74) w i t hi n t he B A s a m pl e s ugge s t e d t ha t f ur t he r di v i s i on ( or r e gr oupi ng) of t he B a ha m a s s a m pl e w a s ne c e s s a r y. F i r s t a N e i ghbor J oi ni ng a na l ys i s us i ng unc or r e c t e d p di s t a nc e s w a s c onduc t e d t o s e e how ha pl ot ype s gr oupe d. T he r e s ul t i ng t r e e s ugge s t e d t w o di s t i nc t l i ne a ge s w i t hi n t he B a ha m a s T he B a ha m a s s a m pl e s w e r e s e pa r a t e d i nt o t w o g r oups a nd ha pl ot ype a nd nuc l e ot i de di ve r s i t i e s w e r e r e c a l c ul a t e d. F o r B a ha m a s 1 ( B A 1) s e ve n s a m pl e s r e s ul t e d i n s i x ha pl ot ype s a nd ha pl ot ype di ve r s i t y w a s e s t i m a t e d a t 0 9524 + 0 09 55 w i t h 33 pol ym or phi c s i t e s obs e r ve d ( = 0. 0196 + 0 0117) F or B a ha m a s 2 ( B A 2) f ou r s a m pl e s r e s ul t e d i n t h r e e ha pl ot ype s a nd ha pl ot ype di ve r s i t y o f 0 8333 + 0 2224 w i t h ni ne pol ym or phi c s i t e s obs e r ve d ( = 0. 0105 + 0 0076) O ve r a l l # S T w a s r e e s t i m a t e d t r e a t i ng B A 1 a nd B A 2 a s s e pa r a t e popul a t i ons a nd t he e s t i m a t e s i nc r e a s e d. T he ove r a l l # S T w a s e s t i m a t e d a s 0. 8963 ( P = 0. 000) i nd i c a t i ng s i gni f i c a nt s t r uc t u r e a m ong a l l p opul a t i ons A l l popul a t i ons w e r e s i gni f i c a nt l y di f f e r e nt f r om e a c h ot he r ba s e d on po pul a t i on pa i r w i s e # S T ( P < 0. 005 ) E xa c t t e s t s of popul a t i on di f f e r e nt i a t i on p r oduc e d c onf l i c t i ng r e s ul t s s ugge s t i ng t ha t a l t hough no ha pl ot ype s a r e s ha r e d a m ong gr oups B A 1 & B A 2 a r e not di f f e r e nt f r om e a c h ot he r or f r om U S V I A l l ot he r c om pa r i s ons r e s ul t e d i n s i gni f i c a nt di f f e r e nc e s ( P < 0. 02) T he non s i gni f i c a nc e i n di f f e r e nc e a m ong t he gr oups i s a r e s ul t of t he l ow f r e que nc i e s of t he ha pl ot ype s a nd t he pe r m ut a t i on pr oc e s s us e d t o a s s e s s s i gni f i c a nc e

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112 T he a ve r a ge unc or r e c t e d p di s t a nc e a m o ng a l l ha pl ot ype s w a s e s t i m a t e d a s 0. 0455 + 0 0224 ( r a nge = 0. 0018 0 0806; T a bl e 3 4) A n unr oot e d N J t r e e ba s e d on unc or r e c t e d p di s t a nc e s r e s ul t e d i n f ou r w e l l s upp or t e d c l a de s c or r e s pondi ng t o F L K B A 1, B e l i z e a nd B A 2 + U S V I ( F i gu r e 3 2A ) B oo t s t r a p va l ue s of t he un r oot e d p di s t a nc e t r e e a l s o i ndi c a t e d a w e l l s uppor t e d g r oup i ng of B A 1, B e l i z e a nd t he B A 2 + U S V I c l a de s M i dpoi nt r oot i ng how e ve r pl a c e d B A 1 c l os e r t o F L K ( not s how n) E s t i m a t e s of a ve r a ge unc or r e c t e d p di s t a nc e s w e r e ge ne r a t e d ba s e d on t he f our c l a de s de t e c t e d i n t he a na l ys i s W i t h i n F L K B e l i z e a nd B A 2 + U S V I a ve r a ge p di s t a nc e s be t w e e n ha pl ot ype s r a nge d f r om a l ow o f 0 0039 + 0. 0038 f or B e l i z e t o a h i gh of 0. 0083 + 0. 0038 f or B A 2 + U S V I W i t hi n B A 1, t he a ve r a ge p di s t a nc e w a s 0. 0 230 + 0 0171. A ve r a ge p di s t a nc e s a m ong c l a de s r a nge d f r om 0. 0488 + 0. 0055 ( F L K t o B A 1) t o 0. 0688 + 0. 0052 ( B A 1 t o B e l i z e ) F or t he de t e r m i na t i on o f M L di s t a nc e s w i t h t he out gr oup, E l y s i a di om e de a t he be s t f i t m ode l w a s T r N + I w i t h s i x s ubs t i t ut i on r a t e s N uc l e ot i de f r e que nc i e s w e r e e s t i m a t e d a s A = 0. 1790, C = 0. 2181 G = 0 254 9 a nd T = 0 3480. T he p r opor t i on of i nva r i a nt s i t e s w a s e s t i m a t e d a s 0. 8711. R a t e va r i a t i on f ol l ow e d a c ont i nuous ga m m a di s t r i but i on e qua l ove r a l l s i t e s T he N J t r e e ba s e d on t hi s m ode l of e vol ut i on r e s ul t e d i n a t r e e ve r y di f f e r e nt f r om t he N J t r e e ba s e d on p di s t a nc e s ( F i gur e 3. 2B ) N o s i gni f i c a nt boot s t r a p s uppor t w a s de t e c t e d i n t he M L di s t a nc e ba s e d t r e e L a c k of s i gni f i c a nt s uppor t f or t he node s de t e c t e d i n t he N J t r e e ba s e d on M L di s t a nc e s i s a r e s ul t of t he l os s of c ons i de r a bl e phyl oge ne t i c i nf or m a t i on w i t h t he e xc l us i on of 3 r d pos i t i ons R e gr e s s i ng 3 r d pos i t i on t r a ns i t i ons a nd t r a ns ve r s i ons a ga i ns t unc or r e c t e d p di s t a nc e s yi e l ds f our di s t i nc t

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113 c l ouds of poi nt s t hr e e o f w hi c h do not i ndi c a t e s i gni f i c a nt s a t ur a t i on of t r a ns i t i ons ( F i gur e 3 3) T he s e t hr e e c l ouds o f poi nt s c o r r e s pond t o w i t hi n popul a t i on va r i a t i on, di ve r ge nt ha pl ot ype E C R 20 ve r s us ot he r m e m be r s of B A 1, a nd va r i a t i on bot h w i t hi n a nd a m ong c l a de s de pi c t e d i n F i gur e 3. 2A T he f i na l c l oud of po i nt s c or r e s ponds t o c om pa r i s ons w i t h t he out gr oup a nd i ndi c a t e s i gni f i c a nt s a t ur a t i on of t r a ns i t i ons T he ove r a l l m e a n M L d i s t a nc e a m ong ha pl ot ype s w a s 0. 0122 + 0 0066 ( r a nge = 0. 0000 0. 0297; T a bl e 3. 4 ) A ve r a ge M L di s t a nc e s a m ong c l a de s r a nge d f r om 0 0078 + 0. 0020 ( B E t o B A 2+ U S V I ) t o 0. 0166 + 0 0036 ( B A 2+ U S V I t o F L K ) I n c om pa r i s on t o t he out gr oup, E l y s i a di om e de a, t he ove r a l l m e a n M L d i s t a nc e w a s 0. 0319 + 0. 0058 w i t h t he r a nge of a ve r a ge M L di s t a nc e e qu i va l e nt t o a m i ni m um of 0. 0265 + 0. 0029 ( t o B A 2/ U S V I ) a nd m a xi m um of 0. 0385 + 0 0052 ( t o B A 1) T he r e l a t i ons hi ps a m ong t he l oc a t i ons c a nnot be c onc l us i ve l y de t e r m i ne d us i ng c ox 1 a nd M L d i s t a nc e s ba s e d on 1 s t a nd 2 n d pos i t i o ns be c a us e of t he l a c k of s i gn a l a t t he w i t hi n s pe c i e s l e ve l O t he r m e t hods s uc h a s s t r i c t m a xi m um l i ke l i hood a na l ys i s ( he ur i s t i c s e a r c h w i t h 30 r a ndom a ddi t i on r e pl i c a t e s a nd T B R s w a ppi ng) ba s e d on a l l pos i t i ons a nd t he out gr oup de t e c t e d hi gh boot s t r a p va l ue s ( 100 r e pl i c a t e s ) c or r e s pondi ng t o t he f ou r l i ne a ge s i n t he unc or r e c t e d p di s t a nc e b a s e d t opol ogy ( F i gur e 3. 2A ) I n t hi s a na l ys i s t he r e l a t i ons hi ps a m ong t he c l a de s w a s u nr e s ol ve d w i t h 64 a nd 53 a s t he boot s t r a p va l ue s f or node s c onne c t i ng B e l i z e + ( B A 2+ U S V I ) a nd B A 1 + F L K r e s pe c t i ve l y. T o de t e r m i ne i f t he a ddi t i on of da t a f r om ot he r ge ne s 16S a nd H i s t one 3, c oul d a i d i n t he r e s ol ut i on o f t he s e node s i ndi vi du a l ha pl ot ype s i n t he f our c l a de s w e r e s e que nc e d ( T a bl e 3. 5) T hr e e of t he f ou r ha pl ot yp e s ( E C R 10, E C R 15 a nd E C R 24) w e r e

