A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China

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A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China

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Title:
A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China
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Curnoe, Darren
Ji, Xueping
Liu, Wu
Bao, Zhende
Taçon, Paul S. C.
Ben, Liang
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PLOS one
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Fossil hominids ( lcsh )
Paleontology -- Pleistocene ( lcsh )
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serial ( sobekcm )

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The number of Late Pleistocene hominin species and the timing of their extinction are issues receiving renewed attention following genomic evidence for interbreeding between the ancestors of some living humans and archaic taxa. Yet, major gaps in the fossil record and uncertainties surrounding the age of key fossils have meant that these questions remain poorly understood. Here we describe and compare a highly unusual femur from Late Pleistocene sediments at Maludong (Yunnan), Southwest China, recovered along with cranial remains that exhibit a mixture of anatomically modern human and archaic traits. Our studies show that the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora. However, the scarcity of later Middle and Late Pleistocene archaic remains in East Asia makes an assessment of systematically relevant character states difficult, warranting caution in assigning the specimen to a species at this time. The Maludong fossil probably samples an archaic population that survived until around 14,000 years ago in the biogeographically complex region of Southwest China.

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K26-05059 ( USFLDC DOI )
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RESEARCHARTICLEAHomininFemurwithArchaicAffinitiesfrom theLatePleistoceneofSouthwestChinaDarrenCurnoe1 ,XuepingJi2 ,WuLiu3,ZhendeBao4,PaulS.C.Taon5,LiangRen41 Palaeontology,GeobiologyandEarthArchivesResearchCentre,SchoolofBiological,Earthand EnvironmentalSciences,UniversityofNewSouthWales,Sydney,NSW,Australia, 2 YunnanInstituteof CulturalRelicsandArchaeology,Kunming,Yunnan,China, 3 KeyLaboratoryofVertebrateEvolutionand HumanOrigins,InstituteofVertebratePaleontologyandPaleoanthropology,ChineseAcademyofSciences, Beijing,China, 4 MengziInstituteofCulturalRelics,Mengzi,Yunnan,China, 5 Place,EvolutionandRockArt HeritageUnit,SchoolofHumanities,GoldCoastCampus,GriffithUniversity,Queensland,Australia Theseauthorscontributedequallytothiswork. d.curnoe@unsw.edu.au (DC); jxpchina@foxmail.com (XJ)AbstractThenumberofLatePleistocenehomininspeciesandthetimingoftheirextinctionare issuesreceivingrenewedattentionfollowinggenomicevidenceforinterbreedingbetween theancestorsofsomelivinghumansandarchaictaxa.Yet,majorgapsinthefossilrecord anduncertaintiessurroundingtheageofkeyfossilshavemeantthatthesequestions remainpoorlyunderstood.Herewedescribeandcompareahighlyunusualfemurfrom LatePleistocenesedimentsatMaludong(Yunnan),SouthwestChina,recoveredalongwith cranialremainsthatexhibitamixtureofanatomicallymodernhumanandarchaictraits.Our studiesshowthattheMaludongfemurhasaffinitiestoarchaichominins,especiallyLower Pleistocenefemora.However,thescarcityoflaterMiddleandLatePleistocenearchaic remainsinEastAsiamakesanassessmentofsystematicallyrelevantcharacterstatesdifficult,warrantingcautioninassigningthespecimentoaspeciesatthistime.TheMaludong fossilprobablysamplesanarchaicpopulationthatsurviveduntilaround14,000yearsago inthebiogeographicallycomplexregionofSouthwestChina.IntroductionThenumberofLatePleistocenearchaichomininspecies,theirbiogeographicaldistribution, andthetimingoftheirextinctionremainimportantbutintractablequestionsinpalaeoanthropology.Theseissueshavebeenbroughtintosharpreliefoverthelasthalf-decadefollowingtheaccumulationofgenomicevidenceforinterbreedingbetweenthePleistocene ancestorsoflivinghumansandarchaichomininsacrossmuchoftheOldWorld[ 1 – 4 ].Yet,in manyregions,archaicremainsaresparseorabsentfromtheLatePleistocenefossilrecord. Thefewexceptionsinclude:1)theNeanderthals( H neanderthalensis )inEurope,WestAsia, andextendingattimesintosouthernSiberia,theyoungestexamplebeingfromMezmaiskaya dating~39ka[ 5 ];2)possiblytheNorthAfricanspecimensDar-es-SoltaneandTmarafrom Morocco[ 6 ],withareportedagerangeof~110to40 – 20kafortheassociatedAterianlithic PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 1/16 OPENACCESS Citation: CurnoeD,JiX,LiuW,BaoZ,TaonPSC, RenL(2015)AHomininFemurwithArchaicAffinities fromtheLatePleistoceneofSouthwestChina.PLoS ONE10(12):e0143332.doi:10.1371/journal. pone.0143332 Editor: DavidCaramelli,UniversityofFlorence, ITALY Received: June3,2015 Accepted: November3,2015 Published: December17,2015 Copyright: 2015Curnoeetal.Thisisanopen accessarticledistributedunderthetermsofthe CreativeCommonsAttributionLicense ,whichpermits unrestricteduse,distribution,andreproductioninany medium,providedtheoriginalauthorandsourceare credited. DataAvailabilityStatement: Allrelevantdataare availableinthepaperanditsSupportingInformation files. Funding: TheauthorswishtothanktheAustralian ResearchCouncil(grantsDP0877603& FT120100168),theYunnanInstituteofCulturalRelics andArchaeology(KeyProjectGrantA-201301),and theUniversityofNewSouthWalesandGriffith Universityforfundingthisresearch. CompetingInterests: Theauthorshavedeclared thatnocompetinginterestsexist.

