The Genetic Ancestry of African Americans, Latinos, and European Americans Across the United ...

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Biology, Chemistry, and Environmental Sciences
Biology, Chemistry, and Environmental Sciences
Faculty Articles and Research
2015
The Genetic Ancestry of African Americans,
Latinos, and European Americans Across the
United States
Katarzyna Bryc
Harvard University
Eric Y. Durand
23andMe
J. Michael Macpherson
Chapman University, [email protected]
David Reich
Harvard University
Joanna Mountain
23andMe
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Recommended Citation
Bryc, Katarzyna, Eric Y. Durand, J. Michael Macpherson, David Reich, and Joanna L. Mountain. "The Genetic Ancestry of African
Americans, Latinos, and European Americans across the United States."The American Journal of Human Genetics96.1 (2015): 37-53.
doi: 10.1016/j.ajhg.2014.11.010
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The Genetic Ancestry of African Americans, Latinos, and European
Americans Across the United States
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This article was originally published inThe American Journal of Human Genetics, volume 96, issue 1, in 2015
and has accompanying data.DOI: 10.1016/j.ajhg.2014.11.010
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ARTICLE
The Genetic Ancestry of African Americans, Latinos,
and European Americans across the United States
Katarzyna Bryc,1,2,* Eric Y. Durand,2 J. Michael Macpherson,3 David Reich,1,4,5
and Joanna L. Mountain2
Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans
(broughtlargelybythetrans-Atlanticslavetrade),shapingtheearlyhistoryofwhatbecametheUnitedStates.Westudiedthegenetic
ancestryof5,269self-describedAfricanAmericans,8,663Latinos,and148,789EuropeanAmericanswhoare23andMecustomersand
showthatthelegacyofthesehistoricalinteractionsisvisibleinthegeneticancestryofpresent-dayAmericans.Wedocumentpervasive
mixedancestryandasymmetricalmaleandfemaleancestrycontributionsinallgroupsstudied.Weshowthatregionalancestrydiffer-
encesreflecthistoricalevents,suchasearlySpanishcolonization,wavesofimmigrationfrommanyregionsofEurope,andforcedrelo-
cationofNativeAmericanswithintheUS.Thisstudyshedslightonthefine-scaledifferencesinancestrywithinandacrosstheUnited
Statesandinformsourunderstandingoftherelationshipbetweenracialandethnicidentitiesandgeneticancestry.
Introduction andareabletodetectlowproportionsofNativeAmerican
ancestry.3–11 Latinos across the Americas have differing
Overthelastseveralhundredyears,theUnitedStateshas proportions of Native American, African, and European
beenthesiteofongoingmixingofpeoplesofcontinental genetic ancestry, shaped by local historical interactions
populationsthatwerepreviouslyseparatedbygeography. withmigrantsbroughtbytheslavetrade,Europeansettle-
NativeAmericans,EuropeanimmigrantstotheAmericas, ment, and indigenous Native American populations.12–18
and Africans brought to the New World largely via the Individuals from countries across South America, the
trans-AtlanticslavetradecametogetherintheNewWorld. Caribbean, and Mexico have different profiles of genetic
Mating between individuals with different continental ancestry molded by each population’s unique history
origins,whichwerefertohereas‘‘populationadmixture,’’ and interactions with local Native American popula-
results in individuals who carry DNA inherited from tions.1,19–25EuropeanAmericansareoftenusedasproxies
multiple populations. Although US government census for Europeans in genetic studies.26 European Americans,
surveysandotherstudiesofhouseholdsintheUShavees- however,haveahistoryofadmixtureofmanygenetically
tablishedfine-scaleself-describedethnicityatthestateand distinct European populations.27,28 Studies have shown
countylevel(seetheUS2010Censusonline),therelation- that European Americans also have non-European
ship between genetic ancestry and self-reported ancestry ancestry, including African, Native American, and Asian,
foreachregionhasnotbeendeeplycharacterized.Under- though it has been poorly quantified with some discor-
standing genetic ancestry of individuals from a self-re- danceamongestimatesevenwithinstudies.29–32
ported population, and differences in ancestry patterns That genetic ancestry of self-described groups varies
amongregions,caninformmedicalstudiesandpersonal- across geographic locations in the US has been docu-
ized medical treatment.1 The genetic ancestry of individ- mented in anecdotal examples but has not previously
uals can also shed light on the history of admixture and been explored systematically. Most early studies of Afri-
migrationswithindifferentregionsoftheUS,whichisof canAmericanshadlimitedresolutionofancestrybecause
interesttohistoriansandsociologists. ofsmallsamplesizesandfewgeneticmarkers,andrecent
Previousstudies haveshownthat African Americansin studies typically have limited geographic scope. Though
theUStypicallycarrysegmentsofDNAshapedbycontri- much work has been done to characterize the genetic di-
butionsfrompeoplesofEurope,Africa,andtheAmericas, versity among Latino populations from across the Amer-
withvariationinAfricanandEuropeanadmixturepropor- icas, it is unclear the extent to which Latinos within
tions across individuals and differences in groups across the US share or mirror these patterns on a national or
parts of the country.2–4 More recent studies that utilized local scale. Most analyses have relied on mitochondrial
high-density genotype data provide reliable individual DNA, Y chromosomes, or small sets of ancestry-informa-
ancestryestimates,illustratethelargevariabilityinAfrican tive markers, and few high-density genome-wide
andEuropeanancestryproportionsatanindividuallevel, SNP studies have explored fine-scale patterns of African
1DepartmentofGenetics,HarvardMedicalSchool,Boston,MA02115,USA;223andMe,Inc.,MountainView,CA94043,USA;3SchoolofComputational
Sciences,ChapmanUniversity,Orange,CA92866,USA;4HowardHughesMedicalInstitute,HarvardMedicalSchool,Boston,MA02115,USA;5BroadInsti-
tuteofMITandHarvard,Cambridge,MA02142,USA
*Correspondence:[email protected]
http://dx.doi.org/10.1016/j.ajhg.2014.11.010.(cid:1)2015TheAuthors
ThisisanopenaccessarticleundertheCCBY-NC-NDlicense(http://creativecommons.org/licenses/by-nc-nd/3.0/).