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114 ba s a l t o t he c l a de s i de nt i f i e d i n t he N J a na l ys i s E C R 3 f r om F L K w a s t he onl y e xc e pt i on t o t hi s T he a ddi t i ona l da t a d i d not yi e l d s i gni f i c a n t br a nc h s uppor t but di d p r ovi de i nf or m a t i on on num be r of pol ym or phi c s i t e s f or t h e s e t w o a ddi t i ona l ge ne s T hi r t y e i ght a nd t hr e e pol ym o r phi c s i t e s w e r e i de nt i f i e d i n t he 16S a nd H i s t one 3 s e que nc e c om pa r i s ons r e s pe c t i ve l y. T he m a xi m um num be r of di f f e r e nc e s obs e r ve d i n t he H i s t one 3 s e que nc e s e xi s t s be t w e e n t he c ox 1 ha pl ot ype s E C R 15 ( B A 1) E C R 10 ( B E ) a nd E C R 22 ( U S V I ) w i t h t w o pol ym or phi s m s f o r e a c h c om pa r i s on w hi l e E C R 3 di f f e r s f r o m a l l ot he r s w i t h onl y one pol ym or phi s m T he F S t e s t o f s e l e c t i ve ne ut r a l i t y f a i l e d t o r e j e c t t h e nul l hypot he s i s of s e l e c t i ve ne ut r a l i t y i n m ut a t i ons f o r B e l i z e B A 1, a nd B A 2+ U S V I I n t he F L K s a m pl e s t hi s hypot he s i s w a s r e j e c t e d a t P = 0 027, s ugge s t i ng n on ne ut r a l m ut a t i ons o r r e c e nt e xpa ns i on. M i s m a t c h di s t r i but i ons i ndi c a t e d t ha t a s udde n e xpa ns i on m ode l w a s t he be s t f i t m ode l f or t he F L K popul a t i on ( P R I = 0. 315 ; P S S D = 0. 34 5 ) E l y s i a s ubor nat a F our t e e n ha pl ot ype s w e r e de f i ne d by 59 pol ym or p hi c s i t e s c ons i s t i ng of 47 t r a ns i t i ons a nd 15 t r a ns ve r s i ons A c c e s s i on num be r s f or E l y s i a s ubor nat a F L K ha pl ot ype s a r e D Q 781349 781 351 ( E S U 14 = D Q 471283) a nd f or E l y s i a s p. I R L D Q 7813 39 781348. P l a nt a t i on K e y ( n = 16) w a s f i xe d f or one ha pl ot ype E S U 14 w hi c h w a s a l s o f ound i n 10 i ndi vi dua l s f r om G r a s s y K e y. N o o t he r ha pl ot ype s w e r e s ha r e d a m ong s a m pl e l oc a t i ons ( T a bl e 3 2) O ve r a l l e s t i m a t e s of ha pl ot ype a nd nuc l e ot i de di ve r s i t y w e r e 0. 7545 + 0 0527 a nd 0. 0475 + 0. 02 35, r e s pe c t i ve l y ( T a bl e 3 3) T he m e a n num be r of pa i r w i s e di f f e r e nc e s a m ong ha pl ot ype s w a s 25. 44 + 11 33. T he l a r ge nu m be r

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115 of pa i r w i s e di f f e r e nc e s a m ong ha pl ot ype s f ound i n t he F l o r i da K e ys ( F L K ) a nd I ndi a n R i ve r L a goo n ( I R L ) pr om pt e d a n i nve s t i ga t i on o f phyl oge ne t i c r e l a t i ons hi ps a m ong ha pl ot ype s F i r s t unc or r e c t e d p di s t a nc e s w e r e e s t i m a t e d f or a l l ha pl ot ype s a nd us e d t o c ons t r uc t a N e i ghbor J oi ni ng t r e e ( F i gur e 3 4A ) w i t h m i dpoi nt r oot i ng T w o di s t i nc t c l a de s w e r e r e c ove r e d r e pr e s e nt i ng F L K a nd I R L O ve r a l l m e a n p di s t a nc e a m ong ha pl ot ype s w a s 0. 0466 + 0 0447 ( r a nge = 0 0016 0. 1003; T a bl e 3. 4 ) M e a n unc or r e c t e d p di s t a nc e s a m ong ha pl ot ype s f ound w i t hi n F L K a nd w i t hi n I R L w e r e l ow ( d = 0 0066 + 0. 0030 a nd 0 0051 + 0. 0020 r e s pe c t i ve l y) T he a v e r a ge unc or r e c t e d p di s t a nc e be t w e e n l oc a t i ons how e ve r w a s s e ve nt e e n t i m e s gr e a t e r T r a ns i t i ons a nd t r a ns ve r s i ons a t 3 r d pos i t i ons w e r e r e gr e s s e d a ga i ns t unc or r e c t e d p di s t a nc e s a nd s a t ur a t i on of t r a ns i t i ons w a s i ndi c a t e d f or I R L F L K a nd E l y s i a pr at e ns i s c om pa r i s ons ( da t a not s how n) W i t h E l y s i a pr at e ns i s a s a n out gr oup, a be s t f i t m ode l of e vol ut i on w a s e s t i m a t e d e xc l udi ng 3 r d pos i t i ons T he m ode l c hos e n w a s a T r N + I w i t h e qua l ga m m a r a t e s a nd p r opor t i on of i nva r i a bl e s i t e s e qua l t o 0 9172. M a xi m um l i ke l i h ood e s t i m a t e s w e r e ge ne r a t e d ba s e d on t hi s m ode l of e vol ut i on a nd us e d t o c ons t r uc t a N J t r e e ( F i gu r e 3. 4B ) T he ba c kbone t opol ogy of t hi s t r e e d i d not di f f e r f r om t ha t of t he unc or r e c t e d p di s t a nc e t r e e a l t hough r e l a t i ons hi ps a m ong i ndi vi dua l ha pl ot ype s w i t hi n c l a de s di d. T he ove r a l l m e a n M L di s t a nc e a m ong ha pl ot ype s w a s 0. 0178 + 0 0190 ( r a nge = 0 0. 0558; T a bl e 3. 4) W i t hi n F L K t he m e a n M L di s t a nc e w a s gr e a t e r t ha n t ha t o bs e r ve d w i t hi n I R L T he m e a n M L di ve r ge nc e e s t i m a t e d f or F L K ha pl ot ype s ve r s us E l y s i a pr at e ns i s w a s 0. 0360 + 0. 0053 a nd f or I R L ha pl o t ype s ve r s us E l y s i a pr at e ns i s t he m e a n di ve r ge nc e w a s s l i ght l y l ow e r ( d = 0. 0250 + 0. 0018 ) ; how e ve r t he m e a n di ve r ge nc e be t w e e n I R L a nd F L K w a s 0. 0375 +

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116 0. 0062, t he hi ghe s t l e ve l r e por t e d he r e S e que nc e s of t he 16S r e gi on f or ha pl ot ype s E S U 1, 2, 5 a nd 11 ( E S U 14 w a s a l r e a dy a va i l a bl e f or bot h ge ne s ) a nd f o r t he H i s t one 3 r e gi on ha pl ot ype s E S U 2 5 a nd 8 w e r e ge ne r a t e d ( T a bl e 3. 5 ) A l a r ge num be r o f pol ym or phi s m s i n 16S ( 25 pol ym or phi c s i t e s ) a nd H i s t one 3 ( 10 pol y m or phi c s i t e s ) s e que nc e s a m ong s e l e c t ha pl ot ype s w e r e de t e c t e d. B e c a us e of t he s e f i ndi ng, I R L a nd F L K w e r e t r e a t e d s e pa r a t e l y i n f ur t he r a na l ys e s W i t hi n t he i ndi vi dua l s f r om F L K t he s a m pl e f r om P l a nt a t i on K e y w a s m onom or phi c w i t h onl y ha pl ot ype E S U 14 ( n = 16 ) a l s o f ound i n t he G r a s s y K e y popul a t i on. T he G r a s s y K e y s a m pl e s ( n = 19) e xhi bi t e d a hi ghe r ha pl ot ype a nd nuc l e ot i de di ve r s i t y. O nl y s i x pol ym or phi c s i t e s w e r e obs e r ve d de f i ni ng f our ha pl ot ype s T he e s t i m a t e d # S T w a s e qua l t o 0. 1572 ( P = 0 005) a nd a l t hough a ha pl ot ype w a s s ha r e d, popul a t i ons w e r e s i gni f i c a nt l y di f f e r e nt f r om e a c h ot he r ba s e d on popul a t i on pa i r w i s e # S T ( P = 0. 002 ) a nd e xa c t t e s t s of popul a t i on di f f e r e nt i a t i on ( P = 0 003) T he s a m pl e s f r om I R L e xhi bi t e d a hi ghe r ha pl ot ype a nd nuc l e ot i de di ve r s i t y t ha n obs e r ve d i n t he G r a s s y K e y s a m pl e E l e ve n po l ym or phi c s i t e s w e r e obs e r ve d ( n = 21) de f i ni ng t e n ha pl ot ype s F S t e s t s of s e l e c t i ve ne ut r a l i t y f a i l e d t o r e j e c t t he n ul l hypot he s i s o f s e l e c t i ve ne ut r a l i t y f o r t he G r a s s y K e y s a m pl e of E l y s i a s ubor nat a ( P = 0. 624 ) a nd t he t e s t c oul d not be a ppl i e d t o t he P l a nt a t i on K e y s a m pl e be c a us e of f i xa t i on f o r one ha pl ot ype C om bi ni ng t he s a m pl e s f r om t he t w o l oc a t i ons s t i l l f a i l e d t o r e j e c t t he nul l hypo t he s i s of s e l e c t i ve ne ut r a l i t y ( P = 0 467)

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117 D I S C U S S I O N W ha t be ga n a s a c om pa r a t i ve popul a t i on s t r uc t ur e s t udy a m ong t hr e e s pe c i e s of s a c ogl os s a n s l ugs de t e c t e d l a r ge de gr e e s of c ox 1 v a r i a t i on w i t hi n put a t i ve s pe c i e s a nd t he di s c ove r y of m ul t i pl e e vol ut i ona r y s i gni f i c a nt uni t s F i r s t I w i l l di s c us s t he s i gni f i c a nt l e ve l s of va r i a t i on de t e c t e d w i t hi n E l y s i a s ubor nat a l i ke a ni m a l s a nd w ha t pos s i bl e s pe c i e s t he y a r e ba s e d on pr e vi ous t a xono m i c de s c r i pt i ons S e c ond, I w i l l e xa m i ne t he r e c e nt l y de s c r i be d s pe c i e s E l y s i a c l ar k i a nd ot he r pot e nt i a l e vol ut i ona r i l y s i gni f i c a nt uni t s w i t hi n E l y s i a c r i s pat a a s t hi s w i l l a f f e c t t he di s c us s i on r e ga r di ng w i t h i n a nd a m ong popul a t i on s t r uc t u r e T h i r d, I w i l l di s c us s t he pot e nt i a l f a c t or s a f f e c t i ng popul a t i on s ubdi vi s i on i n t he t hr e e s pe c i e s A l t ho ugh s a m pl e s i z e s a nd l oc a t i ons a r e l i m i t e d a nd t he e nt i r e r a nge of e a c h t a r ge t e d s pe c i e s di s t r i but i on ha s not be e n s a m pl e d, a n i nt e r e s t i ng pa t t e r n ha s e m e r ge d t ha t c a n be de s c r i b e d a s l ow t o i n t e r m e di a t e t o hi gh i n m ol e c ul a r di ve r s i t y i n w ha t a r e pr e s um e d s i ngl e s pe c i e s c om pa r i s ons E l y s i a s ubor nat a v ar i at i on W ha t w e r e be l i e ve d t o be E l y s i a s ubor nat a i ndi vi d ua l s f r om I R L a nd F L K e xhi bi t e d s i gni f i c a nt nuc l e ot i de va r i a t i on, a l t hough t he onl y e xt e r na l di f f e r e nc e i s i n t he i r s i z e s I n t e r m s of de g r e e of va r i a t i on, t he s e t w o g r oups w e r e a s di f f e r e nt f r om e a c h ot he r a s e a c h w a s t o t he ne xt m os t c l os e l y r e l a t e d s pe c i e s E l y s i a pr at e ns i s F u r t he r s uppor t of a gr e a t e r l e ve l o f di ve r ge nc e a m ong t he s e F l or i da s pe c i m e ns i s a pp a r e nt i n 3 r d pos i t i ons of c ox 1 I n a l l c ur r e nt s pe c i e s c om pa r i s ons w i t hi n P l a c obr a nc hi da e t hi s pos i t i on i s s a t ur a t e d ( s e e C ha pt e r 1) w hi c h i s t he s a m e pa t t e r n obs e r ve d a m ong s a m pl e s f r om I R L a nd F L K O f t he put a t i ve s pe c i e s e xa m i ne d w i t hi n t hi s s t udy, E l y s i a s ubor nat a e xhi bi t s