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industry[ 7 ];3)fossilsfromDenisovaCaveinsouthernSiberiaconsistingofamolarandmanualandpedalphalangesthathavebeendated > 50ka,andwhosephylogeneticpositionhas beeninferredfromrecoveredgenomicDNAsequencestobethesisterspeciestotheNeanderthals[ 2 3 8 ];4)fragmentarycranial,mandibularanddentalremainsfromXujiayaoinNorth Chinadatingintherangeof~125 – 60ka,andexhibitingauniquemorphologyincludingsome similaritiestoNeanderthals[ 9 – 11 ];and5)inSoutheastAsia, H floresiensis [ 12 ]atLiangBua Cave,Flores,dating~74 – 17ka[ 13 ],withitssimilaritiestoLowerPleistoceneandPliocene hominins[ 14 15 ]. ThedearthofLatePleistocenearchaicfossilsmakestheidentificationofanumberofthe speciesinvolvedinepisodesofinterbreedingwithearlyanatomicallymodernhumans(AMH) problematic.Oneprominentexampleistheoccurrenceof “ Denisovan ” DNAinthegenomes ofsomecontemporaryhumansinEastAsiaandAustralo-MelanesiasuggestingtheirPleistoceneancestorsinterbredwiththisanatomicallypoorlyknowntaxon[ 2 3 ].Whilenofossils beyondDenisovaCavehavebeenidentifiedasbelongingtothisgroup,DenisovanmitochondrialdiversitycombinedwiththeobservedstronggeographicpatterningofDenisovanDNAin livingpeopleimplytheywereformerlywidespreadwitharangeextendingperhapsintoSoutheastAsia[ 2 3 16 – 18 ]. Additionally,genomicresearchhasshownthatNeanderthalscontributedmoreDNAto contemporaryEastAsiansthanEuropeansindicatingthatmultipleepisodesofinterbreeding musthaveoccurredunderamodelofcomplexadmixtureanddemographicscenariosacrossa widegeographicarea[ 3 7 19 ].Yet,thereispresentlynodirectevidencefortheiroccupationof AsiaanywhereeastoftheAltaiMountains[ 8 17 ].WhilesomeEastAsianMiddlePleistocene remainslikethosefromMabainSouthChinamightshowaffinitiestoNeanderthals[ 20 ],they areprobablytoooldtoberelatedtothe “ classic ” Neanderthals[ 21 ].Yet,otherinterpretations ofthemorphologyofChineseMiddlePleistocenefossilssuchasfromDalihaveproposeda roleforgeneflowbetweenarchaichomininsandAMHintheemergenceofrecentEastAsian populations[ 22 ]. Pinpointingtheextinctiondateforarchaichomininsisalsoimportantforunderstanding theadaptiveanddemographicresponsesofthesespeciestothearrivalofAMHbeyondrare interbreedingevents[ 1 – 4 8 19 ].Ashomininsfitthedefinitionofmegafauna[ 23 ],thecircum-stancessurroundingtheirextinctionalsopotentiallyaddstounderstandingoftheimpacts AMHhadontheenvironmentduringtheLatePleistoceneandtheirpotentialroleinthe demiseofawiderangeoflarge-bodiedmammalspecies[ 23 ]. Severalofthecurrentauthorshavepreviouslyreportedtheoccurrenceofhominincranial remainsfromtwositesinSouthwestChina(MaludongandLonglinorLaomaocaoCave)that combinearchaichomininandAMHtraits[ 24 25 ].Inthecaseoftheunusualcraniumfrom LonglinCave[ 24 ],itwasrecentlyconcludedthatitsmosaicmorphologyprobablyresults fromhybridisationbetweenAMHandanunknownarchaicspecies,perhapsevenoccurring duringtheearlyHolocene[ 26 ].Asimilarexplanationmightalsoapplytothemorphologyof theMaludongcranialfossils[ 24 25 ],ahypothesiscurrentlyunderinvestigationbyus.Here wereportapartialproximalfemurfromMaludong(Yunnan),SouthwestChina,foundin associationwiththeseunusualcranialremains,whichshowsmorphologicalandphylogenetic affinitiestoarchaichominins.TheMaludonghomininswereallrecoveredfromsediments datedwithAMS14Cofcharcoaltobetweenabout14,310340cal.yrBPand13,590160cal. yrBP[ 24 25 ].Thus,theMaludongfemuristheyoungestfossilwitharchaicmorphology foundtodateandpotentiallyextendstheoverlapofAMHandarchaichomininsinEastAsia to > 50ka. LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 2/16