TheAmericanJournalofHumanGenetics96,37–53,January8,2015 37
andNativeAmericanancestryinindividualslivingacross ResearchCohorts
the US. 23andMecustomerswereinvitedtofilloutweb-basedquestion-
Here,wedescribealarge-scale,nationwidestudyofAfri- naires,includingquestionsonancestryandethnicity,onstateof
canAmericans,Latinos,andEuropeanAmericansbyusing birth, and current zip code of residence. They were also invited
high-density genotype data to examine subtle ancestry to allow their genetic data and survey responses to be used for
research.OnlydataofcustomerswhosignedIRB-approvedcon-
patterns in these three groups across the US. To improve
sentdocumentswereincludedinourstudy.Surveyintroductions
the understanding of the relationship between genetic
areexplicitabouttheirapplicationsinresearch.Forexample,the
ancestry and self-reported ethnic and racial identity, and
ethnicitysurveyintroductiontextstatesthatthesurveyresponses
to characterize heterogeneity in the fine-scale genetic
will be used in ancestry-related research (Table S1 available
ancestry of groups from different parts of the US, we in-
online).
ferred the genetic ancestry of 5,269 self-reported African Self-ReportedAncestry
Americans, 8,663 Latinos, and 148,789 European Ameri- Itisimportanttonotethatancestry,ethnicity,identity,andrace
cans who are 23andMe customers living across the US, are complex labels that result both from visible traits, such as
by using high-density SNPs genotype data from 650K to skincolor,andfromcultural,economic,geographical,andsocial
1M arrays. 23andMe customers take an active role in factors.23,44 As a result, the precise terminology and labels used
participating in research by submitting saliva samples, for describing self-identity can affect survey results, and care
in choice of labels should be utilized. However, we chose to
consentingfordatatobeusedforresearch,andcompleting
maximize our available self-reported ethnicity sample size by
surveys. We generated cohorts of self-reported European
combininginformationfromquestionsaskingforcustomerself-
American,AfricanAmerican,andLatinoindividualsfrom
reportedancestry. We used two survey questions,with different
self-reportedethnicityandidentity.Weobtainedancestry nomenclature, to gaugeresponses aboutidentity, whichhere we
estimates from genotype data by using a Support Vector view as ‘‘the subjective articulation of group membership and
Machine-based algorithm that infers population ancestry affinity.’’45
with Native American, African, and European reference ThefirstquestionismodeledaftertheUScensusnomenclature
panels, leveraging geographic information collected andisamultiquestionsurveythatallowsforchoiceof‘‘Hispanic’’
throughsurveys(seeDurandetal.33).Fordetailsongeno- or‘‘NotHispanic,’’andparticipantswereasked‘‘Whichofthese
typingandancestrydeconvolutionmethods,seeSubjects US Census categories describe your racial identity? Please check
andMethods. all that apply’’ from the following list of ethnicities: ‘‘White,’’
‘‘Black,’’‘‘AmericanIndian,’’‘‘Asian,’’‘‘NativeHawaiian,’’‘‘Other,’’
‘‘Not sure,’’ and ‘‘Other racial identity.’’ For inclusion into our
Subjects and Methods EuropeanAmericancohort,individualshadtoselect‘‘NotHispan-
ic’’and‘‘White,’’butnotanyotheridentity.Forinclusionintoour
Latinocohort,individualshadtoselect‘‘Hispanic,’’withnoother
HumanSubjects
restrictions. For inclusion into our African American cohort,
Allparticipantsweredrawnfromthecustomerbaseof23andMe,
individualshadtoselect‘‘NotHispanic’’and‘‘Black’’andnoother
Inc., a consumer personal genetics company. This data set has
identity.
been described in detail previously.34,35 Participants provided
The second question on identity is a single-choice question,
informedconsentandparticipatedintheresearchonline,under
where respondents were asked to choose ‘‘What best describes
a protocol approved by the external AAHRFP-accredited IRB,
your ancestry/ethnicity?’’ from ‘‘African,’’ ‘‘African American,’’
Ethical&IndependentReviewServices(E&IReview).
‘‘CentralAsian,’’‘‘Declined,’’‘‘EastAsian,’’‘‘European,’’‘‘Latino,’’
‘‘Mideast,’’‘‘Multipleancestries,’’‘‘NativeAmerican,’’‘‘Notsure,’’
Genotyping ‘‘Other,’’‘‘PacificIslander,’’‘‘SouthAsian,’’and‘‘SoutheastAsian.’’
