Genomic Insights into the Ancestry and Demographic History of South America

26 Pages·2015·2.62 MB·English

RESEARCHARTICLE
Genomic Insights into the Ancestry and
Demographic History of South America
JulianR.Homburger1,AndrésMoreno-Estrada1,2*,ChristopherR.Gignoux1,
DominicNelson3,4,ElenaSanchez5,PatriciaOrtiz-Tello1,BernardoA.Pons-Estel6,
EduardoAcevedo-Vasquez7,PedroMiranda8,CarlD.Langefeld9,SimonGravel3,4,Marta
E.Alarcón-Riquelme5,10*,CarlosD.Bustamante1*
1 DepartmentofGenetics,StanfordUniversity,Stanford,California,UnitedStatesofAmerica,2 Laboratorio
NacionaldeGenómicaparalaBiodiversidad(LANGEBIO),CINVESTAV,Irapuato,Guanajuato,Mexico,
3 McGillUniversityandGenomeQuebecInnovationCentre,Montreal,Quebec,Canada,4 Departmentof
HumanGenetics,McGillUniversity,Montreal,Quebec,Canada,5 ArthritisandClinicalImmunology,
OklahomaMedicalResearchFoundation,OklahomaCity,Oklahoma,UnitedStatesofAmerica,6 Sanatorio
Parque,Rosario,Argentina,7 FacultaddeMedicina,UniversidadNacionalMayordeSanMarcos,Hospital
NacionalGuillermoAlmenaraIrigoyen,Lima,Peru,8 CentrodeEstudiosReumatologicos,Santiago,Chile,
9 CenterforPublicHealthGenomics,WakeForestSchoolofMedicine,Winston-Salem,NorthCarolina,
UnitedStatesofAmerica,10 GENYO,CentreforGenomicsandOncologicalResearch:Pfizer/Universityof
Granada/AndalusianRegionalGovernment,Granada,Spain
*[email protected](AME);[email protected](MEAR);
OPENACCESS
[email protected](CDB)
Citation:HomburgerJR,Moreno-EstradaA,
GignouxCR,NelsonD,SanchezE,Ortiz-TelloP,et
al.(2015)GenomicInsightsintotheAncestryand Abstract
DemographicHistoryofSouthAmerica.PLoSGenet
11(12):e1005602.doi:10.1371/journal.pgen.1005602
SouthAmericahasacomplexdemographichistoryshapedbymultiplemigrationand
Editor:EduardoTarazona-Santos,Universidade
admixtureeventsinpre-andpost-colonialtimes.Settledover14,000yearsagobyNative
FederaldeMinasGerais,BRAZIL
Americans,SouthAmericahasexperiencedmigrationsofEuropeanandAfricanindividu-
Received:March31,2015
als,similartootherregionsintheAmericas.However,thetimingandmagnitudeofthese
Accepted:September22,2015 eventsresultedinmarkedlydifferentpatternsofadmixturethroughoutLatinAmerica.We
Published:December4,2015 usegenome-wideSNPdatafor437admixedindividualsfrom5countries(Colombia,Ecua-
dor,Peru,Chile,andArgentina)toexplorethepopulationstructureanddemographichistory
Copyright:©2015Homburgeretal.Thisisanopen
accessarticledistributedunderthetermsofthe ofSouthAmericanLatinos.Wecombinedthesedatawithpopulationreferencepanelsfrom
CreativeCommonsAttributionLicense,whichpermits Africa,Asia,EuropeandtheAmericastoperformglobalancestryanalysisandinferthesub-
unrestricteduse,distribution,andreproductioninany
continentaloriginoftheEuropeanandNativeAmericanancestrycomponentsofthe
medium,providedtheoriginalauthorandsourceare
admixedindividuals.Byapplyingancestry-specificPCAanalyseswefindthatmostofthe
credited.
EuropeanancestryinSouthAmericanLatinosisfromtheIberianPeninsula;however,
DataAvailabilityStatement:Thedataanalyzed
manyindividualstracetheirancestrybacktoItaly,especiallywithinArgentina.Wefinda
herecomprisesbothnewlygeneratedandpreviously
reporteddatasets.Accesstopubliclyavailabledata stronggradientintheNativeAmericanancestrycomponentofSouthAmericanLatinos
setsshouldberequestedthroughthedistribution associatedwithcountryoforiginandthegeographyoflocalindigenouspopulations.For
channelsindicatedineachpublishedstudy.For
example,NativeAmericangenomicsegmentsinPeruviansshowgreateraffinitieswith
newlygenotypedsamples,individualgenotypedata
isavailablethroughdbGaPundertheSusceptibility AndeanindigenouspeopleslikeQuechuaandAymara,whereasNativeAmericanhaplo-
GenesforSLEofAmerindianOrigininHispanics typesfromColombianstendtoclusterwithAmazonianandcoastaltribesfromnorthern
study(accessionnumberphs001025.v1.p1).