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MaterialsandMethodsMeasurementsforasampleofPleistocenefemorawereobtainedfromtheliterature[ 27 – 29 ]. Comparativefossilsweregroupedaccordingtochronology,inthecaseofLowerPleistocene Homo (LPHO)andMiddlePleistocene Homo (MPHO);aninformalgroupingthatrepresents ataxonomicunit,inthecaseoftheNeanderthals( H neanderthalensis ,hereinNEAN);and twosamplesofAMH:MiddlePleistoceneModernHumans(MPMH)andEarlyUpper-Late UpperPalaeolithichumans(EULU).Alistofthespecimensincludedinthesesamplesisprovidedin S1Table .TheonlyspecimenstudieddirectlyinthepresentresearchwasMLDG1678, whichisstoredattheMengziInstituteofCulturalRelics,Mengzi,YunnanProvince,China. PermissiontostudyitwasprovidedbytheYunnanProvincialCultureBureauinaccordance withamemorandumofunderstandingbetweentheBureauandtheUniversityofNewSouth WalesAustralia,andbyco-authorZhendeBao,DirectoroftheMengziInstituteofCultural Relics,whorecoveredthefemurduringexcavationsin1989. CT-scansweremadeofMLDG1678usingaGELightSpeedVCT9scanner,withhelical rotation,0.625mmslicethickness,KVP140kVandcurrent400mA,attheHonghePrefecture FirstHospitalduringJuly2012.ThespecimenwasalignedtotherelativeAPandMLaxesfor scanning.Theexternalandinternalshafthadalreadybeenfreedofmatrixduringcurationso threshold-basedsegmentationwasnotrequired.However,somePlasterofPariswasadded duringrestorationandwehighlightitwhereitisvisiblein Fig1 .Measurementswereselected onaccountoftheiravailabilityonMLDG1678.Subtrochanteric(ST)measurementswere taken10mmbelowthedistaledgeofthelessertrochanter[ 30 31 ],whiletheregionformidshaft(MS)measurementswasselectedfollowingidentificationofapilaster[ 29 ].AllmeasurementsofMLDG1678weremadebyD.CurnoeonCT-scanslicesfollowingstandarddefinitions[ 32 ]andweresubsequentlycheckedontheoriginalspecimen.Becausetheheadis missing,neck-shaftanglewasestimatedusingfourapproaches:1)agoniometerontheoriginal specimen;2)agoniometeronahardcopy(printed)photographofthespecimen;3)theangle toolonadigitalphotousingtheprogram ImageJ ;and4)theangletoolonaCT-scansliceat theapproximatemid-coronalplaneusingtheprogram OsiriX v6.5.Wemeasuredanteroposterior(AP)andmediolateral(ML)externaldiametersandcorticalthicknessdimensionson CT-scanslicesusing OsiriX v6.5.Totalarea(TA)andcorticalarea(CA)attheSTandMS regionswerecalculatedusingthe “ EEM_Macro ” providedbyChristopherRuff(downloaded from: www.hopkinsmedicine.org/fae/cbr.htm ). BodymassforMLDG1678wasestimatedusingtheproductoftheSTAPandSTMLdiametersandformulaefromRef[ 33 ].Bodymasswasoriginallyestimatedforthecomparativefemorain S1Table usingheaddiameters[ 28 ],butthesevaluesmaynotbedirectlycomparableto ourestimateforMLDG1678.Therefore,wereconstructedbodymassagainforthefemorain ourcomparativesamplesusingthesamemethodasemployedforMLDG1678andpublished APandMLvalues.Size-adjustmentwasalsoundertakenonMSareasusingreconstructed bodymass,followingtherecommendationsandmethodofRef[ 34 ]. Inscatterplots,wecomparedMLDG1678withthemedian,95%confidenceinterval(CI) forthemedianand1.5xtheinterquartilerange(1.5IQR)foreachcomparativesample.Sample 95%CIsforthemedianwerecalculatedusingtheformula m 1 : 58 IQRn p[ 35 ].Doingso allowedustovisuallyassessforpossiblesigni canceofmediandifferencesamongsamples [ 35 ].WesupplementedthemwithKruskal-Wallisteststoassessoverallsigni cancecombined with posthoc Mann-Whitneyteststoassesspairsofsamples.Theinclusionof1.5IQRforall samples,equivalentto99.3%coverage(or2.7standarddeviations)fornormallydistributed data[ 35 ],alsoallowedustovisuallyassesstheaf nitiesofMLDG1678inadditiontoitslocationrelativetosamplemedians. LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 3/16

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Weundertookprincipalcomponentanalysis(PCA)andneighbourjoininganalysisusing theout-groupmethod(NJA)withthePASTprogram[ 36 ].Inmultivariatestudiesoffossilsa balancemustbestruckbetweeninformationcontent(numberofvariables)andwithin-group variationofcomparativesamplesinordertoaccountforthevarioussourcesofintrasample variation(numberofobjects).Moreover,arbitrarydecisionsoftenneedtobemadeaboutthe variablestobeemployed.Here,weemphasisedinformationcontentandundertookanalyses thatemployedmetriconlyandcombinedmetricanddiscretedata.Variableswereselectedon accountoftheirabilitytodistinguishbetweenmodernandarchaicfemora,asrevealedthrough ourmorphologicalandunivariatecomparisons.Continuousvariableswereloggedpriorto analysis,whilediscretetraits(presence,absence)werescoredonabinaryscale.ForNJAstudies usingonlycontinuousvariablesweemployedEuclideandistances,butforourmixeddatasets, combiningcontinuousandbinarydata,weusedtheGowerdistance.Resamplingscoreswere calculatedusing100,000replicatesinallNJAinvestigations. Fig1. FemurMLDG1678:(A)Anteriorview.(B)CT-scanslicesatsubtrochanteric,approximatehalf-way andmid-shaftlevels.(C)Posteriorview.(D)CT-scansliceatapproximatelymid-coronalplane,grayscale (left)andcolourdensitymap(right).(E)Superiorviewhighlightingtheoveralloutlineandsuperiorsurfaceof thegreatertrochanter(anterioratleft,lateralattop).(F)CT-scantransverseslicesatapproximatemid-neck level,grayscale(left)andcolourdensitymap(right).(G)Medialview.(H)CT-scanslicesinapproximatemidplane,grayscale(left)andcolourdensitymap(right).(P=plasteraddedin1989duringrestoration). doi:10.1371/journal.pone.0143332.g001 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 4/16