Participants were genotyped as described previously.36 In short, Becauseindividualscouldselectonlyoneresponse,weincluded
DNAextractionandgenotypingwereperformedonsalivasamples individuals who selected‘‘European’’ in ourEuropeanAmerican
byNationalGeneticsInstitute(NGI),aCLIA-licensedclinicallab- cohort, those who selected ‘‘African American’’ in our African
oratory and a subsidiary of Laboratory Corporation of America. Americancohort,andthosewhoselected‘‘Latino’’inourLatino
Samples have been genotyped on one of four genotyping cohort.
platforms.TheV1andV2platformswerevariantsoftheIllumina SomeAfricanAmericanparticipantsincludedinthisstudywere
HumanHap550þBeadChip,includingabout25,000customSNPs recruited through 23andMe’s Roots into the Future project
selectedby23andMe,withatotalofabout560,000SNPs.TheV3 (accessedOctober2013),whichaimedtoincreaseunderstanding
platform was based on the Illumina OmniExpressþ BeadChip, ofhowDNAplaysaroleinhealthandwellness,especiallyfordis-
with customcontenttoimprovetheoverlapwith ourV2 array, easesmorecommonintheAfricanAmericancommunity.Individ-
with atotalof about950,000 SNPs.The V4platformin current ualswhoself-identifiedasAfricanAmerican,black,orAfricanwere
useisafullycustomarray,includingalowerredundancysubset recruitedthrough23andMe’scurrentmembership,atevents,and
ofV2andV3SNPswithadditionalcoverageoflower-frequency viaotherrecruitmentchannels.
codingvariationandabout570,000SNPs.Samplesthatfailedto In the present work, we do not include individuals who self-
reach98.5%callratewerereanalyzed.Individualswhoseanalyses reportashavingmultipleidentities,becausethisrepresentsonly
failedrepeatedlywererecontactedby23andMecustomerservice asmallfractionofindividualsinourdataset.Lowratesofreport-
to provide additional samples, as is done for all 23andMe ingasmultiracialormultiethnicisinlinewithpreviousstudies;an
customers. Customer genetic data have been previously utilized analysisofthe2000USCensusshowsthat95percentofblacks
inassociationstudiesandstudiesofgeneticrelationships.34–43 and 97 percent of whites acknowledge only a single identity.45
38 TheAmericanJournalofHumanGenetics96,37–53,January8,2015
Futurestudiesincludingmultiracialindividualsmightfurtherillu- weexpectthatoursurveydatarepresenthighlyreliableancestry
minatepatternsofgeneticancestryandthecomplexrelationship information, with errors affecting fewer than 1% of survey
withself-identity. responses.
Differencesamongstates,wheredifferentproportionsofpeople GeographicLocationCollection
self-reportasmixedrace,mightexplainsomeregionaldifferences Self-reported state-of-birth survey data was available for 47,473
in genetic ancestry. However, we note that, first, proportionally customers of 23andMe. However, because overlap of these cus-
fewerpeopleidentifyasmixedracethanasasingleidentity,and tomerswithourcohortswaspoor,wealsochosetoincludedata
second,itremainsimportanttoestablishregionaldifferencesin fromaquestiononcurrentzipcodeofresidence.Thisprovided
geneticancestryofself-reportedgroupsevenifthesedifferences anadditional34,351zipcodesofcurrentresidence.Incaseswhere
are driven, to some degree, by regional changes in self-reported boththezipcodeofresidenceandstateofbirthwereavailable,we
identity. More work is needed to determine to what extent usedstate-of-birthinformation.Toobtainstateinformationfrom
regionaldifferencesarearesultofhowpeopletodayreporttheir zipcodes,wetranslatedzipcodestotheirstatelocationsviaanon-
ancestry. Lastly, when available, we excluded individuals who linezipcodedatabase(accessedOctober2013).
answered‘‘No’’toaquestionwhethertheyarelivingintheUS. In total, we had 50,697 individuals with available location
In total, our final sets included 5,269 African Americans, 8,663 information.Aboutonethirdofeachofourcohortshadlocation
Latinos,and148,789EuropeanAmericans. information:1,970AfricanAmericans,2,944Latinos,and45,783
NotesonTerminologyandSelectionofPopulations EuropeanAmericanswereusedinourgeographicanalyses.