SouthAmerica.Usingancestrytractlengthanalysiswemodeledpost-colonialSouthAmeri-
Funding:ThisprojectwassupportedbyNIHgrants canmigrationhistoryastheyoungestinLatinAmericaduringEuropeancolonization(9–14
R01CA141700andRC1AR058621toMEAR;NIH
generationsago),withanadditionalstrongpulseofEuropeanmigrationoccurringbetween
grant1R01GM090087toCDB;NIHNHGRI
3and9generationsago.Thesegeneticfootprintscanimpactourunderstandingof
5U01HG007419-02toCDB;NSFgrantDMS-
PLOSGenetics|DOI:10.1371/journal.pgen.1005602 December4,2015 1/26
TheGeneticAncestryofSouthAmericanLatinos
1201234toCDB.CRGissupportedbyNIH population-leveldifferencesinbiomedicaltraitsand,thus,informfuturemedicalgenetic
T32HG000044.JRHissupportedbyaStanford studiesintheregion.
GraduateFellowship.AMEwassupportedbythe
GeorgeRosenkranzPrizeforHealthCareResearch
inDevelopingCountries.SGandDNaresupported
bytheCanadaResearchChairsprogramandCIHR
operatinggrantMOP-134855.Thefundershadno AuthorSummary
roleinstudydesign,datacollection,analysis,
decisiontopublish,orpreparationofthemanuscript. SouthAmericaishometoover400millionpeoplewhosharearichdemographichistory,
includingsettlementbyNativeAmericans,Europeancolonization,andtheAfricanslave
CompetingInterests:Ihavereadthejournal'spolicy
andtheauthorsofthismanuscripthavethefollowing trade.WeusegenomicdatatoinferwhichpopulationsfromEuropeandtheAmericas
competinginterests:CDBisontheScientificAdvisory contributedtotheseadmixtureevents.Weprovideevidenceformultipleoriginsofthe
BoardsofAncestry.com,Personalis,Liberty NativeAmericanancestryofadmixedSouthAmericanLatinos.TheNativeAmerican
Biosecurity,23andMe’s‘‘RootsintotheFuture’’
ancestralcomponentcorrelatesstronglywithgeography,indicatingthatadmixture
projectandEtalonDX.HeisalsoafounderandChair
occurredbetweenEuropeancolonistsandlocalNativeAmericanpopulationsthroughout
oftheSABofIdentifyGenomics.Noneofthese
SouthAmerica.WealsoshowthattheEuropeanancestryofSouthAmericanLatinos
entitiesplayedaroleinthedesign,interpretation,or
presentationoftheseresults. comesmainlyfromtheIberianpeninsula,however,asignificantnumberofArgentinians
haveEuropeanancestryfromotherSouthernEuropeanregions.Thegeneticsignalof
EuropeanadmixtureinSouthAmericanpopulationsisyoungerthanthesignalobserved
inMexicoandtheCaribbean.WefindevidenceforasecondpulseofEuropeanmigration
tomanyregionsofSouthAmericasubsequenttotheoriginalcolonization.Theseresults
demonstratetheheterogeneousnatureoftheLatinopopulationinSouthAmericaand
helpelucidatethecomplexgeneticandadmixtureeventsthatshapedthepopulationstruc-
tureoftheregion.
Introduction
Ourunderstandingoffine-scalepatternsofpopulationstructureinhumanshasdramatically
increasedwiththeadventanddeploymentoffast,inexpensive,andaccurategenome-wide
technologiesforassayingvariation[1–3].However,ourunderstandingofregionalpatternsof
genomicvariationisquitepoorinmanypartsoftheworldparticularlyinpopulationsthatare
currentlyunderrepresentedinGWASstudies,includingthoseinLatinAmerica[4].Under-
standingpatternsofgenomicvariationisespeciallyimportantforpopulationsthroughoutthe
Americas,whichhaveundergonemultiplerecentadmixtureevents,makingthereconstruction
oftheirevolutionarypastandthedesignofmulti-ethnicmedicalgeneticstudieschallenging.
Recently,studiesinMexico,theCaribbean,andthroughouttheAmericashaveshedlighton
thecomplexdemographicprocessesthatoccurredinthoseregionsandhaveilluminatedhow
differencesinthepre-andpost-colonialhistoryhaveshapeddifferencesingenomicvariation
thatultimatelyimpactvariationincomplexbiomedicaltraits[5–7].TheSouthAmericanland-
massfeaturesuniquegeographic,archaeological,andhistoricalrecordsthataredistinctfrom
otherregionsoftheAmericas[8].Thecontributionsoftheseeventstopatternsofgenomicvar-
iationremainstobelaidouttoagreaterextent.Forexample,incontrasttoNorthAmerica,
SouthAmerica’sindigenouspopulationhistoryderivesfromasinglemigrationwavethatrap-
idlyexpandedsouthwardsthroughouttheAndeanhighlandsandeastwardsintotheAmazon
basin[9].PreviousanalysesofnativeSouthAmericanvariationbasedonmicrosatelliteshave
reportedawest-to-eastdifferenceingeneticdiversitybetweenAndeanandeasternBrazilian
tribesasoneofthestrongestsignalsofsub-continentalgeneticdifferentiation[10–12].The
largesthumansettlementsinSouthAmerica,however,occurredthroughouttheAndeanregion
andlikelyrepresentamajorsourceofNativeAmericanvariationinpresentdaySouth
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TheGeneticAncestryofSouthAmericanLatinos
AmericanLatinos.Characterizingtheextentofsubstructureanddifferentialcontributionof
theseancestralcomponentsisthereforecrucialtounderstandingthegeneticheterogeneityof
theSouthAmericanpopulation.