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Results DescriptionandunivariatecomparisonMLDG1678consistsofa175mmlongproximalsegmentofanadultrightfemurbroken slightlyinferiortotheMSregion( Fig1 ).Itpreservesthegreatertrochanterandamostlycompleteneck.AnisolatedpartialfemoralheadwasalsorecoveredfromMaludong(MLDG1717), butitisunclearwhetherisbelongstoMLDG1678.Thebiomechanicalnecklengthislong,and weestimatethatitmustoriginallyhavemeasured~70mm;assumingMLDG1717providesa reasonableindicationofthesizeoftheheadofMLDG1678.Thus,itwouldhaveresembled LPHO,MPHOandNEAN,withtheirlongbiomechanicalnecks,ratherthanAMH(MPMH andEULU),withtheirshortones[ 37 38 ].ThehorizontalAPdiameteris~27mm,avaluethat wouldsitcomfortablywithintherangeofbotharchaichomininsandAMH[ 39 ]. Anteriorly,althoughtheintertrochantericlineissomewhatobscuredbyplaster,owingto breakageinthisregion,itmusthavebeenfaint.Buttressingoftheproximalmedialdiaphysis canbeseeninanterior,posteriorandmedialviews,andispronounced( Fig1 ).Thegreatertrochanterisalarge[MLbroadandsuperoinferiorly(SI)tall]structurethatbulgesbeyondthelateralwallofthediaphysis.Thesuperiorsurfaceoftheneckispartlymissingalongitsmedial course,andwhatremainsofithasbeenpartiallyobscuredbyplasterduringrestorationofthe specimen( Fig1 ).Posteriorly,theproximaldiaphysisisdominatedbyamassivelessertrochanter,situatedontheapproximatemid-planeoftheshaft,andprojectingslightlymedially( Fig 1 ).CT-scanslicesalsoshowthemassivesizeofthisfeature,whichiscomposedalmostentirely ofcancellousbone( Fig1 ).InAMH,thelessertrochantermostfrequentlyfacesstronglymedially.Whileanteversionofthefemurresultinginamoreposteriorlylocatedlessertrochanteris Table1.MetricdatafortheMaludongfemur(MLDG1678). MLDG1678 Subtrochantericregion Anteroposteriordiameter(mm)22.2 Mediolateraldiameter(mm)28.3 Totalarea(mm2) 493.4 Corticalarea(mm2) 322.6 %-Corticalarea 65.4 Platymericindex(%) 78.4 Neck-shaftangle() ~118 Reconstructedbodymass(kg)50 Mid-shaft Anteroposteriordiameter(mm)24.7 Mediolateraldiameter(mm)22.9 Totalarea(mm2) 444.2 Corticalarea(mm2) 337.0 %-Corticalarea 75.9 Size-adjustedtotalarea18.8 Size-adjustedcorticalarea16.8 Pilastricindex(%) 107.8 Mid-shaft/STarea(%) 90.01Calculatedbydividingtherelevantareabyreconstructedbodymass,afterRef[ 34 ]. doi:10.1371/journal.pone.0143332.t001 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 5/16