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118 t he hi ghe s t pe r c e nt s e que nc e di ve r ge nc e bot h i n un c or r e c t e d p di s t a nc e s a nd M L di s t a nc e s ba s e d on 1 s t a nd 2 n d pos i t i ons onl y ( 9 5 % a nd 3. 8 % r e s pe c t i ve l y) T he s pe c i e s na m e of t he popu l a t i ons i n t he K e ys a nd I ndi a n R i ve r L a goo n i s not a s i m pl e de t e r m i na t i on ba s e d on m o r phol ogy a nd r e f e r e nc e t o t he o r i gi na l E l y s i a s ubor nat a s pe c i e s de s c r i pt i on ( V e r r i l l 1901) S upe r f i c i a l l y bot h popul a t i ons l ook l i ke E l y s i a s ubor nat a ; how e ve r a not he r na m e oc c ur s i n t he l i t e r a t ur e t ha t ha s a d e s c r i pt i on s i m i l a r t o t hi s nom i na l s pe c i e s E l y s i a c auz e M a r c us a nd M a r c us 1957. E l y s i a c auz e w a s de s c r i be d f r om B r a z i l a nd J e ns e n & C l a r k ( 1983 ) di s c us s t he pr e s e nc e of a ne w r e c or d" of E l y s i a c auz e f r om F o r t P i e r c e a nd S e ba s t i a n I nl e t s on t he e a s t c oa s t of F l or i da C onf us i ngl y t he s e a ut hor s a l s o s t a t e t ha t t he y s e pa r a t e d t hr e e s p e c i e s t ha t c l os e l y r e s e m bl e E l y s i a c auz e a l l of w hi c h e xhi bi t s l i ght l y di f f e r e nt f e e di ng ha bi t s but f e e d p r e dom i na nt l y on C aul e r pa s pp. a nd ha ve di f f e r e nt l a r va l de ve l opm e nt t ype s ; pl a nkt ot r ophi c l e c i t hot r ophi c a nd di r e c t m e t a m or phos i s C l a r k ( 1 984) how e ve r s ynonym i z e d E l y s i a s ubor nat a f r om B e r m uda a nd E l y s i a c auz e f r om F l or i da but ga ve l i t t l e e vi de nc e f or w hy. I n C l a r k ( 1994) E l y s i a s ubor nat a i s r e por t e d t o be f a i r l y c om m on t hr oughout t he C a r i bbe a n" a nd t he t ype of de ve l opm e nt i s di r e c t o r e nc a ps ul a t e d m e t a m or phos i s T he i ndi vi dua l s c ol l e c t e d f o r t h i s s t udy f r o m t he F l or i da K e ys c om e f r o m a bor r ow pi t on G r a s s y K e y a nd a c a na l on P l a nt a t i o n K e y a nd w e r e < 1c m i n t ot a l l e ngt h. I ndi vi dua l s w e r e not e d t o s ha r e s om e c ha r a c t e r i s t i c s w i t h E l y s i a papi l l os a, s uc h a s s m a l l t ube r c l e s on t he body a nd da r k pi gm e nt on t he r o l l e d r hi nophor e s O t he r c ha r a c t e r i s t i c s w e r e m or e c ons i s t e nt w i t h E l y s i a s ubor nat a de s c r i pt i ons s uc h a s bl a c k pi gm e nt on t he l i ps a pr om i ne nt pe r i c a r di um e xt e ndi ng of t he l e ngt h of t he body bl a c k pi gm e nt

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119 a l ong t he m a r gi n of t he pa r a podi a a nd bl a c k pi gm e nt s pot s on t he body B ot h P l a nt a t i on a nd G r a s s y K e y s a m pl e s w e r e f ound f e e di ng on a C aul e r pa s p. T he i ndi vi dua l s c ol l e c t e d f r om I R L w e r e e xt r e m e l y s i m i l a r t o t he F l o r i da K e ys i ndi vi dua l s w i t h bl a c k pi gm e nt on t he l i ps pa r a podi a l m a r gi n a nd s pot t e d on t he bo dy. T he pe r i c a r di um e xt e nde d o f t he l e ngt h of t he body but t he ove r a l l l e ngt h ( 1. 5 3c m ) w a s l a r ge r t ha n t he F l or i da K e ys i ndi vi dua l s T he I R L i ndi vi dua l s w e r e f ound on C aul e r pa pr ol i f e r a S pe c i m e ns f r om bot h l oc a t i ons a l s o s ha r e a di s t i nc t i ve l y l i ght e ne d f oot r e gi on a nd hi ghl y p i gm e nt e d pa r a podi a I n a n e l e c t r ophor e t i c a na l ys i s of F l or i d a e l ys i i ds N ut t a l l ( 1987) s a m pl e d E l y s i a s ubor nat a f r om t he G r a s s y K e y bor r ow pi t a nd a l oc a t i on i n t he I ndi a n R i ve r L a goon a t T i t us vi l l e F l or i da a nd f ound t ha t t he t w o s a m pl e l oc a t i ons w e r e ge ne t i c a l l y di s t i nc t R a dul a r da t a f or t he t w o s a m pl e l oc a t i ons w e r e a l s o s i gni f i c a nt l y d i f f e r e nt N ut t a l l a l s o i nc l ude d a s t r i pe d" E l y s i a s ubor nat a f r om B i g P i ne K e y, w hi c h i s m os t l i ke l y E l y s i a pr at e ns i s O r t e a & E s pi nos a 1996. T he phe ne t i c r e s ul t s of N ut t a l l ( 1987 ) i ndi c a t e d t ha t E l y s i a s ubor nat a gr oupe d w i t h E l y s i a pr at e ns i s a nd t ha t E l y s i a ( I ndi a n R i ve r ) i s t he ne xt m os t c l os e l y r e l a t e d l i ne a ge w hi c h a gr e e s w i t h t he f i ndi ngs pr e s e nt e d he r e ( F i gur e 3. 4 ) A l t hough I c a nnot c onf i r m w ha t s pe c i e s i s i nvol ve d i n t hi s s t udy w i t hout f ur t he r m or phol ogi c a l a nd l i f e hi s t or y a s s e s s m e nt s t he F l or i da K e ys s pe c i m e ns a r e m os t l i ke l y E l y s i a s ubor nat a a nd t he I R L s pe c i m e ns a r e a n un na m e d s pe c i e s or pos s i bl y E l y s i a c auz e ( s e ns u M a r c us & M a r c us 1957) T he l a r ge va r i a t i on i n c ox 1 16S a nd H i s t one 3 s e que nc e s be t w e e n F L K a n d I R L s pe c i m e ns s ugge s t s t ha t t he s e a r e e vol ut i ona r i l y s i gni f i c a nt uni t s ; how e ve r f ur t he r i nve s t i ga t i on o f m or phol ogi c a l a nd ge ne t i c va r i a t i on i s

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120 c l e a r l y w a r r a nt e d be c a us e of t he i ns uf f i c i e nt l y de t a i l e d or i gi na l s pe c i e s de s c r i pt i ons a nd t he r e a s ons out l i n e d pr e vi ous l y. E l y s i a c r i s pat a v ar i at i on W i t hi n t he s a m pl e s of E l y s i a c r i s pat a f r om t he C a r i bbe a n, f our di s t i nc t l i ne a ge s w e r e de t e c t e d. O ne of t he s e l i ne a ge s F L K ha s s ubs e que nt l y be e n de s c r i be d a s a s e pa r a t e s pe c i e s E l y s i a c l ar k i ( P i e r c e e t a l 2006) T he di ve r ge nc e e s t i m a t e s i n c ox 1 a r e i nt e r m e di a t e w he n c om pa r e d t o t he unc o r r e c t e d p di s t a nc e s e s t i m a t e d f or E l y s i a t uc a ( l ow ) a nd E l y s i a s ubor nat a vs E l y s i a s p. I R L ( hi g h) S t r i c t m a xi m um l i ke l i hood a na l ys i s of a l l pos i t i ons di d r e c ove r t he f ou r di s t i nc t c l a de s ( not s how n) but di d not s he d m or e l i ght on t he r e l a t i ons hi ps a m ong t he s e c l a de s nor d i d t he i nc l us i on o f s e que nc e s f r om t w o ot he r ge ne s T he c ox 1 d i ve r ge nc e s a nd i nf or m a t i on r e ga r di ng v a r i a t i on i n t w o ot he r ge ne s 16S a nd H i s t one 3 s ugge s t t ha t a l l t he s e popul a t i o ns a r e e vol ut i ona r y s i gni f i c a nt uni t s I nt e r e s t i ngl y, t he m a xi m um num be r o f di f f e r e nc e s obs e r ve d i n t he H i s t one 3 s e que nc e s e xi s t be t w e e n t he c ox 1 ha pl ot ype s f r om B A 1, B E a nd U S V I F o r t he 16S ge ne t he gr e a t e s t num be r of di f f e r e nc e s i s f ound w he n c om pa r i ng t he B A 1 ha pl ot ype E C R 15, t o a l l l i s t e d a bove A m o r e c om pr e he ns i ve s ur ve y ( m or e l oc a t i ons a nd l a r ge r s a m pl e s i z e s ) of c ox 1 va r i a t i on i n E c r i s pat a i n t he C a r i bbe a n d e t e c t e d s i gni f i c a nt s t r uc t ur i ng a nd l a r ge de gr e e s of va r i a t i on a m ong ge ogr a phi c a l l y c l os e l oc a t i ons e s pe c i a l l y i n t he B a ha m a s ( P K r ug pe r s ona l c om m uni c a t i on ) ; t he r e f or e t he da t a pr e s e nt e d he r e a r e onl y a s m a l l por t i on of t he ove r a l l va r i a t i on p r e s e nt B e c a us e of t he l ow l e ve l of ge ne t i c va r i a t i on i n t he nuc l e a r ge ne H i s t one 3, c a ut i ona r y a ppr oa c h ha s be e n t a ke n a nd t he