PreviousstudiesonSouthAmericanLatinopopulationshaveeitherusedalimitednumber
ofgeneticmarkerstoevaluatecontinental-levelpatternsofpopulationstructureorfocusedon
particulargeographicregions[13–18].Manyofthesestudiesandothershavedemonstrateda
largeamountofgeneticdiversityinNativeAmericanandmestizopopulations,especially
betweendifferentgeographicregions[11–13,19].Wangetal.analyzedmultiplemestizopopu-
lationsthroughoutSouthAmericausing678microsatellitemarkers[13]andfoundevidenceof
correlationsbetweenancestrycomponentsandgeography.TheGalanteret.al.andRuiz-
Linaresetal.studies[15,16]usedalimitedsetofancestryinformativemarkerstoanalyzethe
globalancestryproportionsthroughoutLatinAmerica.However,duetothesmallernumbers
ofmarkers,thesestudieswereunabletoperformanalysesthatrelyupondensegeneticinfor-
mationsuchaslocalancestryinference,ancestryspecificprincipalcomponentsanalysis,and
demographicmodelingbaseduponancestrytractlength.RecentworkinBrazilusingdense
genomicinformationhasdemonstratedthatindividualsdiffermarkedlyinancestrypropor-
tionsbothwithinandbetweenpopulationsinmetropolitanregionsofSouthAmerica[20].
TheyalsodemonstratesignificantvariationwithintheEuropeanandAfricanancestry
components.
Here,weexpanduponpreviousworkbyfocusingonadmixedpopulationsfromfivecoun-
triesinSpanishspeakingSouthAmerica(Argentina,Chile,Colombia,Ecuador,andPeru),
spanningmuchoftheAndeanregionofthecontinent.SimilartootherareasinLatinAmerica,
SouthAmericahasexperiencedmultiplemigrationandadmixtureevents,includingNative
Americansettlement,Europeancolonization,andtheAfricanslavetrade.However,thetiming
andmagnitudeofmigrationwavesfromamyriadofcontinentalandsubcontinentalancestral
groupsvariesdramaticallythroughoutthecontinentandaffectsthepopulationgeneticprofile
oftheregionatalocalscale.
TheearliestsettlementsinSouthAmericadatebackover14,000yearsago[8].NativeAmer-
icansdevelopedmultiplecivilizationsthroughoutthecontinent,includingsettlementsinthe
Andes,theAmazon,andalongthecoasts.Inthe16thcentury,Europeancolonizationandcon-
questledtoadramaticpopulationbottleneckintheNativeAmericanpopulationaswellasan
increasinginfluxofEuropeanmigrants,quicklyfollowedbyadmixturewithWestAfricans
broughttotheAmericasthroughtheslavetrade.Duringthefollowingcenturies,therewas
continuousadmixturebetweenEuropean,NativeAmericans,andAfricanindividuals.Early
EuropeanmigrationintotheSpanishSouthAmericancoloniescamemainlyfromtheIberian
Peninsula.Spanishconquistadorsintheearly16thcenturyconqueredmanyoftheindigenous
populationsintheAndeanregionofSouthAmerica,establishingSouthAmericancolonies
throughoutthecontinent[21].Allfiveofthecountriesstudiedherewereoriginallypartofthe
SpanishviceroyaltyofPeru.TheseSpanishcoloniesfollowedseparatebutrelateddevelopmen-
talpaths,eventuallysplittingintotheviceroyaltiesofPeru,NewGranada,andRiodelaPlata.
ThePeruviancolonywasamajorsourceofsilverfortheSpanishEmpire,whilethecoloniesin
RiodelaPlata(includingpresentdayArgentina)andNewGranada(includingColombiaand
Ecuador)becameimportantcommercialcenters[21,22].TheSpanishcoloniesinSouthAmer-
icacontinuedtoreceiveimmigrationfromEuropeconcurrentwithadmixturewithNative
Americanpopulations.Inthe19thand20thcenturies,thereisevidenceofincreasedmigration
frommanyregionsofSouthernEurope,especiallyinArgentina[23,24].