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seeninrecenthumans[ 40 ],thecombinationofitsposteriororientationandmassivesizein MLDG1678wouldberare(ifpresentatall)inAMH. Thepectineallineisacrest-likebuttressrunningSIalongthemedianplaneoftheposterior diaphysisfromthebaseofthelessertrochanterinferiorly( Fig1 ).Thehypotrochantericfossais extensiveSIandML,mergingacrossawideareawiththeglutealcrest( S1Fig ),ratherthan beingadistinctandnarrowfossathatdistinguishesthelateralwallofthefemurfromthe weaklydevelopedproximo-lateralbuttress,asistypicallyseenwhenthisfeatureisdevelopedin AMHfemora.ItcloselyresemblestheconditionseeninNEANinitsmorphology,whichis probablyautapomorphicforthisgroup[ 41 ].Theintertrochantericcrestismostlymissing(not preserved),andismoderatelydevelopedinferiorly.Thequadratetubercleisnotpreserved. In Table1 wepresentmetricdataforMLDG1678.ValuesfortheMaludongfemurarecomparedwithsummarystatisticsforcomparativesamplesinFigs 2 and 3 .AttheSTlevel,theAP diameterfailedtoshowsignificantmediandifferencesamonggroups( Fig2A ).Thevaluefor MLDG1678issmall(22.2mm),beingclosesttotheLPHOmedian,butsitswithin1.5IQRof allsamplesexceptMPMH( Fig2A ).TheMLdiameterwasalsocharacterisedbyanabsenceof significantmediandifferences( Fig2B ).MLDG1678possessesasmallMLdiameter(28.3 mm),againmostsimilartotheLPHOmedian,butoutsideofthesmall1.5IQRofthissample, andwithin1.5IQRofallothers( Fig2B ).TAattheSTlevellackedsignificancewhenaKruskalWallistestwasperformed,but posthoc Mann-Whitneytestsrevealedasignificantdifference betweenNEANandEULUmedians( p 0.038).TAforMLDG1678(493.4mm2)isunsurprisinglysmall,andonceagainismostsimilartotheLPHOmedian.However,itsvaluesitswith 1.5IQRofallsamplesexceptNEAN( Fig2C ).MediandifferencesforCAalsolackedsignificancewithaKruskal-Wallistest,but posthoc Mann-WhitneytestsrevealedasignificantdifferencebetweenLPHOandNEAN( p 0.019),andNEANandEULU( p 0.032).CAforthe Maludongfemur(322.6mm2)isalsoverysmall,againbeingmostsimilartotheLPHO median,andwith1.5IQRonlyofLPHOandEULU( Fig2D ). Fortheindex%-CA(CA/TAx100),mediandifferenceswerefoundtobenon-significant. Moreover,the%-CAforMLDG1678(65.4%)wasmostsimilartotheLPHOandEULUmedians,butsatwithin1.5IQRofallsamples( Fig2E ).Intermsoftheplatymericindex,aKruskalWallistestrevealedsignificantdifferencesamongsamplemedians( p 0.040): posthoc comparisonsrevealedsignificantdifferencesbetweenMPHOandNEAN( p 0.016),andNEANand EULU( p 0.014)( Fig2F ).Withahighplatymericindex(78.4%),theshaftoftheMaludong femurisreasonablycircularattheSTlevel,beingmostsimilartothemedianforNEAN( Fig 2F ).Whiletheneck-shaftanglealsolackedsignificancewithaKruskal-Wallistest, posthoc Mann-WhitneytestsrevealedsignificantmediandifferencesbetweenMPHOandMPMH ( p 0.035),NEANandMPMH( p 0.008),andNEANandEULU( p 0.035)( Fig2G ).TheneckshaftangleofMLDG1678isestimatedtoliewithinthenarrowrangeof116 – 120,andtaking themedianofthis(c118),itwasfoundtobewithin1.5IQRofMPHOandEULU,andequalto thenegative1.5IQRvalueforNEAN( Fig2G ). WereconstructedbodymassforMLDG1678tobelow(50kg),avalueverysimilartothe LPHOandMPHOmedians,butwithin1.5IQRofallsamples;although,itisclearlysmallby PleistoceneAMHstandards( Fig2H ).Kruskal-Wallisand posthoc Mann-Whitneytestsfailed torevealanysignificantdifferencesamongsamplemedians. TheMSAPdiameterwascharacterisedbysignificantmediandifferences(KruskalWallis: p 0.002).Specifically, posthoc testsrevealedimportantdifferencesbetweenallarchaicsamples andMPMH(MannWhitney: p 0.022 – 0.0067),betweenLPHOandMPHO( p 0.012),and LPHOandEULU( p 0.011)( Fig3A ).Thus,thisvariableservestodistinguisharchaicfemora fromPleistoceneAMHones.TheMLDG1678valueissmall(24.7mm)andfoundtobemost similartothemediansofLPHOandMPHO( Fig3A ).Itdid,however,sitwithin1.5IQRofall LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 6/16

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Fig2. Scatterplotscomparingsamplemediansforsubtrochanteric(ST)variables,neck-shaftangleandreconstructedbodymass:(A)Anteroposterior(AP ) diameter(mm).(B)Mediolateral(ML)diameter(mm).(C)Totalarea(TA:mm2).(D)Corticalarea(CA:mm2).(E)%-Corticalarea(%-CA).(F)Platymericindex (%).(G)Neck-shaftangle().(H)Reconstructedbodymass(kg).(Errorbars=95%confidenceintervalofmedian[dark]and1.5xinterquartilerange[ light]; Abbreviations:LPHO=LowerPleistocene Homo ;MPHO=MiddlePleistocene Homo ;NEAN=Neanderthals;MPMH=MiddlePleistoceneModernHumans; EULU=EarlyUpper-LateUpperPalaeolithichumans[see S1Table ]). doi:10.1371/journal.pone.0143332.g002 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 7/16

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Fig3. Scatterplotscomparingsamplemediansformid-shaft(MS)variables,size-adjustedvariablesandmid-shaft/subtrochantericareaindex:(A) Anteroposterior(AP)diameter(mm).(B)Mediolateral(ML)diameter(mm).(C)Totalarea(TA:mm2).(D)Corticalarea(CA:mm2).(E)%-Corticalarea (%-CA).(F)Size-adjustedtotalarea.(G)Size-adjustedcorticalarea.(H)Pilastricindex(%).(I)Mid-shaft/subtrochanteric(MS/ST)areaindex (%).(Error bars=95%confidenceintervalofmedian[dark]and1.5xinterquartilerange[light];Abbreviations:LPHO=LowerPleistocene Homo ;MPHO=Middle Pleistocene Homo ;NEAN=Neanderthals;MPMH=MiddlePleistoceneModernHumans;EULU=EarlyUpper-LateUpperPalaeolithichumans[see S1 Table ]). doi:10.1371/journal.pone.0143332.g003 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 8/16