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121 F l or i da K e ys s pe c i m e ns a r e t r e a t e d a s a popul a t i on i n a n a t t e m p t t o e xa m i ne how m i t oc hondr i a l ge ne t i c va r i a t i on i s pa r t i t i one d. W i t hi n and am ong popul at i on v ar i at i on A l t hough a s pur i ous e f f e c t of s a m pl e s i z e a nd ge ogr a phi c br e a dt h o f s a m pl i ng c a nnot be di s c ount e d, di f f e r e nt p r oc e s s e s m a y be a f f e c t i ng popul a t i on s t r uc t ur i ng i n t he s pe c i e s s t udi e d he r e T he r a nge s of t he t hr e e s pe c i e s s a m pl e d he r e a r e l a r ge r t ha n t he s a m pl i ng r a nge : E l y s i a t u c a i s f ound t hr oughout t h e C a r i bbe a n a nd i n B r a z i l E l y s i a s ubor nat a i s f ound t hr oughout t he C a r i bbe a n a nd i n B e r m uda a nd B r a z i l a nd E l y s i a c r i s pat a i s f ound t hr oughout t he C a r i bbe a n a nd t he B a ha m a s I nc r e a s e d s a m pl i ng of i ndi vi dua l s a t l oc a t i ons a nd s a m pl i ng o f m o r e l oc a t i ons i nc r e a s e s t he pot e nt i a l of de t e c t i ng m or e ha pl ot ype s e i t he r uni que or s ha r e d. T o i l l us t r a t e t he da nge r s of s a m pl i ng a l i m i t e d po r t i on o f a s pe c i e s r a nge i t i s i ns t r uc t i ve t o r e vi e w t he s t udi e s of L e e & F oi ghi l ( 2004 2005 ) I n a s e r i e s of pa pe r s on t he phyl oge ogr a phy of t he s c or c he d m us s e l B r ac hi dont e s e x us t us t he a ut hor s e xa m i ne d popul a t i on ge ne t i c s t r uc t u r e on bo t h s m a l l ( G ul f & A t l a nt i c ) a nd l a r ge s c a l e s ( G ul f A t l a nt i c & C a r i bbe a n) C ons e que nt l y, t he y ha d t o r e vi s e t he i r o r i gi na l c onc l us i on r e ga r di ng a F l or i da vi c a r i a nt e ve nt r e s ul t i ng i n s i gni f i c a nt ge ne t i c di vi s i ons be t w e e n t he G ul f a nd A t l a nt i c l i ne a ge s S i gn i f i c a nt s ha r i ng of pr e s um e d A t l a nt i c l i ne a ge s w i t h t he s out he r n C a r i bbe a n l oc a t i ons w a s de t e c t e d, s ugge s t i ng a nor t hw a r d e xpa ns i on of B r ac hi dont e s e x us t us l i ne a ge s i ns t e a d of a F l or i da vi c a r i a nt e ve nt c a us i ng di ve r ge nc e a m ong popul a t i ons ( L e e & F oi ghi l 2005 ) T he i nc r e a s e d s a m pl i ng of t he e nt i r e r a nge o f B r ac hi dont e s e x us t us i l l us t r a t e s how br oa d s c a l e s a m pl i ng c a n i nf l ue nc e c onc l us i ons a bout ha pl ot yp e e nde m i c i t y a nd t he r ol e o f vi c a r i a nt

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122 pr oc e s s e s I n one s e ns e c onc l us i ons a bout i ndi vi d ua l popul a t i ons w oul d not be s i gni f i c a nt l y a f f e c t e d w i t h l a r ge r s a m pl i ng br e a dt h F or e xa m pl e i f a popu l a t i on unde r w e nt r e pe a t e d bot t l e ne c ks s a m pl i ng a not he r l oc a t i on w oul d not a f f e c t t he de t e c t i on of bot t l e ne c ks T he de t e c t i on of ha pl ot ype s i n ot h e r l oc a t i ons how e ve r c a n ha ve a s i gni f i c a nt e f f e c t on c onc l us i ons m a de a bout ge ne f l ow be t w e e n l oc a t i ons a nd t he r ol e o f vi c a r i a nt pr oc e s s e s i n s ha pi ng ha pl ot ype di s t r i but i ons a s oppos e d t o l i f e hi s t or y t r a i t s o r de m ogr a phi c s pe c i f i c pr oc e s s e s A n obvi ous pa t t e r n i n va r i a t i on w i t hi n t he t hr e e s p e c i e s c onc e r ns di ve r s i t y e s t i m a t e s ( h & ) de gr e e of va r i a t i on a m ong ha pl o t ype s a nd popul a t i on s ubdi vi s i on: E l y s i a c r i s pat a a l w a ys e xhi bi t e d t he hi ghe s t l e ve l s of di ve r s i t y, va r i a t i on a nd popul a t i on s ubdi vi s i on. I n t e r m s o f r a nki ng ba s e d on t he s e pa r a m e t e r s E l y s i a t uc a w a s s e c ond, f ol l ow e d by E l y s i a s ubor nat a ( F L K ) a nd l a s t l y, E l y s i a s p. I R L ( no # S T e s t i m a t e a va i l a bl e ) W i t h s a m pl e l oc a t i ons a s t he popul a t i o n uni t s A M O V A a na l ys e s yi e l de d l a r ge di f f e r e nc e s a m ong # S T va l ue s w i t h E l y s i a c r i s pat a e xhi bi t i ng a va l ue of 0 8963, E l y s i a t uc a a va l ue of 0 6696 a nd l a s t l y E l y s i a s ub or nat a a va l ue of 0. 1572 I n t e r m s of ove r a l l ha pl ot ype di ve r ge nc e s ( M L di s t a nc e s ) f or m ul t i pl e l oc a t i ons t he l e a s t di ve r ge nt ha pl ot ype s w e r e f ound i n E l y s i a s ubor nat a i n t he F l or i da K e ys ( 0 15 + 0. 16% ) f o l l ow e d by E l y s i a t uc a ( 0. 55 + 0 34% ) a nd E l y s i a c r i s pat a ( 1. 1 + 0. 66% ) ( T a bl e 3 4) L i t t l e va r i a t i on w i t hi n t he F l or i da K e ys E l y s i a s ubor nat a w a s de t e c t e d e s pe c i a l l y w he n c om pa r e d t o a l l ot he r s pe c i e s or put a t i ve s pe c i e s ( T a bl e 3. 3 ) E l y s i a c r i s pat a F L K ha s gr e a t e r ha pl ot ype a nd nuc l e ot i de di ve r s i t y t ha n E l y s i a s ubor nat a ( h = 0. 79 a nd 0 61 a nd = 0. 0032 a nd 0 0024, r e s pe c t i ve l y) T he s e t w o s pe c i e s di f f e r i n l i f e h i s t or y

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123 c ha r a c t e r i s t i c s a l t hough i nf or m a t i on on kl e pt opl a s t y i s not a va i l a bl e f or E l y s i a s ubor nat a ( T a bl e 3 6) I n t e r m s of f e e di ng pr e f e r e nc e s E l y s i a c r i s pat a F L K a ppe a r s t o f e e d on m ul t i pl e a l ga l t ype s i nc l udi ng B r y ops i s s p. a nd P e ni c i l l us s p. w he r e a s E l y s i a s ubor nat a i s a s pe c i a l i s t on C aul e r pa s pp. C l a r k ( 1994) s t a t e s t ha t di r e c t o r e nc a ps ul a t e d m e t a m or phos i s i s t he l a r va l de ve l opm e nt a l t ype of E l y s i a s ubor nat a a nd t i m e t o ha t c hi ng i s 13 14 da ys ( C l a r k e t a l 1979 T hi ba ul t e t a l 20 01) A l t hough s a m pl e s i z e s of E l y s i a c r i s pat a a r e s m a l l f r om l oc a t i ons i n t he F l or i da K e ys s ha r i ng of ha pl ot ype s oc c ur s be t w e e n t he t w o l oc a t i ons ( S uga r l oa f a nd G r a s s y K e ys ) S i ng l e i ndi vi dua l s f r om P l a nt a t i on K e y ( E C R 3) a nd a n of f s hor e r e e f a t W e s t e r n D r y R oc ks ( E C R 1) a l s o s ha r e ha pl ot ype s but w e r e no t i nc l ude d i n t he ove r a l l a n a l ys i s T he f i ndi ng o f ha pl ot ype s ha r i ng a m ong l oc a t i ons w i t hi n t he F l o r i da K e ys s e e m s s ur pr i s i ng gi ve n t ha t E l y s i a s ubor nat a e xhi bi t s di r e c t de ve l opm e nt S uc h a c o m pl e x ha bi t a t a s t he F l or i da K e ys m os t l i ke l y ha s m i c r o s c a l e vi c a r i a nt p r oc e s s e s ( e g. l oc a l c ur r e nt s ) oc c ur r i ng t ha t a f f e c t t he di s t r i but i on of l a r va e i n w a ys t ha t a r e not de t e c t a bl e w i t h t he c u r r e nt s a m pl i ng F ur t he r s a m pl i ng i n t he K e ys a nd t h r oughout t he C a r i bbe a n i s ne c e s s a r y t o unde r s t a nd popul a t i on ge ne t i c s t r uc t ur e w i t hi n bot h s pe c i e s a nd t he i m pa c t of t he s e di f f e r e nt t ype s of de ve l opm e nt O nl y t w o of t he s pe c i e s s t udi e d he r e E l y s i a t uc a a nd E l y s i a c r i s pat a w e r e s a m pl e d i n F l or i da a nd t he B a ha m a s I nt e r e s t i ngl y t he s e t w o s pe c i e s e xhi bi t s i gni f i c a nt l y di f f e r e nt pa t t e r ns i n ha pl ot ype di s t r i b ut i ons nuc l e ot i de di ve r s i t y a nd popul a t i on s ubdi vi s i on ( T a bl e s 3 2, 3. 3 a nd 3 6) S i gni f i c a nt s ha r i ng o f ha pl ot ype s oc c ur s i n E l y s i a t uc a s a m pl e s f r om t he B a ha m a s a nd t he F l o r i da K e ys w i t h a