Toexploretheimpactofthiscomplexdemographichistoryuponthecurrentgeneticstruc-
tureofSouthAmericanLatinopopulations,weanalyzesinglenucleotidepolymorphism(SNP)
genotypingdatafrom436unrelatedadmixedsamples,including175Argentinians,119
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TheGeneticAncestryofSouthAmericanLatinos
Peruvians,27Chileans,19Ecuadorians,and96Colombians.Wecombinedthesedatawithref-
erencepanelsofEuropeanandNativeAmericanpopulations,andappliedadmixturedeconvo-
lutionmethodstotracebacktheoriginofeachancestrycomponentwithinEuropeandthe
Americas.Wealsoanalyzedthelengthdistributionofancestralsegmentsinadmixedindividu-
alstotesthypothesesaboutpastmigrationpatternsandexaminewhetherdifferentcountries
haveexperienceddifferentgenetichistories.
ResultsandDiscussion
Globalancestrycomposition
TocharacterizetheancestralcomponentsofSouthAmericanLatinoindividualsfromColom-
bia,Ecuador,Peru,Chile,andArgentina,weappliedunsupervisedclusteringmodelsandprin-
cipalcomponentsanalysistogenotypedatafromancestralandadmixedpopulations(Fig1)
(seeMethods).Thisdatasetcontains436admixedSouthAmericanindividualstogetherwith
204EuropeanindividualsfromthePOPRESstudy[1],50Yorubanand50HanChinesefrom
the1000GenomesProject[3],and493unmaskedNativeAmericanindividualsfromReich
etal.2012[9].TheSouthAmericanindividualsshowedvaryingproportionsofEuropean,
NativeAmericanand,toalesserextent,WestAfricanancestryinPCAspace,supportingthe
notionofabroadrangeofglobalancestrypatternsthroughoutSouthAmerica.Weobserved
somedispersionofNativeAmericanindividualsawayfromthemainancestralclusterdueto
thepresenceofEuropeanadmixture.
WethenranclusteringmodelsforK=2throughK=15ancestralpopulationswith
ADMIXTURE[25]onatotalof1,233individuals.CrossvalidationerrorsfortheADMIX-
TUREanalysisareshowninS2Fig.TheminimumCVerrorwasobservedatK=13.When
clusteringisperformedassumingK=4ancestralpopulations(Fig1C),thealgorithmseparates
theindividualsintofourmajorcontinentalclusters.Averagecontinentalancestryproportions
foreachoftheadmixedpopulationsareshowninTable1.Asexpectedfromhistoricalrecords
[21,22]andpreviousresultsfromotherLatinopopulationsintheCaribbean[6]andMexico
[5],SouthAmericanLatinoindividualsshowamixtureofEuropean,NativeAmerican,and
Africanancestry.However,somepopulations,especiallythoseinPeru,Chile,andArgentina,
tendtohaveasmallerproportionofAfricanancestrythanseeninLatinopopulationsinthe
Caribbean(p<2.2x10−16,Wilcoxontest,S6Fig),alsoobservedinpreviousanalyses[13,16–
18].Wefindsignificantdifferencesinglobalancestryproportionsbetweencountrieswithin
SouthAmerica.ThePeruvianindividualstendtohaveahigherproportionofNativeAmerican
ancestrythanindividualsfromanyoftheotherSouthAmericanpopulations(TukeyHSD
Test,p<0.001vs.Argentina,Chile,Colombia,Ecuador;S3Fig).WeobservedmultiplePeru-
vianindividualswitha>25%proportionofEastAsianancestry,whichisnotsurprisinggiven
thattherewerelargeAsianmigrationstoPeruespeciallyduringthe19thandearly20thcentury
wherelaborersfromGuandong(formerlyCanton)provinceinChinawerebroughttothe
country[26].PeruopeneditsborderstoAsianimmigrationin1849,anditisestimatedthat
over87,000ChineseindividualsenteredPerubetween1859and1874[22].ThisEastAsian
ancestrycomponentisalsoseenintheNorthernAmerindianindividuals.Theseindividuals
arefromEskimo,Aleut,andNa-Denepopulationsandtheobservedclusteringisconsistent
withthehypothesisofmultiplewavesofgeneflowfromAsiatoAmericasuggestedbyaprevi-
ousstudy[9].AthighervaluesofKinADMIXTURE,theseindividualsareassignedtotheir
ownADMIXTUREcomponent,indicatingauniqueancestrycomponentthatisseparatefrom
theEastAsiancluster(Fig1andS5Fig).
TheArgentinianpopulationhasasignificantlyhigherproportionofEuropeanancestry
thanthePeruvian,Chilean,andEcuadorianpopulations(TukeyHSDTest,p=0.018vs.Chile,
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TheGeneticAncestryofSouthAmericanLatinos
Fig1.GlobalancestryanalysisofSouthAmericanpopulations.(a)PrincipalComponentsAnalysisofadmixedindividualsandcontinentalreference
panels.Eachindividualisrepresentedasapointcoloredbycountry,region,orcontinentoforigin.(b)Mapofsampledpopulations.Countriesoforiginfor
admixedSouthAmericansarehighlightedandcoloredasin(a).(c)ADMIXTUREplotofadmixedindividualsandcontinentalreferencepanels.Each
individualisrepresentedasathinverticalbar.Thecolorsrepresenttheproportionofancestryassignedtoeachclusterforeachindividual.K=4andK=13
modelsareshownabove,K=2throughK=15modelsareavailableinS4andS5Figs.