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samplesexceptMPMH( Fig3A ).TheMLdiameterwasalsofoundtoshowsignificantdifferencesamongsamplemedians( p 0.018),onlythistimeEULUwasdistinguishablefromMPHO andNEAN( p 0.024& p 0.002)( Fig3B ).TheMaludongMLdiameter(22.9mm)isverysmall andwasnotespeciallysimilartoanysamplemedian,butdidliewithin1.5IQRofLPHOand EULU( Fig3B ).AsattheMSregion,TAlackedsignificanceinaKruskal-Wallistest.Thesmall areaforMLDG1678(444.2mm2)wasmostsimilartotheLPHOmedian,butdidsitwithin 1.5IQRofallsamples( Fig3C ).WhileMSCAalsolackedoverallsignificance, posthoc MannWhitneytestsrevealedasignificantdifferencebetweenNEANandEULUmedians( p 0.039) ( Fig3D ).TheMaludongfemurCAisverysmall(337.0mm2),butsatwithin1.5IQRofallsamplesexceptMPMH( Fig3D ).%-CAwasfoundtoexhibitsignificantmediandifferencesamong samples( p 0.005),with posthoc testsshowingthistobethecasebetweenLPHOandMPHO ( p 0.025),MPHOandNEAN( p 0.049),MPHOandMPMH( p 0.009),andMPHOandEULU ( p 0.001)( Fig3E ).%-CAinMLDG1678(75.9%)wasvirtuallyidenticaltotheLPHOmedian, butitdidsitwithin1.5IQRofallsamples( Fig3E ). Wealsocalculatedsize-adjustedTAandCAusingreconstructedbodymass.Size-adjusted TAlackedoverallsignificance,but posthoc Mann-WhitneytestsrevealedasignificantdifferencebetweenMPMHandEULU( p 0.016)( Fig3F ).TheverysmallvalueforMLDG1678(8.8) wasmostsimilartotheLPHOmedian,although,notespeciallyclosetoit.Itsvaluedid,however,sitwithin1.5IQRofallsamplesexceptNEAN( Fig3F ).Significantmediandifferences werefoundforsize-adjustedCA( p 0.044),with posthoc testsshowingimportantdifferences betweenMPHOandEULU( p 0.029),andMPMHandEULU( p 0.037)( Fig3G ).Thesmall valuefortheMaludongfemur(6.7)wasmostsimilartotheEULUmedian,butitdidliewithin 1.5IQRofallsamplesexceptMPMH( Fig3G ). ThepilastricindexwasfoundtostronglydistinguisharchaichomininfromAMHfemora (KruskalWallis: p 7.4E-07)( Fig3H ).MannWhitneytestsshowedthatmediandifferenceswere significantbetweenallarchaicandAMHmedians:archaicversusMPMH( p 0.001 – 0.0003)and archaicversusEULU( p 0.001 – 2.07E-05).TheMaludongfemur(107.8%)wasfoundtobeintermediatebetweenarchaicandAMHmedians,butwithin1.5IQRofallsamples( Fig3H ). Finally,wealsocalculatedanindexcomparingtheMSTAandSTTA(MSTA/STTAx100) andfoundmediandifferencestobesignificant(Kruskal-Wallis: p 0.043)( Fig3I ).Mann-WhitneytestsrevealedthatMPMHtypicallypossesssignificantlythickershaftsattheSTlevelcomparedwitharchaicfemora( p 0.033 – 0.023),butnotEULU( Fig3I ).TheMS/STareaindexfor MLDG1678(90%)wasmostsimilartothemedianforEULU,butagainsatwithin1.5IQRof allsamples( Fig3I ).MultivariateanalysesAlthoughthemetricvaluesforMLDG1678mostoftenshowedstrongestaffinitytotheLPHO median,theindividualvaluesforthespecimenwereoftenfoundtoliewithin1.5IQRofmost comparativesamples.Thus,itsaffinitiesaredifficulttoresolvesatisfactorilyusingunivariate methodsalone,necessitatingdeploymentofamultivariatestrategy(see MaterialsandMethods ; S1 and S2 Appendices). TheresultsofPCAemploying10continuousvariablesand26Pleistocenefemoraaresummarisedasanobjectplotforprincipalcomponent(PC)1versusPC2in Fig4 (seealso, S2 and S3 Tables).PC1,accountingfor52.86%oftotalvariance,showedextensiveoverlapofAMH (MPMHandEULU)andallarchaicfemora.HighestloadingvariablesforPC1wereSTTA andSTCA.Thus,thisPChighlightedstrongsimilaritiesbetweenAMHandarchaicfemora, especiallyattheSTlevel,whicharelikelytoreflectcommondevelopmentalresponsestoindividualdifferencesinfemoralneckorientationandpelvicproportions[ 28 ].Incontrast,PC2 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 9/16

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(28.92%ofvariance)clearlydistinguishedmodernandarchaicfemora( Fig4 ),thehighestloadingvariablebeingMSrelativecorticalarea(%-corticalarea).Thisindexexpressesdisparities betweensubperiostealdepositionandendostealresorptionofboneduringdevelopmentandis thoughttobeameasureofbothdifferentialdevelopmentalandagingprocessesaswellasstructuralreinforcementofthediaphysis[ 28 ].TheresultsofPCAsuggestafundamentaldifference betweenarchaicandAMHfemorainthisregard,asnotedaboveinunivariatecomparisons, andalsosuggestedinsomepreviousinvestigationsofPleistocenefemora[ 28 ].Aminimal spanningtreeindicatedthattheshortestdistancewasbetweenMLDG1678andKNM-ER Fig4.Objectplotfromprincipalcomponentanalysisof10continuousvariables:PC1(52.85%)versusPC2(28.92%)(AMHfemoralabeledinblack; archaichomininsinblue;minimalspanningtreeshown). doi:10.1371/journal.pone.0143332.g004 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 10/16