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124 G ul f / A t l a nt i c s pl i t s i m i l a r t o ot he r s t udi e s i n t hi s r e gi on ( A vi s e 1992 ) E l y s i a c r i s pat a doe s not e xhi bi t a s i m i l a r bi oge ogr a phi c pa t t e r n, a s no ha pl ot ype s a r e s ha r e d a m ong br oa d s c a l e l oc a t i ons I n r e ga r ds t o l i ne a ge di s t r i b ut i on a m ong s a m pl e s i t e s of E l y s i a c r i s pat a t he onl y r e gi on w he r e a ny of t he f ou r di s t i nc t l i ne a ge s ( F i gur e 3. 2A ) ove r l a ppe d w a s i n t he B a ha m a s W i t hi n t w o s i t e s i n t he B a ha m a s B i m i ni & C ha nne l C a y, i ndi vi dua l s w e r e c ol l e c t e d s i m ul t a ne ous l y t ha t e xh i bi t e d ha pl ot ype s be l ongi ng t o c l a de s B A 1 a nd B A 2. A n e xa m pl e of t hi s a r e ha pl ot ype s E C R 20 a nd E C R 21 f ound i n t w o i ndi vi dua l s f r om B i m i ni t ha t w e r e c ol l e c t e d on t he s a m e r oc k. A l t hough t he e nt i r e di s t r i but i on ha s not be e n s a m pl e d f or e i t he r s pe c i e s t he s t r i ki ng di f f e r e nc e i n ha pl ot ype di s t r i but i on i s puz z l i ng a s bot h E l y s i a c r i s pat a a nd E t uc a e xhi bi t l e c i t hot r oph i c l a r va l de ve l opm e nt T he m a j or di f f e r e nc e s be t w e e n t he t w o s pe c i e s a r e i n f e e di ng p r e f e r e nc e a nd de gr e e of k l e pt opl a s t y ( T a bl e 3. 6) E l y s i a t uc a di s pl a ys a s t r ong f e e di ng pr e f e r e nc e f or H al i m e da s p. ( J e ns e n, 1983 a nd pe r s obs e r v. ) w hi l e E l y s i a c r i s pat a f e e ds on non c a l c a r e ous a l ga e of t he f a m i l y B r yops i da c e a e a nd c a l c a r e ous a l ga e of t he f a m i l y U dot e a c e a e ( C ur t i s e t a l 2004) E l y s i a c r i s pat a h a s l ong be e n c ons i de r e d a s t r ong kl e pt opl a s t s pe c i e s pr om pt i ng i t s c a t e gor i z a t i on a s a L e ve l 6 kl e pt opl a s t ( s e ns u C l a r k, 1992) T hi s l e ve l i s c ha r a c t e r i z e d a s l ong t e r m f un c t i ona l r e t e nt i on o f c hl or op l a s t s a nd t he a bi l i t y t o pr oduc e phot os ynt ha t e f or pe r i ods gr e a t e r t ha n 1 w e e k ( C l a r k, 1992) E l y s i a t uc a how e ve r i s a L e ve l 5 kl e pt opl a s t w hi c h i s c ha r a c t e r i z e d a s m e di um t e r m f unc t i ona l r e t e nt i on of c hl or opl a s t s ( ~ 5 da ys ) a nd no pho t os ynt ha t e pr oduc t i on w i t hi n 1 w e e k of s t a r va t i on ( C l a r k & B us a c c a 1978)

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125 I f a s pe c i e s f e e ds on one t ype of a l ga a nd t ha t a l ga di e s of f t he n t he a dul t s ha ve t o m ove or di e a nd of f s pr i ng p r oduc e d m a y ha ve t o s e a r c h f a r t he r a br oa d f o r t he i r f ood c hoi c e I f t he y a r e a bl e t o pr oduc e ne c e s s a r y e ne r gy f r om r e s our c e s c ol l e c t e d pr e vi ous l y ( i e c hl or opl a s t s ) a nd t he i r f ood c hoi c e i s not l i m i t e d t o one t ype of a l ga a ni m a l s m a y be a bl e t o s ur vi ve i n a l oc a t i on f or a l onge r pe r i od of t i m e T he s pe c i a l i s t / ge ne r a l i s t s t r a t e gy c oupl e d w i t h kl e pt opl a s t y c oul d e xpl a i n t he s t r uc t u r e obs e r ve d be t w e e n s l ug s pe c i e s i n t he K e ys a nd B a ha m a s F or E l y s i a t uc a a s pe c i a l i s t a nd not a s good a kl e pt opl a s t t he a dul t s w oul d ha ve t o s e a r c h f or t he a ppr opr i a t e f oo d s our c e I f t he a ppr op r i a t e f ood s our c e i s not a va i l a bl e or i n c l os e p r oxi m i t y, t he n a dul t s w oul d not be a bl e t o pe r s i s t f or a l ong pe r i od. S pe c i f i c s r e ga r di ng l a r va l m e t a m o r ph os i s a r e unknow n a t t hi s t i m e T he pa t t e r n of s i gni f i c a nt s ha r i ng o f h a pl ot ype s be t w e e n t he B a ha m a s a nd t he F l o r i da K e ys how e ve r s ugge s t s t ha t t he i r p l a nkt oni c l i f e pr i o r t o m e t a m or phos i s i s e xt e ns i ve e na bl i ng l ong di s t a nc e di s pe r s a l F o r t he ge ne r a l i s t f e e de r a nd e xc e l l e nt kl e pt opl a s t E l y s i a c r i s pat a, m or e i nf o r m a t i on i s a va i l a bl e i n t e r m s of t i m e t o m e t a m o r phos i s I n t he l a bor a t or y, P i e r c e e t a l ( 2006) doc um e nt e d t i m e t o m e t a m or phos i s f or bot h F L K a nd U S V I a ni m a l s t o be 4 5 da ys a l t hough t he t i m e t o ha t c hi ng w a s l onge r i n t he F L K s pe c i m e ns a t 28 35 da ys ve r s us 19 da ys f or t he U S V I s pe c i m e ns A l ong pe r i od t o ha t c hi ng a nd t he a bi l i t y t o us e m u l t i pl e a l ga l s pe c i e s c oul d a l l ow popul a t i ons t o pe r s i s t i n pa r t i c ul a r l oc a t i ons f o r l onge r pe r i ods o f t i m e A s a c ons e que nc e of l onge r pe r s i s t e nc e s i gni f i c a nt br oa d a nd m i c r o s c a l e popul a t i on s t r uc t ur e c oul d r e s ul t S uppor t f or t hi s hypot he s i s i s e vi de nt f r om t he l a c k of ha pl ot ype s h a r i ng a m ong b r oa d a nd s m a l l s c a l e l oc a t i ons of E l y s i a c r i s pat a.

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12 6 A not he r pos s i bl e e xpl a na t i on f or t he i nc r e a s e d l e v e l of popul a t i on s ubdi vi s i on i n E l y s i a c r i s pat a c oul d be r a pi d f l uc t ua t i ons i n popu l a t i on s i z e c oupl e d w i t h va r y i ng s e l e c t i ve pr e s s ur e a nd r e t e nt i on of a nc e s t r a l pol ym or phi s m s I n r e f e r e nc e t o popul a t i on s i z e C l a r k ( 1994) r e por t e d a n a ppr oxi m a t e l y 10 f o l d r e duc t i on i n t he popul a t i on s i z e of a ni m a l s a t G r a s s y K e y f r om t he 1970's t o t he 90's N o s i m i l a r da t a e xi s t f o r t he ot he r l oc a t i ons s a m pl e d he r e C ol l e c t or s w o r ki ng i n t he F l or i da K e ys ha ve obs e r ve d l ow t o hi gh de ns i t y popul a t i ons i n t he s a m e l oc a t i on s pa nni ng t he c our s e of 2 ye a r s ( 2002 2004; S E M a s s e y, pe r s c om m ) w hi c h m a y be a s s oc i a t e d w i t h t he i r l i f e c yc l e T he F L K s a m pl e s a na l yz e d he r e w e r e c ol l e c t e d i n 2000 a nd 2002. T he s e obs e r va t i ons on popul a t i on s i z e pr ovi de a t l e a s t c i r c um s t a nt i a l e vi d e nc e of f l uc t ua t i ons pot e nt i a l l y r a pi d. E vi de nc e f or s e l e c t i on i n t he F L K popul a t i on w a s de t e c t e d us i ng t he F S t e s t of F u ( 1997) a nd a goodne s s of f i t t e s t i ndi c a t e d t ha t a s udde n e xpa ns i on m ode l e xpl a i ne d t he m i s m a t c h di s t r i but i on of pa i r w i s e di f f e r e nc e s F or a l l ot he r popul a t i ons s e l e c t i ve ne ut r a l i t y c oul d not be r e j e c t e d a nd t he m i s m a t c h di s t r i but i ons w e r e not uni m oda l W i t hi n s pe c i e s i t a ppe a r s t ha t l a r va l de ve l opm e nt t ype m a y not be a good pr e di c t or of popul a t i on s ubdi vi s i on. A ni m a l s w i t h t he s a m e t ype of de ve l opm e nt e xhi bi t di f f e r e nt pa t t e r ns of s ubdi vi s i on, a s obs e r ve d i n E l y s i a t uc a a nd E l y s i a c r i s pat a a l t hough t he i m por t a nc e of t he t i m e t o m e t a m or phos i s c a nnot be di s c ount e d. F e e di ng p r e f e r e nc e s a nd de gr e e of k l e pt opl a s t y m a y e xpl a i n t he obs e r v e d di f f e r e nc e s a nd w a r r a nt f u r t he r i nve s t i ga t i on. A s not e d a bove e xa m i na t i on of t he s e s pe c i e s a c r os s t he i r r a nge i s a l s o ne c e s s a r y t o f ul l y c om pr e he nd ge ne t i c va r i a t i on a n d i t s pot e nt i a l c a us e s