doi:10.1371/journal.pgen.1005602.g001
p=0.129vs.Colombia,p<0.001vs.PeruandEcuador)withsomeindividualshavingcloseto
100%Europeanancestry(S3Fig).Evenso,thereisalargerangeofancestryproportionswithin
individualsfromArgentina,consistentwithpreviousresultsbasedonasmallnumberofances-
tryinformativemarkersandbloodgroupantigens[17,27,28].Thisvarianceismostlikelya
resultofthecontrastinghistoriesofdifferentArgentineanregions.Forexample,theoriginal
SpanishsettlersofArgentinacamethroughthePacific/Andeanregion[21].However,as
Argentinadeveloped,individualsfromSpainandSouthernEuropesettledthroughoutthe
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TheGeneticAncestryofSouthAmericanLatinos
Table1. GlobalancestryproportionsestimatedthroughADMIXTUREK=4.
Population European NativeAmerican WestAfrican EastAsian
Argentina 0.673 0.277 0.036 0.014
Chile 0.572 0.387 0.025 0.017
Colombia 0.625 0.274 0.092 0.009
Ecuador 0.408 0.501 0.068 0.023
Peru 0.260 0.683 0.032 0.025
doi:10.1371/journal.pgen.1005602.t001
coastalregionsontheAtlantic[23].WealsoobservedasmallnumberofArgentinianindividu-
alswithrelativelyhighamountsofAfricanancestry,whereastherestoftheindividualshavea
verylowAfricanancestrycomponent.Thisdiversityisreflectedinthelargerangeinancestry
proportionsseenwithinArgentinaandisconsistentwithpreviousstudies[17,28,29].
AthigherorderKs(K=13inFig1),weobservedsignificantsubstructureinboththeNative
AmericanandEuropeanpopulations.TheNorth-SouthgradientamongEuropeanpopulations
isstronglycorrelatedwiththelatitudeofeachcountry’scapital(p<2.2X10−16,linearregres-
sion),withasouthernEuropeancomponent(lightblue)mostprominentinSpain,Portugal,
Italy,andGreece.MostoftheadmixedLatinoindividualsinthesamplehaveahighproportion
ofthissouthernEuropeancomponent,suggestingthattheEuropeansinvolvedinadmixture
eventsinSouthAmericaarefromtheIberianPeninsulaandMediterraneanEurope.This
observationisconsistentwithhistoricalmigrationpatternsandmaintainedculturalinfluence
[19].Ontheotherhand,theprimaryclusterofNativeancestryisreflectiveofthelocalindige-
nousdiversity.WefindthatacomponentoftheNativeAmericanancestryinthePeruvian
samplesissharedwithlocalAndeannativegroups,suchasQuechuaandAymara,andthatof
ColombiansismorecloselysharedwiththeSouthernandCentralAmerindiangroups(Fig1,
K=13).Incontrast,weseethattheNativeAmericancomponentinArgentinaandChileis
sharedbetweencomponentsfromCentral/SouthernNativeAmericanandAndeanNative
Americangroups,showingawiderrangeofancestraloriginsthatweexplorebelowinfurther
analyses(Fig1C,K=13).
SexbiasedancestryisanimportantfeatureofmanyLatinAmericanpopulations,andhas
beenobservedanddescribedthoroughlyinmanypreviousresearcharticles[6,18].European
migrantstotheAmericasweremainlymale,especiallyduringtheearlieryearsofcolonization.
ThishasresultedinincreasedAmerindianancestryontheX-chromosomewhencomparedto
theautosomes.Afterexcludingadmixedmalesfromtheanalysis,wehadadmixedindividuals
fromonlyfourpopulations:Argentina,Chile,Colombia,andPeru.WecomparedADMIX-
TUREestimatesatK=3ofautosomalandX-chromosomalancestry(S7Fig).Wefindan
increaseinNativeAmericanancestryontheX-chromosomecomparedtotheautosomes(S8
Fig,Wilcoxonp<0.001).Thisissuggestiveofthefactthattherewasanoverabundanceof
EuropeanmalesandAmerindianfemalesthatparticipatedintheadmixtureprocess.
SubcontinentalancestrycomponentsinSouthAmerica
Toidentifytheadmixedindividuals’subcontinentallineagesrootedwithinEuropeandSouth
America,weperformedancestry-specificPCAanalysis.ASPCAisatechniquedevelopedto
performprincipalcomponentsanalysisonthefractionofanindividual’sancestryfromaspe-
cificcontinentalorigin.IncontrasttoPCA,whichisperformedonindividual(unphased)dip-
loidgenotypecalls,ASPCAisperformedonphasedhaploidgenomesconditionalonancestry
calls(seeMethodsfordetails).