Throughoutthemanuscript,theterm‘‘NativeAmericanancestry’’
referstoestimatesofgeneticancestryfromindigenousAmericans AncestryAnalyses
foundacrossNorth,Central,andSouthAmerica,andwedistin- AncestryComposition
guishthistermfrompresent-dayNativeAmericanslivinginthe We apply Ancestry Composition, a three-step pipeline that effi-
US.Weusetheterm‘‘NativeAmerican’’torefertoindigenouspeo- ciently and accurately identifies the ancestral origin of chromo-
plesoftheAmericas,acknowledgingthatsomepeoplemayprefer somal segments in admixed individuals, which is described in
othertermssuchas‘‘AmericanIndian.’’OurestimatesofAfrican Durandetal.33Weapplythemethodtogenotypedatathathave
ancestry specifically aim to infer ancestry of sub-Saharan Africa beenphasedviaareimplementationofBeagle.46AncestryCompo-
and does not include ancestry from North Africa. We note that sition applies a string kernel support vector machines classifier
theterm‘‘Latino’’hasmanymeaningsindifferentcontexts,and to assign ancestry labels to short local phased genomic regions,
inourcase,weuseittorefertoindividualslivingintheUSwho which are processed via an autoregressive pair hidden Markov
self-reportaseither‘‘Latino’’or‘‘Hispanic.’’ model to simultaneously correct phasing errors and produce
Ourworkrepresentsasnapshotintimeofgeneticancestryand reconciled local ancestry estimates and confidence scores based
identity,andfutureworkisneededtoinformthedynamicchanges on the initialassignment. Lastly, these confidenceestimates are
andforcesthatshapesocialinteractions. recalibrated by isotonic regression models. This results in both
We note that our cohorts are likely to have ancestry from precision and recall estimates that are greater than 0.90 across
many African populations, but because of current reference many populations, and on a continental level, have rates of
sample availability, our resolution of West African ancestries is 0.982–0.994forprecisionandrecallratesof0.935–0.993,depend-
outside the scope of our study. Likewise, our estimates of ing on populations (see Table 1 from Durand et al.33). We note
Native American ancestry arise from a summary over many thathere,andthroughoutthemanuscript,Africanancestrycorre-
distinct subpopulations, but we are limited in scope because of spondstosub-SaharanAfricanancestry(includingWestAfrican,
insufficient sample sizes from subpopulations, so we currently East African, Central, and South African populations, but
use individuals from Central and South American together as a excludingNorthAfricanpopulationsfromthereferenceset).For
reference set (see Durand et al.33 for a list of populations and more details on our ancestry estimation method, see Durand
samplesizes). etal.33
ValidationofSelf-ReportedIdentitySurveyResults AggregatingLocalAncestryInformation
Toverifythatourself-reportedethnicitieswerereliable,weexam- 23andMe’s Ancestry Composition methodprovides estimates of
inedtheconsistencyofethnicitysurveyresponseswhenindivid- ancestry proportions for several worldwide populations at each
ualscompletedbothancestryandethnicitysurveys.Becausethe windowof thegenome.To estimategenome-wide ancestry pro-
structure of the two surveys is different and multiple selections portionsofEuropean,African,andNativeAmericanancestry,we
wereallowedinonesurveybutnottheother,weexaminedthe aggregate over populations to estimate the total likelihood of
replication rate of the primary ethnicity from the single-choice eachpopulation,andwithamajoritythresholdof0.51,ifanywin-
ethnicitysurveyinthemultiple-selectionsurvey. dowhasamajorityofacontinentalancestry,weincludeitinthe
In addition to structural differences, the survey content used calculation of genome-wide ancestry, which is estimated as the
very different nomenclature, and therefore we believe our esti- numberofwindowspassingthethresholdforeachancestryover
matederrorratestobeoverestimatesofthetrueerrorrate,because the total number of windows. Some windows might not pass
itislikelythatsomeindividualschoosetoidentifywithonelabel our threshold for any population, so they remain unassigned,
butnottheother(i.e.,‘‘AfricanAmerican’’butnot‘‘black’’).Dis- making it possible for estimates for all ancestries to not sum to
crepancies in the question nomenclatures are likely to increase 100%, resulting in population averages that likewise might not
the error rate. Furthermore, because the two surveys could be sum to 100%. We allow for this unspecified ancestry to reduce
completedatdifferenttimes,eitherbeforeorafterobtainingper- theerrorratesofourassignments,so,insomesense,ourestimates
sonalancestryresults,itispossiblethatviewinggeneticancestry mightbeviewedaslowerboundsonancestry,anditispossible
resultsmighthaveledtoachangeinself-reportedancestry.Such thatindividualscarrymoreancestrythanestimated.Inpractice,
achangewouldbetalliedasanerrorinourestimates,butinstead wetypicallyassignnearlyallwindows,withanaverageofabout
reflectsatruechangeinperceivedself-identityovertime.Overall, 1%–2%unassignedancestry,sowedonotexpectittoaffectour
TheAmericanJournalofHumanGenetics96,37–53,January8,2015 39
results,withtheexceptionofNativeAmericanancestry,whichwe 74.8%, of the mean proportion of African ancestry in African
discussbelow. Americans.
GeneratingtheDistributionofAncestryTracts ToquantifydifferencesinAfricanancestrydrivingmeanstate
Wegenerateancestrysegmentsasdefinedascontinuousblocksof differences,weexaminedthedistributionsofestimatesofAfrican
ancestry,estimatingthebestguessofancestryateachwindowto ancestry in African Americans from the District of Columbia
define segments of each ancestry. Assigning the most likely (D.C.) and Georgia, which had at least 50 individuals with the
ancestryateachwindowresultsinfewerspuriousancestrybreaks lowest and highest mean African ancestry proportions
andallowsforasmallerupwardbiasinadmixturedates,because (FigureS1E).We finda qualitativeshiftin thetwo distributions
breaksinancestrysegmentspushestimatesofdatesfurtherback of African ancestry, with D.C. showing a reduced mode, higher
intime.Wemeasuresegmentlengthsbyusinggeneticdistances, variance,andaheavierlowertailofAfricanancestry,correspond-
by mapping segment start and end physical positions to the ingtomoreAfricanAmericanswithbelow-averageancestrythan
HapMapgeneticmap. Georgia. Qualitative differences in the distributions of African
AdmixtureDating ancestryproportionsinAfricanAmericansfromstateswithhigher
Toestimatethetimeframeofadmixtureevents,wetestasimple andlowermeanancestryappeartobedrivenbybothashiftinthe
two-event,three-populationadmixturemodelviaTRACTS.47We mode of the distribution as well as a heavier left tail reflecting
use a grid-search optimization to find four optimal parameters moreindividualswithaminorityofAfricanancestry(FigureS1).