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127 P opul a t i on s pe c i f i c de m ogr a phy ne e ds t o be e xpl o r e d m or e f ul l y w i t h t he a ddi t i on of gr e a t e r s a m pl e s i z e s T he di f f e r e nc e s not e d i n t he m i s m a t c h di s t r i but i ons be t w e e n t he s a m pl e l oc a t i ons / c l a de s of E l y s i a c r i s pat a hi ghl i gh t t he pot e nt i a l f or popul a t i on s pe c i f i c pr oc e s s e s t o ha ve a s i gni f i c a nt i m pa c t on popu l a t i o n s ubdi vi s i on. P r e vi ous l i t e r a t ur e on s pe c i e s de s c r i pt i ons a nd s pe c i e s oc c ur r e nc e i s c onf us i ng a nd pot e nt i a l l y c ont r a di c t or y s uc h t ha t i de nt i f i c a t i o n of s pe c i e s c a n be di f f i c ul t E l y s i a s ubor nat a a nd s i m i l a r l ooki ng a ni m a l s a r e a good e xa m pl e of t he p r obl e m s i nhe r e nt i n c ur r e nt pl a c obr a nc hi d s l ug t a xonom y. O bvi ous l y, f ur t he r s t udy ba s e d on m or phol ogy be ha vi or a nd ge ne t i c s i s ne c e s s a r y t o de t e r m i ne ho w t o di f f e r e nt i a t e t he s e a ni m a l s f r om e a c h ot he r I t i s i m por t a nt t o s a m pl e t he s e a ni m a l s a c r os s t he i r r a nge s o t ha t l e ve l s of m or p hol ogi c a l a nd ge ne t i c va r i a t i on c a n be de t e r m i ne d a nd s pe c i e s de s i gna t i ons c a n be m a de i n a c om pa r a t i ve f r a m e w or k

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128 R E F E R E N C E S A V I S E J C 1992 M ol e c ul a r popul a t i on s t r uc t u r e a nd t he bi oge ogr a phi c hi s t or y of a r e gi ona l f a una : a c a s e hi s t or y w i t h l e s s o ns f or c ons e r va t i on bi ol ogy. O i k os 63: 62 76. B H A U D M 1998. T he s pr e a di ng pot e nt i a l o f pol yc ha e t e l a r va e doe s not pr e di c t a dul t di s t r i but i ons ; c ons e que nc e s f or c ondi t i ons o f r e c r ui t m e nt H y dr obi ol ogi a, 375/ 376: 35 47. B U R T O N R S 1983. P r ot e i n pol ym o r phi s m s a nd ge ne t i c di f f e r e nt i a t i on of m a r i ne i nve r t e br a t e popul a t i ons M ar i ne B i ol ogy L e t t e r s 4: 193 206 C L A R K K B 1984. N e w r e c or ds a nd s ynonym i e s of B e r m uda O pi s t hobr a nc hs ( G a s t r opoda ) N aut i l us 98: 85 97 C L A R K K B 1992. P l a nt l i ke a ni m a l s a n d a ni m a l l i ke pl a nt s : s ym bi ot i c c oe vol ut i on of a s c ogl os s a n ( = s a c ogl os s a n) m ol l us ks t he i r a l ga l pr e y, a nd a l ga l pl a s t i ds P p. 515 5 30 i n A l gae and Sy m bi os i s : P l ant s A ni m al s F ungi V i r us e s I nt e r ac t i ons E x pl or e d W R e i s s e r ( e d. ) B i opr e s s L t d. B r i s t ol U K C L A R K K B 1994. A s c ogl os s a n ( = S a c ogl os s a ) m ol l us c s i n t he F l or i da K e ys : r a r e m a r i ne i nve r t e br a t e s a t s pe c i a l r i s k B u l l e t i n of M ar i ne Sc i e nc e 54: 900 916.

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129 C L A R K K B & B U S U C C A M 1978 F e e di ng s pe c i f i c i t y a nd c hl or opl a s t r e t e nt i on i n f our t r op i c a l a s c ogl os s a w i t h a di s c us s i on of e xt e nt of c hl or opl a s t s ym bi os i s a nd t he e vol ut i on o f t he or de r J our nal of M ol l us c an St udi e s 44: 272 282. C L A R K K B B U S A C C A M & S T I R T S H 19 79. N ut r i t i ona l a s pe c t s of de ve l opm e nt of t he a s c ogl os s a n, E l y s i a c au z e P p. 11 24 i n R e pr oduc t i v e E c ol ogy of M ar i ne I nv e r t e br at e s S S t a nc yk ( e d. ) U ni ve r s i t y S out h C a r ol i na P r e s s ; 283pgs C U R T I S N E M A S S E Y S E S C H W A R T Z J A T A G I H O F H & P I E R C E S K 2004. T he i nt r a c e l l ul a r f unc t i ona l c hl or op l a s t s i n a dul t E l y s i a c r i s pat a c om e f r o m s e ve r a l a l ga l s pe c i e s a nd a r e di f f e r e nt f r om t hos e i n j uve ni l e s l ugs I nt e gr at i v e and C om par at i v e B i ol ogy 44: 686 E X C O F F I E R L 2004. P a t t e r ns of D N A s e que nc e di ve r s i t y a nd ge ne t i c s t r uc t ur e a f t e r a r a nge e xpa ns i on: l e s s ons f r om t he i nf i ni t e i s l a nd m ode l M ol e c ul ar E c ol ogy 13: 853 64. E X C O F F I E R L L A V A L G & S C H N E I D E R S 2005. A r l e qui n ve r 3. 0 : A n i nt e gr a t e d s of t w a r e pa c ka ge f or popul a t i on ge ne t i c s da t a a na l ys i s E v ol ut i onar y B i oi nf or m at i c s O nl i ne 1: 47 50. F O L M E R O B L A C K M H O E H W L U T Z R & V R I J E N H O E K R 1994. D N A pr i m e r s f o r a m pl i f i c a t i on of m i t oc hondr i a l c yt oc hr om e c oxi da s e s ubuni t I f r om di ve r s e m e t a z oa n i nve r t e br a t e s M ar i ne B i ol ogy 3: 294 299 F U Y X 1997 S t a t i s t i c a l t e s t s of ne ut r a l i t y o f m ut a t i ons a ga i ns t popul a t i on gr ow t h, hi t c hhi ki ng a nd ba c kgr ound s e l e c t i on. G e ne t i c s 147: 915 925.

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130 G R E E N E R W & M U S C A T I N E L 1972. S ym bi os i s i n s a c ogl os s a n opi s t hobr a nc hs : phot os ynt he t i c pr oduc t s of a ni m a l c hl or opl a s t a s s oc i a t i ons M ar i ne B i ol ogy 14: 253 259. H E D G E C O C K D 1986. I s ge ne f l ow f r om pe l a gi c l a r va l di s pe r s a l i m por t a nt i n t he a da pt a t i on a nd e vol ut i on of m a r i ne i nve r t e br a t e s ? B ul l e t i n of M ar r i ne Sc i e nc e 39: 550 564. H E L L B E R G M E 1996 D e pe nde nc e of ge ne f l o w on ge ogr a phi c di s t a nc e i n t w o s ol i t a r y c or a l s w i t h di f f e r e nt l a r va l di s pe r s a l c a pa bi l i t i e s E v ol ut i on 50: 1167 1175. K Y L E C J & B O U L D I N G E G 2000 C om pa r a t i ve popul a t i on ge ne t i c s t r uc t ur e of m a r i ne ga s t r opods ( L i t t or i na s pp. ) w i t h a nd w i t hout pe l a gi c l a r va l d i s pe r s a l M ar i n e B i ol ogy 137: 835 845 J E N S E N K R 1983. F a c t or s a f f e c t i ng f e e di ng s e l e c t i vi t y i n he r bi vo r ous A s c ogl os s a ( M ol l us c a : O pi s t hobr a nc hi a ) J our nal of E x pe r i m e nt al M ar i ne B i ol ogy and E c ol ogy 66: 135 148. J E N S E N K R 1993. M or phol ogi c a l a da pt a t i ons a nd pl a s t i c i t y of r a dul a r t e e t h of t he S a c ogl os s a ( = A s c ogl os s a ) ( M ol l us c a : O pi s t hobr a nc hi a ) i n r e l a t i on t o t he i r f ood pl a nt s B i ol ogi c al J our nal of t he L i nne an Soc i e t y 48: 135 155 J E N S E N K R & C L A R K K B 1983 A nnot a t e d c he c kl i s t of F l or i da a s c ogl os s a n O pi s t hobr a nc hi a N aut i l us 97: 1 13 L E E T & F O I G H I L D 2004 H i dde n F l o r i di a n bi odi ve r s i t y: m i t oc hond r i a l a nd nuc l e a r ge ne t r e e s r e ve a l f our c r ypt i c s pe c i e s w i t hi n t he s c or c he d m us s e l B r ac hi dont e s e x us t us s pe c i e s c om pl e x. M ol e c ul ar E c ol ogy 13: 3 527 3542.

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131 L E E T & F O I G H I L D 2005 P l a c i ng t he F l o r i di a n m a r i ne ge ne t i c di s j unc t i on i nt o a r e gi ona l e vol ut i ona r y c ont e xt us i ng t he s c or c he d m us s e l B r ac hi dont e s e x us t us s pe c i e s c om pl e x. E v ol ut i on 59: 2139 21 58. M A R C U S E & M A R C U S E V 1957 O n O pi s t hobr a nc hi a f r om B r a z i l J our nal of t he L i nne an Soc i e t y of L ondon Z ool ogy 43: 390 486. M A R I N A & R O S J 2004. C he m i c a l de f e ns e s i n s a c ogl os s a n opi s t hobr a nc hs : t a xonom i c t r e nds a nd e vol ut i ve i m pl i c a t i ons Sc i e nt i a M ar i na 68: 227 241 N E I M 1987 M ol e c ul ar E v ol ut i onar y G e ne t i c s C ol um bi a U ni ve r s i t y P r e s s N e w Y or k, N Y N U T T A L L T R 1987 A n e l e c t r opho r e t i c a na l ys i s of C a r i bbe a n e l ys i i d t a xonom y ( O pi s t hobr a nc hi a : A s c ogl os s a ) P h. D D i s s e r t a t i on. F l or i da I ns t i t ut e o f T e c hnol ogy. 68 pgs P I E R C E S K B I R O N R W & R U M P H O M E 1996. E ndos ym bi ot i c c hl or opl a s t s i n m ol l us c a n c e l l s c ont a i n pr ot e i ns s y nt he s i z e d a f t e r pl a s t i d c a pt ur e J our nal of E x pe r i m e nt al B i ol ogy 199: 2323 2330. P I E R C E S K C U R T I S N E M A S S E Y S E B A S S A L K A R L S A & F I N N E Y C M 2006. A m or phol og i c a l a nd m ol e c ul a r c om pa r i s on be t w e e n E l y s i a c r i s pat a a nd a ne w s pe c i e s of kl e pt opl a s t i c s a c ogl os s a n s e a s l ug f r om t he F l o r i da K e ys M ol l us c an R e s e ar c h 26: 23 28 R A Y M O N D M & R O U S S E T F 1995. A n e xa c t t e s t f or popul a t i on di f f e r e nt i a t i on E v ol u t i on 49: 1280 1283