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Fig2.Europeanancestryspecificanalysis.(a)EuropeanAncestrySpecificPCAofhaploidgenomesfromColombiaandEcuadorwithgreaterthan25%
estimatedEuropeanancestrycombinedwith2,882haploidgenomesfromthePOPRESdataset.AdmixedLatinoindividualsareshowninshadesofgrey,
whileEuropeanindividualsarecoloredaccordingtoregionandrepresentedasatwo-charactercountrycode.(b)EuropeanAncestrySpecificPCAofhaploid
genomesfromPeru,Chile,andArgentinawithgreaterthan25%estimatedEuropeanancestrycombinedwiththesamereferenceEuropeandatasetasin
(a).Theinsetmapshowsthecolor-codedregionswithinEuropeofthePOPRESreferencepanel.TomaximizeSNPoverlapbetweendatasets,ASPCA
analyseswereperformedseparatelyforeachsubsetofSouthAmericanLatinopopulations(seeMethods).
doi:10.1371/journal.pgen.1005602.g002
ToexploretheirEuropeanorigins,wecombinedouradmixedindividualswiththePOPRES
Europeandataset[1]andperformedASPCAonthemergeddataset(Fig2).Duetothelimited
overlapbetweenthePOPRESdatasetandoursamples,weperformedASPCAontheArgentin-
ian,Chilean,andPeruvianhaplotypesseparatelyfromtheColombianandEcuadorianhaplo-
types.TheEuropeanreferencesamplesclusteraccordingtogeography[30].Wefindthatthe
majorityoftheEuropeanhaplotypesoftheadmixedsamplesclusterwithIberianandSouthern
Europeans,consistentwithhistoricalrecordsandpreviousreports[6,31].However,we
observedinterestingdifferencesbetweencountriesinSouthAmerica.Forexample,Argentina
showedthehighestnumberofEuropeanhaplotypesthatclusterintheItalianpeninsula.This
isconsistentwithrecentmigrationeventsfromItalytoArgentinainthelate19thandearly20th
centuries[22].Between1880and1930,2.3millionofthe4.7millionmigrantstoArgentina
hadItaliannationality[24].WealsofindthatArgentinahasthelargestrangeintheEuropean
ancestrycomponentsandevenincludestwohaploidgenomesthatclusternearindividuals
fromGermany,Poland,andHungaryinthetoprightoftheASPCAplot(Fig2).Noother
SouthAmericanpopulationshowedsampleswithsuchdistantancestryfromtheIberianclus-
ter,norotherLatinosamplesfrompreviousstudiesintheCaribbeanandMexico[5,6].
TofurtherourinvestigationoftheEuropeancomponentbeyondtheSpanishancestry
foundintheIberianPeninsula,wecombinedmaskedsamplesfromtheCanaryIslandswith
SouthAmericanindividualsfromColombiaandEcuador.TheCanaryIslandswerecolonized
bytheSpanishintheearly15thcenturyandbecameastoppingpointforSpanishontheirway
totheAmericas.Here,wefindundifferentiatedpatternsofancestrybetweentheEuropean
componentofthesethreepopulations(S9Fig),suggestingthattheEuropeanancestryofthese
groupseitheroriginatedfromasimilarsourceontheIberianpeninsulaorthatmethodsof
increasedresolutionareneededtountanglemoresubtledifferences.
ToinvestigatetheNativeAmericancomponentoftheSouthAmericanindividuals’ances-
try,wecombinedoursampleswiththosefrom49NativeAmericanpopulationspreviously
genotyped[9].WeremovedNativeAmericansamplesthatappearedasoutliersinASPCA
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TheGeneticAncestryofSouthAmericanLatinos
Fig3.NativeAmericanancestryspecificanalysis.NativeAmericanAncestrySpecificPCAofallLatinohaploidgenomeswithgreaterthan25%
estimatedNativeAmericanancestry.Eachmaskedhaploidgenomefromadmixedindividualsisrepresentedbyasinglepointcoloredbypopulationoforigin.
NativeAmericanhaploidgenomesareplottedasthefirstthreelettersofthepopulationnameandcoloredaccordingtotheregionalgroupings.The
approximatesamplinglocationforeachoftheNativeAmericanparentalpopulationsisshownonthemapofLatinAmerica.
doi:10.1371/journal.pgen.1005602.g003
spaceandthatweregeographicallydistantfromSouthAmerica(seeMethodsandS10Fig).We
alsoexcludedNativeAmericanindividualswithgreaterthan10%estimatedEuropeanances-
try,aswefoundtheseindividualswerebiasingtheprincipalcomponentsanalysistowardsa
European/NativeAmericanaxis(S11,S12andS13Figs).Forvisualizationpurposes,Native
AmericanpopulationsweregroupedcorrespondingtothelabelsusedinReichetal.[9]and
arereferencedgeographically(seeS1Tableformapping).