for the times of two admixture events and the proportions of Wepositthatdifferencesamongstatescouldbeduetodifferences
admixture.Wearelimitedtosimpleadmixturemodelsresulting inadmixture,differencesinself-identity,ordifferencesinpatterns
fromthecomputationallyintensivegridsearch,becausewewere ofassortativemating,wherebyindividualswithsimilarancestry
unabletoobtainlikelihoodconvergencewithanyofthebuilt-in mightpreferentially mate. For example, greater levels of admix-
optimizers.Themodeltestedisasfollows:twopopulationsadmix ture with Europeans would both shift the mode and result in
t1 generationsago, with proportion frac1 and 1 (cid:2) frac1, respec- moreAfricanAmericanindividualswhohaveaminorityofAfri-
tively.Athirdpopulationlatermixesint2generationsago,with canancestry.Alternatively,ashifttowardAfricanAmericanself-
proportionfrac2. identity for individuals with a majority of European ancestry
Bothourancestrysegmentsandpriorresultssupportedamodel (possibly because of changes in cultural or social forces) would
withanearlierdateofNativeAmericanadmixture.25,47 Weesti- likewiseresultinlowerestimatesofmeanAfricanancestry.Lastly,
matedlikelihoodsoverplausiblegridofadmixturetimesandfrac- assortativematingwouldworktomaintainorincreasethevari-
tionsforAfricanAmericans,Latinos,andEuropeanAmericansto ance in ancestry proportions, though assortative mating alone
estimatedatesofinitialNativeAmericanandEuropeanadmixture could not shift the mean proportion of African ancestry in a
and subsequentAfricanadmixture.Thesedates areestimatedas population.
the best fit for a pulse admixture event: because they represent SexBiasinAncestryContributions
anaverageover morecontinuousor multiple migrations, initial Sexbiasinancestrycontributions,oftenassessedthroughancestry
admixtureislikelytohavebegunearlier. ofmtDNAandYchromosomehaplogroups,isalsomanifestedin
LowerEstimatesofAfricanAncestryin23andMeAfricanAmericans unequalestimatesofancestryproportionsontheXchromosome,
Unlike previous estimates of the mean proportion of African whichhasaninheritancepatternthatdiffersbetweenmalesand
ancestry,whichtypicallyhaverangedfrom77%to93%African females.TheXchromosomemorecloselyfollowsfemaleancestry
ancestry,2–4,48–62 our estimates, depending on exclusions, are contributionsbecausemalescontributehalfasmanyXchromo-
73%or75%.Thereareseveralpossibleexplanationsforourlow somes. Comparing ancestry on the X chromosome to the auto-
mean African ancestry. If our Ancestry Composition estimates somalancestryallowsustoinferwhetherthatancestryhistorically
are downward biased, then the African Americans might have entered via males (lower X ancestry) or by females (higher X
levelsofAfricanancestryconsistentwithotherstudies,andourre- ancestry). Under equal ancestral contributions from both males
sultsaresimplyunderestimates.However,ourAncestryComposi- andfemales,theXchromosomeshouldshowthesamelevelsof
tionestimatesareextremelywellcalibratedforAfricanAmericans admixtureasthegenome-wideestimates.Tolookforevidenceof
from the 1000 Genomes Project and their consensus estimates, unequalmaleandfemaleancestrycontributionsinourcohorts,
and we see no evidence of a downward bias (see Figure 5 from weexaminedancestryontheXchromosome(NRYregion),which
Durandetal.33). follows a different pattern of inheritance from the autosomes.
Themeanancestryproportionof23andMeself-reportedAfrican In particular, estimates of ancestry on the X chromosome have
Americans is about 73%. A small fraction, about 2%, of African been shown to have higher African ancestry in African Ameri-
Americans carry less than 2% African ancestry, which is far less cans.9WecalculateancestryontheXchromosomeastheestimate
thantypicallyseeninmostAfricanAmericans(FigureS18Aavail- ofancestryonjustwindowsontheX,andwecomparetogenome-
able online). Further investigation reveals that the majority of wideestimates(whichdothemselvesincludetheXchromosome).
these individuals (88%)have predominantlyEuropeanancestry, Itshouldbenotedthatthesecalculationsdifferamongmalesand
and others carry East Asian, South Asian, and Southeast Asian females,becausetheXchromosomeisdiploidinfemalesandthus
ancestry, roughly in proportion to the frequencies found in hastwiceasmanywindowsincalculationofgenome-widemean
the 23andMe database overall. Given the large number of non- proportions. However, our results still allow a peek into sex
AfricanAmericanindividualsinthe23andMedatabase,evenan bias because the overall contribution of the X chromosome to
exceedinglowsurveyerrorrateof0.02%couldbesufficienttoac- the genome-wide estimates is small. We note that because our
countforthenumberofoutlierindividualswedetect.Hence,we ancestryestimationmethodconservativelyassignsNativeAmer-
posit that these individuals represent survey errors rather than icanancestry,weexpectthatmuchoftheremainingunassigned
trueself-reportedAfricanAmericans.Exclusionofthese108self- ancestry might be due to Native American ancestry assigned as
reported African Americans with less than 2% African ancestry broadly East Asian/Native American, which is not included in
from mean ancestry calculations results in a moderate rise, to thesevalues(seeFigure5inDurandetal.33).