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132 R Z H E T S K Y A & S I T N I K O V A T 1996 W he n i s i t s a f e t o us e a n ove r s i m pl i f i e d s ubs t i t ut i on m ode l i n t r e e m a ki ng? M ol e c ul ar B i ol ogy and E v ol ut i on 13: 1255 1265. R O G E R S A R & H A R P E N D I N G H C 1992 P o pul a t i on gr ow t h m a ke s w a ve s i n t he di s t r i but i on of pa i r w i s e ge ne t i c di f f e r e nc e s M ol e c ul ar B i ol ogy and E v ol ut i on 9 : 552 555. P O S A D A D & C R A N D A L L K A 1998 M O D E L T E S T : t e s t i ng t he m ode l of D N A s ubs t i t ut i on. B i o i nf or m at i c s 14: 817 818 R U M P H O M E S U M M E R E J & M A N H A R T J R 2000 S o l a r pow e r e d s e a s l ugs M ol l us c / a l ga l c hl or opl a s t s ym bi os i s P l ant P hy s i ol ogy 123: 29 38 S L A T K I N M & H U D S O N R R 1991. P a i r w i s e c om pa r i s ons of m i t oc hondr i a l D N A s e que nc e s i n s t a bl e a nd e xpone nt i a l l y gr ow i ng popul a t i ons G e ne t i c s 129: 555 562. S W O F F O R D D L 1998. P A U P 4 0: P hyl oge ne t i c A na l ys i s U s i ng P a r s i m ony a nd O t he r M e t hods S i na ue r A s s oc i a t e s M a s s a c hu s e t t s T A Y L O R D L 1968 C hl or opl a s t s a s s ym bi ot i c o r ga ne l l e s i n t he di ge s t i ve gl a nd of E l y s i a v i r i di s ( G a s t r op oda : O pi s t hobr a nc hi a ) J our nal of t he M ar i ne B i ol ogi c al A s s oc i at i on of t he U ni t e d K i ngdom 48: 1 15.

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133 T H I B A U T T M E I N E S Z A A M A D E P C H A R R I E R S D E A N G E L I S K I E R A R D I S M A N G I A L A J O L M E L N I C K J & V I D A L V 2001 E l y s i a s ubor nat a ( M ol l us c a ) a pot e nt i a l c ont r ol a ge nt of t he a l ga C aul e r pa t ax i f ol i a ( C hl or ophyt a ) i n t he M e di t e r r a ne a n S e a J our nal of t he M ar i ne B i ol og i c al A s s oc i at i on of t he U ni t e d K i ngdom 81: 497 504 T O D D C D L A M B E R T W J & T H O R P E J P 1998. T he ge ne t i c s t r uc t ur e of i nt e r t i da l p opul a t i ons o f t w o s pe c i e s of nudi br a nc h m ol l us c s w i t h pl a nkt ot r oph i c a nd pe l a gi c l e c i t hot r ophi c l a r va l s t a ge s : a r e pe l a gi c l a r va e f or di s pe r s a l ? J our nal of E x pe r i m e nt al M ar i ne B i ol ogy and E c ol ogy 228: 1 28. W A L S H H E M E T Z G E R D A & H I G U C H I R 199 1. C he l e x m e di um f or s i m pl e e xt r a c t i on of D N A f o r P C R ba s e d t ypi ng f r om f or e ns i c m a t e r i a l B i oT e c hni que s 10: 506 513 W A U G H G D & C L A R K K B 1986. S e a s ona l a nd ge ogr a phi c va r i a t i on i n c hl or ophyl l l e ve l o f E l y s i a t uc a ( A s c ogl os s a : O pi s t hobr a nc hi a ) M a r i ne B i ol ogy 92: 483 487.

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134 T a bl e 3. 1: P r i m e r s us e d i n a m pl i f i c a t i on o f t h r e e s pe c i e s of s a c ogl os s a n s T he f i r s t t w o l i s t e d a r e t he c ox 1 pr i m e r s of F ol m e r e t a l ( 1996) T he r e m a i ni ng pr i m e r s a r e s pe c i e s s pe c i f i c pr i m e r s m a de f o r t hi s s t udy. E S U E T U a nd E C R r e f e r t o E l y s i a s ubor nat a, E l y s i a t uc a a nd E l y s i a c r i s pat a r e s pe c t i ve l y. T he e s t i m a t e d f r a gm e nt s i z e i s pr ovi de d f or t he f or w a r d ( F ) a nd r e ve r s e ( R ) p r i m e r c om bi na t i o ns P r i m e r N a m e 5' 3' S e que nc e F r a gm e nt S i z e L C O 1490 G G T C A A C A A A T C A T A A A G A T A T T G G H C O 2198 T A A A C T T C A G G G T G A C C A A A A A A T C A 700bp E S U C O 1F T G G G A C T T C A G G T G C T T T T T E S U C O 1R A A T A G G A T C C C C T C C T C C A 680bp E T U C O 1F 1 G A T G T G G T C T G G T T G G A A C A E T U C O 1R 1 A T T G G G T C C C C A C C T C C T 670bp E C R C O 1F 2 T G T G G T T T A G T C G G G A C T G G E C R C O 1R 3 T A A T T G C T C C A G C A A G C A C A 630bp

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135 T a bl e 3. 2: C yt oc hr om e c ox i da s e s ubuni t I ha pl ot y pe s by l oc a t i on f o r s pe c i e s of s a c ogl os s a ns I n t he t e xt ha pl ot ype s a r e r e f e r e nc e d us i ng t he s pe c i e s na m e a bbr e vi a t i on ( i e E T U f or E l y s i a t uc a a nd E C R f o r E l y s i a c r i s pat a ) f ol l ow e d by t he ha pl ot ype num be r D a s he s i ndi c a t e t he a bs e nc e of t hos e num be r e d ha pl ot ype s f o r a pa r t i c ul a r s pe c i e s B A 1 a nd B A 2 unde r E l y s i a c r i s pat a r e f e r t o B a ha m a ns c l a de 1 a nd 2 r e s pe c t i ve l y. E l y s i a t u c a E l y s i a c r i s p a t a E l y s i a s u b o r n a t a H a p l o t y p e G O M ( N = 5 ) F L K ( N = 1 3 ) B A ( N = 1 9 ) F L K ( N = 2 5 ) B E ( N = 7 ) B A ( N = 1 1 ) U S V I ( N = 6 ) I R L ( N = 2 1 ) F L K ( N = 3 5 ) 1 1 1 1 1 2 1 1 7 3 1 3 1 4 1 1 1 5 1 2 1 6 2 2 1 1 7 1 2 1 8 8 3 5 9 1 1 1 1 0 2 1 2 1 1 1 5 1 1 2 1 1 1 1 3 6 3 1 ( B A 2 ) 7 1 4 1 2 ( B A 2 ) 2 6 1 5 1 1 ( B A 1 ) 1 6 1 1 ( B A 1 ) 1 7 2 1 ( B A 1 ) 1 8 1 ( B A 1 ) 1 9 2 ( B A 1 ) 2 0 1 ( B A 1 ) 2 1 1 ( B A 2 ) 2 2 2 2 3 2 2 4 1 2 5 1

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136 T a bl e 3. 3: H a pl ot ype a nd nuc l e ot i de di ve r s i t y e s t i m a t e s + s t a nda r d de vi a t i ons f or t hr e e s pe c i e s of s a c ogl os s a ns E s t i m a t e s i n bol d a r e ove r a l l e s t i m a t e s of di ve r s i t y f or e a c h put a t i ve s pe c i e s L oc a t i ons r e f e r s t o b r oa d s c a l e s a m pl e s i t e s S pe c i e s / L oc a t i on H a pl ot ype ( h) d i ve r s i t y N uc l e ot i de ( ) di ve r s i t y E l y s i a s ubor nat a 0. 7545 + 0 0527 0. 0475 + 0 0235 F l or i da K e ys G r a s s y 0. 6140 + 0 0750 0. 0024 + 0 0018 P l a nt a t i on 0 0 I ndi a n R i ve r L a goon 0. 8476 + 0 0588 0. 0038 + 0 0025 E l y s i a t uc a 0. 8919 + 0. 0332 0. 0121 + 0 0065 G ul f o f M e xi c o 1. 0000 + 0 1265 0. 0040 + 0 0031 F l or i da K e ys 0. 7821 + 0 1045 0. 0038 + 0 0026 B a ha m a s 0. 8070 + 0 0790 0. 0069 + 0 0041 E l y s i a c r i s pat a 0. 9345 + 0 0237 0. 0395 + 0 0197 F l or i da K e ys 0. 7900 + 0 0738 0. 0032 + 0 0021 B e l i z e 0. 5238 + 0 2086 0. 0017 + 0 0016 B a ha m a s 0. 9636 + 0 0510 0. 0416 + 0 0224 1 0. 9524 + 0 0955 0. 0196 + 0 0117 2 0. 8333 + 0 22 24 0. 0105 + 0 0076 U S V I 0. 8667 + 0 1291 0. 0032 + 0 0025

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137 T a bl e 3. 4: S um m a r y of unc or r e c t e d p a nd m a xi m u m l i ke l i hood ( M L ) di s t a nc e s V a l ue s i ndi c a t e t he a ve r a ge di s t a nc e s ove r a l l a nd be t w e e n c l a de s f or bot h unc o r r e c t e d p a nd c or r e c t e d M L di s t a nc e s A ve r a ge M L di s t a nc e s t o t he out gr oups a r e i ndi c a t e d a nd w he r e a ppl i c a bl e m i ni m um a nd m a xi m um di s t a nc e s a r e i ndi c a t e d f or be t w e e n c l a de a nd out gr oup c om pa r i s ons D i s t a nc e s C om pa r i s ons E l y s i a t uc a E l y s i a c r i s pat a E l y s i a s ubor nat a l i ke a ni m a l s U nc or r e c t e d p O ve r a l l 0 0 1 9 0 + 0 0 1 2 3 0 0 4 5 5 + 0 0 2 2 4 0 0 4 6 6 + 0 0 4 4 7 B e t w e e n C l a de s 0 0 3 1 8 + 0 0 0 4 2 0 0 4 8 8 + 0 0 0 5 5 (mi n ) 0 0 6 8 8 + 0 0 0 5 2 (m ax ) 0 0 9 4 8 + 0 0 0 2 7 M L O ve r a l l 0 0 0 5 5 + 0 0 0 5 3 0 0 1 1 2 + 0 0 0 6 6 0 0 1 7 8 + 0 0 1 9 0 B e t w e e n C l a de s 0 0 1 0 5 + 0 0 0 3 4 0 0 0 7 8 + 0 0 0 2 0 (mi n ) 0 0 1 6 6 + 0 0 0 3 6 (m ax ) 0 0 3 7 5 + 0 0 0 6 2 O ut gr oups 0 0 5 2 2 + 0 0 0 5 9 1 0 0 5 8 7 + 0 0 0 5 1 2 0 0 2 6 5 + 0 0 0 2 9 (mi n ) 0 0 3 8 5 + 0 0 0 5 2 (m ax ) 0 0 2 5 0 + 0 0 0 1 8 (mi n ) 0 0 3 6 0 + 0 0 0 5 3 (m ax ) 1 ve r s us E l y s i a be nne t t ae 2 ve r s us E l y s i a pus i l l a