WefindthattheNativeAmericancomponentoftheSouthAmericanhaplotypesclusters
alongagradientbetweentheAndeanAmerindianpopulationsandtheSouthernAmerindian
populationsalongASPC1andASPC2(Fig3).Notably,theNativeAmericanancestryinthe
admixedSouthAmericanindividualsisdrasticallydifferentfromthegeneticcomponents
observedamongCentralandNorthernNativeAmericangroups,suchasKaqchikelinGuate-
malaandZapotecorTepehuanoinMexico.Noneofthesegroupsshowedcloseaffinitieswith
Latino-derivedSouthAmericanhaplotypes,supportingthenotionofahighlysubstructured
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TheGeneticAncestryofSouthAmericanLatinos
architectureoftheNativeAmericancomponentamongLatinosfromdifferentregionsacross
LatinAmerica.
OurASPCAanalysisrevealedthatSouthAmericannativehaplotypesclusterprimarilyinto
twogroups:onerepresentedbycentralAndeanindividuals,suchasQuechuaandAymara,and
anothergroupthatincludesmostoftheremainingnativepopulationsfromSouthAmerica.
ThedifferentiationbetweentheAndeanAmerindiansandotherSouthAmerindiansisconsis-
tentwithpreviousresultsusingYchromosomeandmtDNAanalyses[11,12],andsuggests
thatthemountainrangeoftheAndesactedasamajorgeographicbarriertogeneflowduring
NativeAmericanevolution.ThiscreatedfurtherpopulationstructureamongSouthNative
AmericangroupsseparatingpopulationsintheAmazonandeastcoastalregionsfromhigh-
landpopulationsintheAndes.Interestingly,anumberofthepopulationsclassifiedasAndean
suchastheHulliche,Inga,andYahganclusteredclosetotheSouthern/AmazonianNative
AmericansandfarfromtheotherAndeanNativeAmericanssuchastheQuechuaand
Aymara.Reichetal.in2012[9]suggestedthat,basedonlinguisticaffinities,thesepopulations
wouldbeexpectedtoclusterwiththeAymaraandQuechuapopulations.Indeed,amongthe
samplesfromthemainAmazonianclusterinFig3,thesearetheonlyonesspreadingtowards
theQuechua/Aymaracluster,supportingtheideaofpre-Columbianadmixtureeventsgiving
risetopopulationsliketheInga,Huilliche,andYahganalongtheAndes.Theseparation
betweentheAndeanandotherSouthAmericanpopulationsisconsistentwiththehypotheses
ofeithermultiplemigrationroutesintoSouthAmerica,withanearlysplitsoonaftercrossing
theIsthmusofPanama,orrestrictedlevelsofgeneflowshortlyafterestablishmentofNative
Americansettlementsinthecontinent[8,11,12,32].Likewise,theclusteringofnorthernArgen-
tinianWichiandParaguayanGuaraniandTobawithlowlandgroupsfromBrazilandColom-
bia,suggestsanAmazonianoriginofNativeAmericanmigrationintotheGranChacoand
Pampasareasratherthanstrongevidenceofatrans-Andeanroute.Thebranchingpatternof
theseancestralmigrationshavedirectlyimpactedthegeneticprofileofpresentdaySouth
AmericanLatinopopulations,evenbetweenneighboringcountriessuchasArgentinaand
Chile.Wedetailthesepatternsinwhatfollows.
Theclusteringofthemaskedhaploidgenomesfromtheadmixedindividualstendedtobe
populationspecific(Fig3).WefindthatthePeruvianindividualsclustermorecloselywiththe
AndeanNativeAmericanindividualsthanwithanyotherNativeAmericangroup,suggesting
thattheNativeAmericancomponentofthePeruvianpopulationismainlyfromtheAndean
region.WhiletheAndeanNativeAmericansandPeruvianindividualsclusterclosely,manyof
themdonotoverlap.BoththeQuechuaandAymaraindividualsarefromtheCentralAndes,
whiletheadmixedindividualsarefromLima.MitochondrialandY-chromosomalstudiesof
Andeanancestryhaveindicatedthatthereisrelativelylowgeographically-correlatedgenetic
diversityintheAndeanregion,likelyduetothehistoricallyhighergeneflowandpopulation
sizeintheAndeanregion[11,12].Whilethereseemstobelessgeographiccorrelationinances-
tryintheAndeanNativeAmericansthaninotherNativeAmericanpopulations,somegeo-
graphicstratificationmaybedetectedthroughhigh-densitygenotypingthatwasnotdetected
usingmitochondrialorY-chromosomalanalysis.Inotherpopulationswithlowerlevelsof
geneticdifferentiation,suchasEuropeans,highdensitygenotypingdatarevealedcorrelations
betweengeographyandancestry[30].Also,ourreferencepanelhaslittlerepresentationfrom
coastalPeruvianNativeAmericans,andthesegroupsmayalsohavecontributedtotheadmix-
tureprocessincosmopolitanareas.