40 TheAmericanJournalofHumanGenetics96,37–53,January8,2015
Toinferestimatesofmaleandfemalecontributionsfromeach age,predictingself-reportedancestrybyusingproportionAfrican
ancestralpopulation,weestimatedthemaleandfemalefractions ancestry,sex,age,intercept,andinteractionvariables.
of ancestry that total the genome-wide estimates and minimize
themeansquareerroroftheXchromosomeancestryestimates.
We assume that overall male and female contributions are each ValidationofNon-EuropeanAncestryinAfrican
P P
50% ( popfpop;male¼0:5 and popfpop;female¼0:5). We assume AmericansandEuropeanAmericans
thatthetotalcontributionfrommalesandfemalesofapopulation AlthoughourAncestryCompositionestimatesarewellcalibrated
givesrisetotheautosomalancestryfraction(fpop,maleþfpop,female¼ and have been shown to accurately estimate African, European,
autopop). We then compute, via a grid search, the predicted and Native American ancestry in tests of precision and recall,33
X chromosome estimates from fpop,male, fpop,female for each we wereconcernedthat low levelsof non-Europeanancestry in
pop˛fAfrican;NativeAmerican;Europeang, which are calculated, as EuropeanAmericansthatwedetectedmightrepresentanartifact
inLindetal.,6as of Ancestry Composition. Hence, we pursued several lines of
Xbpop¼fpop0;m:5ale,1þþ2,0f:p5op,;f2emale¼fpop;maleþ12:5,fpop;female iNnavteivsteigAamtioenrictaonparnocveisdteryevinidEeunrcoeptehaantAemstiemricaatenssoafreArforibcuasntaanndd
notartifacts.
Wechoosetheparametersofmaleandfemalecontributionsthat Comparisonwith1000GenomesProjectConsensusEstimates
minimizethemeansquarederroroftheXancestryestimatesand Comparisonsofourestimateswiththosepublishedbythe1000
the predicted Xbpop. These are the estimates of male and female GenomesConsortiumshowthehighconsistencyacrosspopula-
ancestry fractions under a single simplistic population mixture tionsandindividuals.WecompareestimatesacrossAmericansof
eventthatbestfitourXchromosomeancestryestimatesobserved. AfricanAncestryinSWUSA(ASW),ColombiansfromMedellin,
PopulationSizeCorrelations Colombia (CLM), Mexican Ancestry from Los Angeles USA
Fromthe2010CensusBrief‘‘TheBlackPopulation’’availableon- (MXL),andPuertoRicansfromPuertoRico(PUR).Wenotethat
line,wecalculatedthecorrelationbetweenthenumberofreported our estimates of Native American ancestry are conservative.
African Americans living in a state and our sample of African Indeed,whenourAncestryCompositionassignmentprobabilities
Americansfromthatstate.Thecorrelationisstrong,withpvalue do not pass over the confidence threshold, including signals of
of9.5310(cid:2)14,suggestingthatourlowsamplesizesfromstatesin NativeAmericanancestrytogetherwithgeneralEastAsian/Native
theUSMountainWestisexpectedfromestimatesofpopulation American ancestry (but not East Asian) recapitulates estimates
sizes. fromthe1000GenomesProjectconsensusestimates.Fiveindivid-
AfricanancestryinEuropeanAmericansmostfrequentlyoccurs uals from the ASW population from the 1000 Genomes Project
inindividualsfromstateswithhighproportionsofAfricanAmer- havepoorconsistencyintheirestimates.Theseindividualshave
icansandisrareinstateswithfewAfricanAmericans.Thisobser- alargeamountofNativeAmericanancestrythatwasnotmodeled
vationledustolookatthecorrelationbetweenpopulationsize(as bythe1000GenomesProjectestimates.Thattheseparticularindi-
apercentofstatepopulationusingself-reportedethnicityfromthe vidualsweresampledinOklahoma,andcarrysignificantNative
2010USCensus)andstatemeanlevelsofancestry. American ancestry, is supported by our own high estimates of
Toexaminetheinteractionbetweenproportionsofminorities NativeAmericanancestryin23andMeself-reportedAfricanAmer-
and ancestry, we used the 2010 US Census demographic survey icansfromOklahoma.
by state. We compare the state population proportion to the EstimatesofAfricanandNativeAmericanAncestryinEuropeans
mean estimated admixture proportion of individuals from that We looked at whether all individuals who are expected to carry
state, fitting linear regressions, and generating figures with solely European ancestry also have similar rates of detection of
geom_smooth(method¼‘‘lm,’’formula¼y~x)fromtheggplot2 non-European ancestry. To this end, we generated a cohort of
packageinR. 15,289customersof23andMewhoreportedthatallfouroftheir
WefindthatAfricanancestryinEuropeanAmericansisstrongly grandparentswereborn inthesameEuropeancountry. The use
correlatedwiththepopulationproportionofAfricanAmericansin offour-grandparentbirth-countryhasbeenutilizedasaproxyfor
eachstate.WefindthatthehigherthestateproportionofAfrican assessingancestry.27,63WethenexaminedAncestryComposition
Americans,themoreAfricanancestryisfoundinEuropeanAmer- resultsfortheseindividualsandcalculatedatwhatratewedetected
icansfromthatstate,reflectingthecomplexinteractionofgenetic atleast1%Africanandatleast1%NativeAmericanancestry.