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138 T a bl e 3. 5: A c c e s s i on num be r s f or s e que nc e s of 16 S a nd H i s t one 3 ge ne r e gi ons D a s he s i ndi c a t e t ha t s e que nc e s a r e not a va i l a bl e f o r t hos e ha pl ot ype s H a pl ot ype 16S H i s t one 3 E C R 3 D Q 480197 D Q 534788 E C R 10 D Q 480199 D Q 534790 E C R 15 D Q 781366 D Q 7 81368 E C R 24 D Q 781367 D Q 781369 E S U 1 D Q 781370 E S U 2 D Q 781371 D Q 781374 E S U 5 D Q 781372 D Q 781375 E S U 8 D Q 781376 E S U 11 D Q 781373 E S U 14 D Q 480165 D Q 534765

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139 T a bl e 3. 6: R e s ul t s of ove r a l l e s t i m a t e s of S T a nd s e l e c t l i f e hi s t or y t r a i t s f or t hr e e s pe c i e s of s a c ogl os s a ns F or l a r va l de ve l opm e nt t ype : 2 = l e c i t hot r ophi c a nd 3 = di r e c t de ve l opm e nt F o r kl e pt op l a s t y l e ve l : 5 = m e di um t e r m f unc t i ona l r e t e nt i on of c hl or opl a s t s phot os ynt ha t e pr oduc e d > 24 hou r s w i t h f unc t i on c e a s i ng w i t hi n 1 w e e k o f s t a r va t i on; 6 = l ong t e r m f unc t i ona l r e t e nt i on, phot os ynt ha t e pr oduc e d f or > 1 w e e k. S pe c i e s O ve r a l l S T F e e di ng P r e f e r e nc e L a r va l D e ve l opm e nt T ype K l e pt opl a s t y L e ve l E l y s i a t uc a 0. 6696 P < 0 0001 H al i m e da s pp . 2 5 E l y s i a c r i s pat a 0. 8963 P < 0 0001 H al i m e da, P e ni c i l l us 2 6 E l y s i a s ubor nat a 0. 1572 P = 0 005 C aul e r pa s pp. 3 ?

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140 F i gur e 3. 1 : R e s ul t s of N e i ghbor J oi ni ng ( N J ) a na l y s i s of E l y s i a t uc a c ox 1 ha pl ot ype s f r om t he G ul f o f M e xi c o ( G O M ) F l or i da K e ys ( F L K ) a nd t he B a ha m a s ( B A ) B oot s t r a p va l ue s ba s e d on 1000 r e pl i c a t e s a r e i ndi c a t e d a bove t he br a nc he s A ) M i dpoi nt r oot i ng of N J t r e e ba s e d on unc or r e c t e d p di s t a nc e s B ) N J t r e e r oo t e d w i t h E l y s i a be nne t t ae a nd E l y s i a ( = E l y s i e l l a) pus i l l a ba s e d on M L di s t a nc e s e xc l udi ng 3 r d pos i t i ons

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141 F i gur e 3. 2 : R e s ul t s of N e i ghbor J oi ni ng ( N J ) a na l y s i s of E l y s i a c r i s pat a c ox 1 ha pl ot ype s f r om F l or i d a K e ys ( F L K ) B e l i z e B a ha m a s ( B A 1 & B A 2) a nd t he U ni t e d S t a t e s V i r gi n I s l a nds ( U S V I ) B oot s t r a p va l ue s ba s e d on 10 00 r e pl i c a t e s a r e i ndi c a t e d a bove t he br a nc he s A ) U nr oo t e d N J t r e e ba s e d on unc or r e c t e d p di s t a nc e s B ) N J t r e e r oot e d w i t h E l y s i a ( = T r i dac hi e l l a) di om e de a ba s e d on M L di s t a nc e s e xc l udi ng 3 r d pos i t i ons

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142 F i gur e 3. 3 : R e gr e s s i on of 3 r d p os i t i on t r a ns i t i ons ( ) a nd t r a ns ve r s i ons ( ) a ga i ns t unc or r e c t e d p di s t a nc e s f or E l y s i a c r i s pat a ha pl ot ype s a nd E l y s i a di om e de a. T he non l i ne a r r e l a t i ons hi p i ndi c a t i ng a t t he s pe c i e s l e ve l i ndi c a t e s s a t ur a t i on. B oxe s a r ound di s t i nc t i ve c l ouds of poi nt s a r e r e l a t e d t o w i t hi n di ve r ge nt ha pl ot ype E C R 20, a m ong l oc a t i ons a nd c om pa r i s ons t o E l y s i a di om e de a r e s pe c t i ve l y.

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143 F i gur e 3. 4 : R e s ul t s of N e i ghbor J oi ni ng ( N J ) a na l y s i s of E l y s i a s ubor nat a c ox 1 ha pl ot ype s f r om t he F l or i da K e ys ( F L K ) a nd I ndi a n R i ve r L a goon ( I R L ) B o ot s t r a p va l ue s ba s e d on 1000 r e pl i c a t e s a r e i ndi c a t e d a bove t he br a nc he s A ) M i dpoi nt r oot i ng of N J t r e e ba s e d on unc or r e c t e d p d i s t a nc e s B ) N J t r e e r oot e d w i t h E l y s i a pr at e ns i s ba s e d on M L di s t a nc e s e xc l udi ng 3 r d pos i t i ons

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A B O U T T H E A U T H O R A nna L e e B a s s r e c e i ve d he r B S i n Z ool ogy f r o m t he U ni ve r s i t y of G e or gi a a nd a M S i n Z ool ogy f r om L oui s i a na S t a t e U ni ve r s i t y S he be ga n he r bi o l ogy c a r e e r on a be a c h i n t he C a r i bbe a n s t udyi ng t he popul a t i on e c ol ogy of ha w ks bi l l m a r i ne t u r t l e s A f t e r m a ny m o s qui t o bi t e s a nd r a i n, s he de c i de d t o a ppl y ot he r t e c hni que s t o t he s t udy of a ni m a l s T hus be ga n he r us e o f m ol e c ul a r t e c hni que s f or s t udi e s on be ha vi or a nd c ons e r va t i on l e a di ng t o t he pub l i c a t i on of ove r 20 s c i e nt i f i c a r t i c l e s or s pe c i a l r e po r t s on a va r i e t y of or ga ni s m s A f t e r w or ki ng w i t h m a ny gr a dua t e s t ude nt s gove r nm e nt a ge nc i e s a nd f a c ul t y m e m be r s A nna l e f t a s a l a r i e d pos i t i on f o r gr a dua t e s c hool S he be ga n r e s e a r c h on ot he r i nt e r e s t s s ys t e m a t i c s a nd m a r i ne i nve r t e br a t e s a nd qui c kl y l e a r ne d of t he c ha l l e nge s c onduc t i ng r e s e a r c h i n t h e s e f i e l ds T hr ough a l l t he di f f i c ul t i e s a nd bl a nk ge l s he r l ove o f di ve r s i t y a nd f a s c i na t i o n w i t h t he be a ut y of t he opi s t hobr a nc hs ha s ne ve r c e a s e d.


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2006.
3 520
ABSTRACT: Members of the family Placobranchidae have been the focus of numerous studies because of their interesting physiological adaptations (kleptochemistry and kleptoplasty) and ecological associations with marine algae. More than 100 species have been described since the 1800's, but no determination of phylogenetic relationships in the family has occurred. DNA sequences from two mitochondrial genes (large subunit ribosomal and cytochrome c oxidase subunit I) and one nuclear gene (Histone 3) were used to reconstruct relationships among 34 nominal species within the Placobranchidae. Strong support for terminal nodes was found using Bayesian phylogenetic methods; however, a "soft" polytomy was detected at internal nodes. In general, the results confirm the paraphyly of Elysia. Proposals for the designation of the genera, Thallepus Swainson, 1840 and Tridachia Deshayes, 1857 and delineation of species are presented.^ How intrinsic factors affect speciation rates in groups of animals has been a central focus in evolutionary biology. Adaptive radiation associated with food choice has been postulated for the opisthobranch order Sacoglossa. An increase in the rate of cladogenesis was detected within the family Placobranchidae and intrinsic factors such as larval development, kleptoplasty and food choice were investigated as potential key innovations. Ancestral state reconstruction of characters suggests that food choice played a dominant role in influencing speciation rate within the family Placobranchidae. Life history strategy may play an important role in structuring genetic variation throughout the geographic range of a species. Members of the sacoglossan family Placobranchidae Gray, 1840, exhibit variation in life history strategies such as feeding preference and degree of kleptoplasty that could be influential in population structuring.^ ^Three species, Elysia subornata Verrill, 1901, Elysia tuca Marcus and Marcus, 1967, and Elysia crispata Mrch, 1863 were sampled from several locations in an attempt to quantify genetic variation as indicated by cytochrome c oxidase subunit I gene sequencing. Elysia crispata exhibited the highest degree of population subdivision followed by Elysia tuca and Elysia subornata. Nucleotide and haplotype diversity also revealed the same general ranking of species. Preliminary conclusions suggest that diversity in feeding preference and degree of kleptoplasty play significant roles in population subdivision of these species.
502
Dissertation (Ph.D.)--University of South Florida, 2006.
504
Includes bibliographical references.
516
Text (Electronic dissertation) in PDF format.
538
System requirements: World Wide Web browser and PDF reader.
Mode of access: World Wide Web.
500
Title from PDF of title page.
Document formatted into pages; contains 143 pages.
Includes vita.
590
Co-adviser: Earl McCoy, Ph.D.
Co-adviser: Stephen Karl, Ph.D.
653
Phylogeny.
Population genetics.
Mitochondrial DNA.
Nuclear DNA.
Cladogenesis.
690
Dissertations, Academic
z USF
x Biology
Doctoral.
773
t USF Electronic Theses and Dissertations.
4 856
u http://digital.lib.usf.edu/?e14.1725