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1481A,aspecimenbelongingtoAfricanearly Homo [ 42 43 ],followedbyTabun1,whichis likelytobelonginNEAN( Fig4 ). WeperformedNJAonthesamedatasetemployingKNM-ER1472(alsoearly Homo [ 43 ]) asanout-group.Theresultingtreealsoshowedacleardistinctionbetweenarchaicandmodern humanfemora,although,thedivisiondidnotreceivestrongsupportinbootstrapanalysis( Fig 5 ).MLDG1678clusteredinabranchalongwithKNM-ER1481A,whichwasfoundin100% oftreesduring100,000replicatesinourresamplingresults( Fig5 ).Thus,thistreeconfirmed thepheneticandphylogeneticaffinitiesoftheMaludongfemurtoearly Homo Fig5.Neighbor-joiningtreefromananalysisof10continuousvariables(AMHfemoralabeledin black;archaichomininsinblue;bootstrapscoresarefrom100,000replicateswithonlythose 60% shown). doi:10.1371/journal.pone.0143332.g005 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 11/16

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ThefinalNJAweperformedincluded15variables(binaryandcontinuous)andemployed comparativesamplemedians(see MaterialsandMethods ; Table2 ; S2Appendix ).Thistime, LPHOwasusedastheout-group.TheresultingtreeplacedMLDG1678asthemostbasal branchseparatetoabranchcontainingMPHO,MPMHandEULU( Fig6 ).ThebranchcontainingMLDG1678wasfoundin100%oftreesduring100,000bootstrapreplicates( Fig6 ). TheresultsshowedtheMaludongfemurtobehighlyplesiomorphicandmorphologicallyand phylogeneticallydistinctfromMiddleandLatePleistocenehominins.DiscussionandConclusionsInlightoftheabsenceofarchaichomininsfrommainlandEurasiayoungerthanabout39ka [ 5 11 17 20 ]itwouldbereasonabletoexpectMLDG1678tosampleanUpperPalaeolithic individual,givenitsyounggeologicalage(i.e.~14.0ka).Instead,ourcomparisonswithPleistocenefemorarevealtheMaludongspecimentobemorphologicallydistinctfromAMH.Moreover,ofthe15traitssummarisedin Table2 ,eightaresharedwitharchaichomininstothe exclusionofPleistoceneAMHfemora,andafurthertwoareunusualinMLDG1678byLate Pleistocenehomininstandards.TheothersfailedtodistinguishAMHfromoneormore archaicsamples,sohavelittlebearingdirectlyontheaffinitiesofMLDG1678( Table2 ).Itis strikingthatforthefivediscretetraitscompared,theMaludongfemursharesstatesonlywith archaichominins,differentiatingthemallfromAMH( Table2 ).Noteworthy,overall,isits:1) smallSTTAandCA,thelatterbeingsuggestiveoflowresistancetoaxialloads[ 28 ];2)relativelyhighplatymericindex,indicatingitsshafttoberathercircularattheSTlevel;3)small MSAPandMLdiameters,whichcouldreflectrelativelylowlevels,although,thelevelofbuttressingseenintheMaludongfemursuggestsotherwiseandperhapsinsteadresultsfromits smallbodysize[ 34 ];and4)moderatepilastricindexvalue,associatedwiththepresenceofa Table2.ComparisonofsystematicallyrelevanttraitsinMLDG16781. MLDG1678LPHOMPHONEANMPMHEULU 1.BiomechanicalnecklengthLongLongLongLongShortShort 2.Lessertrochanter:large,posteriorlyorientedPresentPresentVariableAbsentAbsentAbsent 3.PronouncedmedialbuttressingPresentPresentPresentPresentAbsentAbsent 4.MarkedglutealbuttressAbsentAbsentAbsentAbsentPresentPresent 5.HypotrochantericfossamergeswithglutealbuttressPresentAbsentAbsentPresentAbsentAbsent 6.STTotalareaSmallSmallSmallLargeModerateModerate 7.STCorticalareaVerysmallSmallModerateLargeModerateModerate 8.PlatymericindexLargeSmallSmallLargeLargeSmall 9.Neck-shaftangleLowLowLowLowHighLow 10.MSAPdiameterSmallSmallSmallModerateLargeModerate 11.MSMLdiameterVerysmallSmallLargeLargeSmallSmall 12.MSSize-adjustedcorticalareaSmallSmallLargeLargeLargeSmall 13.MS%-CorticalareaLowLowHighLowLowLow 14.PillastricindexModerateLowLowLowHighHigh 15.Mid-shaft/STareaLowLowLowLowHighLow1Abbreviations:LPHO=LowerPleistocene Homo ;MPHO=MiddlePleistocene Homo ;NEAN=Neanderthals;MPMH=MiddlePleistoceneModern Humans;EULU=EarlyUpper-LateUpperPalaeolithichumans.ST=subtrochantericregion;MS=mid-shaftregion;AP=anteroposteriordiameter; ML=mediolateraldiameter. Samplecompositions,see S1Table doi:10.1371/journal.pone.0143332.t002 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 12/16