ancestry,historicaladmixture,culture,andself-identifiedancestry. IndependentValidationofAfricanAncestryinEuropeanAmericansviaf4
LogisticRegressionModelingofSelf-Identity Statistics
We examine the probabilistic relationship between self-identity Weusedf4statisticsfromtheADMIXTOOLSsoftwarepackageto
and genetically inferred ancestry. To explore the interaction be- confirmthepresenceofAfricanancestry.64Weusedthef4ratio
tween genetic ancestry and self-reported identity, we estimated test, designed to estimate the proportion of admixture from a
the proportion of individuals that identify as African American relatedancestralpopulation,tocompareadmixtureinEuropean
andEuropeanAmerican,partitionedbylevelsofAfricanancestry. Americans versus reference European individuals. We tested
JointlyconsideringthecohortsofEuropeanAmericansandAfri- whether European Americans with estimated African ancestry
canAmericans,weexaminedtherelationshipbetweenanindivid- showedanyadmixturefromAfricansbyusingourcohortsofindi-
ual’sgenome-wideAfricanancestryproportionandwhetherthey vidualswithestimatedAfricanancestryandreferencepopulations
self-reportasEuropeanAmericanorAfricanAmerican.Wenotea from the 1000 Genomes Project data set. Admixture would be
strongdependenceontheamountofAfricanancestry,withindi- expectedtoresultinestimatesofasignificantlydifferentfrom1.
vidualscarryinglessthan20%Africanancestryidentifyinglargely Detection of Native American mtDNA in European Americans and
asEuropeanAmerican,andthosewithgreaterthan50%reporting AfricanAmericans
asAfricanAmerican.Totestthesignificanceofthisrelationship, ThemitochondrialDNA(mtDNA)haplogroupsA2,B2,B4b,C1b,
wefitalogisticregressionmodel,usingPython’sstatsmodelspack- C1c,C1d,andD1aremostprevalentlyfoundintheAmericasand
TheAmericanJournalofHumanGenetics96,37–53,January8,2015 41
ican,EastAsian,sub-SaharanAfrican,MiddleEastern,andOcean-
Table1. ComparisonofGenome-wideAncestryEstimatesandX
ChromosomeEstimatesinAfricanAmericans,Latinos,and ianancestryproportions.WeusethesupervisedalgorithmforK¼
EuropeanAmericans 6,with9,694referenceindividualsrepresentingthesixaforemen-
Ancestry tionedpopulations. WeranADMIXTUREon269,229 autosomal
markers after pruning SNPs to have r2 < 0.5, via PLINK.67 To
Estimate African NativeAmerican European
reducecomputationtime,weexaminedconsistencyofmethods
AfricanAmericans on the African Americans whom we estimated to have at least
1%NativeAmericanancestry,EuropeanAmericansestimatedto
Genome-wide 73.2% 0.8% 24.0%
haveatleast1%NativeAmericanancestry,andEuropeanAmeri-
Xchromosome 76.9% 0.9% 19.8% cansestimatedtohaveatleast1%Africanancestry.
Relativeincrease þ5.1% þ13.6% (cid:2)17.7%
ordecreaseonX
Results
pvalue 4.4310(cid:2)17*** 0.078 7.8310(cid:2)24***
Latinos
Self-reported survey data was used to generate cohorts
Genome-wide 6.2% 18.0% 65.1% of African Americans, Latinos, and European Americans.
Out of 35,524 self-reported ‘‘European’’ individuals,
Xchromosome 6.8% 19.4% 56.7%
35,279 selected ‘‘white’’ on the ethnicity survey, yielding
Relativeincrease þ9.0% þ7.4% (cid:2)13.0% a per-survey error estimate of 0.2%. Out of 1,560 self-re-
ordecreaseonX
ported ‘‘Latino’’ individuals, 1,540 selected ‘‘Hispanic,’’
pvalue 0.008** 2.4310(cid:2)10*** 4.2310(cid:2)94*** giving a per-survey error estimate of 0.7%. Lastly, out of
EuropeanAmericans 1,327 self-reported ‘‘African American’’ individuals, 1,287
selected ‘‘black,’’ resulting in a per-survey error rate esti-
Genome-wide 0.19% 0.18% 98.6%
mateof1.1%.Formoredetailsonourcross-surveyvalida-
Xchromosome 0.19% 0.22% 98.4%
tion,seeSubjectsandMethods.
Relativeincrease (cid:2)0.04% þ23.73% (cid:2)0.1%
ordecreaseonX
TheGeneticLandscapeoftheUS
pvalue 0.99 6.6310(cid:2)10*** 8.0310(cid:2)5***
PatternsofGeneticAncestryofSelf-ReportedAfricanAmericans
MeanestimatesofAfrican,NativeAmerican,andEuropeanancestryareshown. Genome-wide ancestry estimates of African Americans
pvaluesprovidedarecalculatedbytwo-sidedStudent’sttestonindividual show average proportions of 73.2% African, 24.0% Euro-
ancestry estimates for each cohort per ancestry, with no multiple testing
correction. Significance is assigned as *p < 0.05, **p value < 0.01, and pean, and 0.8% Native American ancestry (Table 1). We
***p value < 0.001. Relative increase on the X chromosome is calculated find systematic differences across states in the US in
as the absolute difference, X chromosome estimate minus genome-wide
meanancestryproportionsofself-reportedAfricanAmeri-
estimate,dividedbythegenome-wideestimate.