Argentinianindividualsshowabroaderrangeofindigenousancestry:someclustercloserto
theSouthern/AmazonianNativeAmericans,whileothersclusterwiththeLatinoPeruvians
andtheAndeangroup,reflectingarichdiversityofpre-ColumbianrootsinArgentina,whose
geographyspansthebreadthofthecontinentfromtheAndestotheAtlantic,thusabsorbing
PLOSGenetics|DOI:10.1371/journal.pgen.1005602 December4,2015 9/26
TheGeneticAncestryofSouthAmericanLatinos
haplotypesfrombothmajorstreamsofNativeAmericanmigration.Wefindonlyamarginal
relationshipbetweenclusteringandsamplinglocationwithinArgentina.Wefindthatsam-
plinglatitudeismarginallyassociatedwithASPC1inalinearregression(p=0.025,S14Fig),
andnotsignificantlyassociatedwithASPC2(p=0.3387,S15Fig).Wefindnosignificantlinear
relationshipbetweenlongitudeandASPCs(p=0.322vs.ASPC1andp=0.844vs.ASPC2;S16
andS17Figs).However,wedonotexpectthesamplinglocationsinourcurrentsampletobe
indicativeofanindividual’shistorytothisdegreeofresolution.Mostindividualsweresampled
athospitalsinmajorcitiesthroughoutArgentina,withthelargestnumberofindividualssam-
pledinBuenosAires.Becauseofrecentmajormigrationsofindividuals,especiallyfromrural
tourbanareas,currentlocationmaynotbeindicativeofthelocationofanindividual’sances-
tors.TherehasalsobeenrecentintraregionalmigrationthroughoutSouthAmerica,especially
inurbanregionssuchasBuenosAires[33,34].Thiscouldbecontributingtothegeneticdiver-
sityweobservewithintheArgentinianindividuals’NativeAmericanancestry.Asampling
schemebaseduponthe“fourgrandparent”ancestryprinciple,suchastheoneusedinthe
EuropeanPOPRES[1]study,alongwithmorerepresentationfordifferentregionsthroughout
Argentinamaybetterelucidatefinerscalestructureinthecountry,althoughthisisalsoknown
tobeimperfect[17].
Incontrast,theColombianandEcuadorianLatinohaplotypestendtoclusterwithgeo-
graphicallynearbySouthernNativeAmericans,suchastheWayuu,Piapoco,andTicunafrom
Colombia.TheEcuadorianindividualsclusterfartherawayfromthisancestralgroupthanthe
Colombians,whichcouldbeduetothelackofEcuadorianNativeAmericangroupsintheref-
erencepanelorbetheresultofadmixturewithAndeanNativeAmericanlineages.
TheChileanindividualsclustertowardsthemiddleoftheadmixedgroup,betweenthe
AndeanclusterandtheChileanHuillicheandYaghansamples.TheNativeAmericanreference
panelusedheredoesnotincludemanyNativeAmericansfromSouthernChile.Onlytwohap-
loidgenomesfromoneHullicheindividualareinthesubsetofthereferencepanelusedfor
analysisduetothehighproportionofEuropeanancestryintheremainingHullicheindividu-
als.ThelackofrepresentationofHullicheandotherChileanNativeAmericanscouldexplain
whywedonotseeastrongdifferentiationoftheadmixedChileanhaploidgenomes.Adeeper
samplingeffortisneededtoassessfine-scalegeneticpatternswithinChile.Wefindthatthe
NativeAmericanancestryofadmixedLatinosisassociatedwithpopulationoforigin(ANOVA
p<2x10−16forbothASPC1andASPC2).Thisisconsistentwithmanypreviousresultsin
populationhistoryanalysis,whichhavealsoshownstrongcorrelationbetweengeographicfea-
turesandancestry.
TofurtherinvestigatethedifferencesbetweentheEuropeanandNativeAmericanancestry
componentsofSouthAmericanindividuals,weusedGERMLINE[35]toidentifygenomic
regionsofidentitybydescent(IBD)intheadmixedindividualsandcomparedthepatternsof
IBDmatchingwithinandamongpopulationstothelocalancestrycallsinferredthroughout
eachIBDmatch.Wefind12,348segmentsofIBDsharedwithinpopulationscomparedwith
only4,941segmentsofIBDsharedbetweenpopulations.Onaverage,theindividualsfrom
ColombiasharethemostIBDwithinthepopulation(15.2cM),followedbyChile(3.42cM),
Ecuador(2.58cM),Peru(2.06cM),andArgentina(0.84cM).Wefindthatsegmentsshared
betweenpopulationsareshorterthanthosesharedwithinpopulations(Wilcoxp<2.2e-16).
ForIBDsegmentsthatcouldbeidentifiedusingahaploidcomparison,wecalculatedforeach
segmenttheproportionofEuropean,NativeAmerican,andAfricanlocalancestry.We
findthatinbothwithinandbetweenpopulations,longerIBDsegmentshaveahigherpropor-
tionofEuropeanancestry(linearregression,p=4.04x10−16).Theeffectsizebaseduponlinear
regressionisgreaterinIBDsegmentssharedbetweenpopulations(β=0.050±0.0084s.e.,
p=3.7x10−9)thaninIBDsegmentssharedwithinpopulations(β=0.0076±0.0011s.e.,
PLOSGenetics|DOI:10.1371/journal.pgen.1005602 December4,2015 10/26