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weaklydevelopedfemoralpilaster,afeatureoftentakentodistinguishAMHfromarchaic hominins[ 44 ]( Table2 ). Puttingtheresultsofouranalysestogether,MLDG1678showsmorphologicalandphylogeneticaffinitiestoarchaicfemora,particularlyLowerPleistoceneearly Homo .Weconclude, therefore,thattheMaludongfemurrepresentsanindividualthatprobablybelongedtoan archaictaxonratherthanAMH.Justwhichtaxonitrepresentsisdifficulttodetermine,however,becauseofthescarcityofLatePleistocenehomininfemorafromEastAsia.Italsoremains unclearwhetherLatePleistocenearchaicgroupsfromwesternEurasiaprovidethemostappropriatemodelforEastAsianhomininsduringthisperiod.InthecaseofAMH,though,wedid includefemorafromEastAsia,includingthefourfromMinatogawa,andMLDG1678was foundtobeverydistinctfromthem. ItisintriguingthatsuchaplesiomorphichominincouldhavesurvivedatMaludonguntil neartheendofthePleistocene.Yet,thisfindingappliesalsoto H floresiensis ,withitsapparent minimumgeologicalageonlyslightlyolderthanMLDG1678[ 13 ]. Homofloresiensis hasonly beenfoundontheislandofFloresineasternIndonesiathough,anditsoccurrencehasbeen explainedbyislandbiogeography[ 45 46 ].Moreover,theMaludongfemurisdistinctfromthe highlyunusualfemoraofthisspecies,withitsuniquemosaicoftraitsincludingresemblances to Australopithecus taxa[ 47 ].OnepossibleexplanationisthattheMaludongfemursamples thepopulationpresentlyknownonlyfromDenisovaCaveintheAltairegionanddubbedthe Fig6.Neighbor-joiningtreefromananalysisof15variables(5discreteand10continuous)using comparativesamplemediansasOTUs. (Bootstrapscoresarefrom100,000replicates;Abbreviations: LPHO=LowerPleistocene Homo ;MPHO=MiddlePleistocene Homo ;NEAN=Neanderthals; MPMH=MiddlePleistoceneModernHumans;EULU=EarlyUpper-LateUpperPalaeolithichumans[see S1 Table ]). doi:10.1371/journal.pone.0143332.g006 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 13/16

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“ Denisovans ” [ 2 3 ].Anothercandidateisthepresentlyunnamedtaxonrepresentedbythe Xujiayaofossils[ 9 – 11 ].However,theabsenceoffemorafrombothofthesegroupsmakesthese scenariosimpossibletotestatpresent.Besides,thesimilaritiesofMLDG1678toLowerPleistocenehomininsimpliesthatotherpossibilitiesshouldbeconsidered,suchasalatesurviving descendentofaLowerPleistoceneEastAsiangroup[ 48 ]oreventheDmanisihominins[ 49 ]. YunnanProvinceischaracterisedbycomplextopographyassociatedwithHimalayanuplift andextrusionoftheIndochinablockresultinginvicariousbiogeographicdivisions[ 50 ].Itis oneof20floristicendemiccentresinChina,comprisingsubtropicalevergreenbroad-leaved andsclerophyllousforests,andcontainshighlevelsofpalaeoendemism[ 50 – 52 ].Theregion aroundMaludongisalsobiogeographicallyonthenorthernedgeoftropicalSoutheastAsia [ 50 ].Thus,theMaludongfemurmightrepresentarelic,tropicallyadapted,archaicpopulation thatsurvivedrelativelylateinthebiogeographicallycomplexregionofSouthwestChina.SupportingInformationS1Appendix.TenvariablematrixemployedinPCAandNJAofindividualfossils. (DOCX) S2Appendix.FifteenvariablematrixusedforNJAwithsamplesasOTUs. (DOCX) S1Fig.LateralviewofMLDG1678. (DOCX) S1Table.Compositionofcomparativesamples. (DOCX) S2Table.ResultsofPCA. (DOCX) S3Table.VariableloadingsfromPCA. (DOCX)AcknowledgmentsWewishtothankananonymousreviewerandtheeditor(DavidCaramelli)forveryhelpful commentsonthemanuscript.WeareverygratefulalsotoKanningBai,YunshengZhuand MianFanoftheHongheInstituteofCulturalRelicsandArchaeologyforlogisticalsupport duringourresearch.AuthorContributionsConceivedanddesignedtheexperiments:DCXJ.Performedtheexperiments:DCXJ.Analyzed thedata:DCXJ.Contributedreagents/materials/analysistools:DCXJZBLR.Wrotethepaper: DCXJWLZBPTLR.References1. GreenRE,KrauseJ,BriggsAW,MaricicT,StenzelU,KircherM,etal.AdraftsequenceoftheNeandertalgenome.Science2010;328:710 – 722.doi: 10.1126/science.1188021 PMID: 20448178 2. ReichD,GreenRE,KircherM,KrauseJ,PattersonN,DurandEY,etal.Genetichistoryofanarchaic hominingroupfromDenisovaCaveinSiberia.Nature2010;468:1053 – 1060.doi: 10.1038/ nature09710 PMID: 21179161 LateArchaicHomininfromSouthwestChina PLOSONE|DOI:10.1371/journal.pone.0143332December17,2015 14/16

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