cans(Figure1andTableS2).Onaverage,thehighestlevels
ofAfrican ancestryarefound inAfrican Americans living
arelikelytobeNative-American-specifichaplogroupsbecausethey in or born in the South, especially South Carolina and
arerarelyfoundoutsideoftheAmericas.Weassessedthefraction Georgia (Figure 1Aand Table S3). We find lower propor-
ofindividualsthatcarrythesehaplogroupstovalidatethelikeli- tions of African ancestry in the Northeast, the Midwest,
hood of Native American ancestry in European Americans and the Pacific Northwest, and California. The amount of
AfricanAmericansandshowthatthesehaplogroupsarevirtually
NativeAmericanancestryestimatedforAfricanAmericans
absentinEuropeancontrols.BecausemtDNAhaplogroupsareas-
alsovariesacrossstatesintheUS.Morethan5%ofAfrican
signedbyclassificationwithSNPsthatsegregateontheselineages,
Americansareestimatedtocarryatleast2%NativeAmer-
theseorthogonalresultsprovideanindependentlineofsupport
ican ancestry genome-wide (Figures S1 and 1D). African
for ourestimated NativeAmericanancestry in European Ameri-
Americans in the West and Southwest on average carry
cansandAfricanAmericans.
DistributionofAncestrySegmentStartPositions higher levels of Native American ancestry, a trend that is
Regions of the genome that have structural variation or show largely driven by individuals with less than 2% Native
strong linkage disequilibrium (LD) have been shown both to Americanancestry (Figure 1B). With a lower threshold of
confoundadmixturemappingandtoinfluencethedetectionof 1% Native American ancestry, we estimate that about
population substructure in studies using Principal Components 22% of African Americans carry some Native American
Analysis (PCA).27,63,65 If such regions were to drive artifacts of ancestry(FigureS2).
spuriousancestry,wewouldexpectthatsegmentsoflocalancestry
We used the lengths of segments of European, African,
wouldprobablyoccuraroundtheseregions,ratherthaninauni-
andNativeAmericanancestrytoestimateabest-fitmodel
form distribution acrossthe genome. To this end, we examined
ofadmixturehistoryamongthesepopulationsforAfrican
thestartingpositionsofallAfricanandNativeAmericanancestry
Americans(FigureS3).Weestimate that initialadmixture
segmentsinEuropeanAmericansandNativeAmericanancestryin
between Europeans and Native Americans occurred 12
AfricanAmericans.
ComparisonwithADMIXTUREGenome-wideEstimates generations ago, followed by subsequent African admix-
WeappliedADMIXTURE,66amodel-basedestimationofancestry ture 6 generations ago, consistent with other admixture
proportions, to estimate proportions of European, Native Amer- inferencemethodsdatingAfricanAmericanadmixture.A
42 TheAmericanJournalofHumanGenetics96,37–53,January8,2015
A B
Mean
Mean
Native
African
American
ancestry
ancestry
0.80 0.0100
0.0075
0.75
0.0050
0.70
0.0025
0.65
0.0000
C D
Self−reported African Americans
with > 2% Native American ancestry
Mean
European Percent of
ancestry African
Americans
0.30
0.25 10
0.20
5
0.15
0
Figure1. TheDistributionofAncestryofSelf-ReportedAfricanAmericansacrosstheUS
(A)DifferencesinlevelsofAfricanancestryinAfricanAmericans(blue).
(B)DifferencesinlevelsofNativeAmericanancestryinAfricanAmericans(orange).
(C)DifferencesinlevelsofEuropeanancestryofAfricanAmericans(red),fromeachstate.Stateswithfewerthantenindividualsare
excludedingray.
(D)Thegeographicdistributionofself-reportedAfricanAmericanswithNativeAmericanancestry.TheproportionofAfricanAmericans
ineachstatewhohave2%ormoreNativeAmericanancestryisshownbyshadeofgreen.Stateswithfewerthan20individualsare
excludedingray.
sex bias in African American ancestry, with greater male highest mean levels of African ancestry in Latinos living
EuropeanandfemaleAfricancontributions,hasbeensug- in or born in states in the South, especially Louisiana,
gested through mtDNA, Y chromosome, and autosomal the Midwest, and Atlantic (Figure 2A). Further stratifica-
studies.6 On average, across African Americans, we esti- tion of individuals by their self-reported population
matethattheXchromosomehasa5%increaseinAfrican affiliation (e.g., ‘‘Mexican,’’ ‘‘Puerto Rican,’’ or ‘‘Domin-
ancestryand18%reductioninEuropeanancestryrelative ican’’) reveals a diversity in genetic ancestry, consistent
togenome-wideestimates(seeTable1).Throughcompar- with previous work studying these populations (see
ison of estimates of X chromosome and genome-wide FigureS5andTableS5).10,20,24,25,68,69WefindthatLatinos
African and European ancestry proportions, we estimate who, besides reporting as ‘‘Hispanic,’’ also self-report as
that approximately 5% ofancestors of African Americans MexicanorCentralAmerican,carrymoreNativeAmerican
were European females and 19% were European males ancestrythanLatinosoverall;thosealsowhoself-reportas
(TableS4). black, Puerto Rican, or Dominican have higher levels of
PatternsofGeneticAncestryofSelf-ReportedLatinos African ancestry; and those who additionally self-report
LatinosencompassnearlyallpossiblecombinationsofAf- as white, Cuban, or South American have on average
rican,NativeAmerican,andEuropeanancestries,withthe higherlevelsofEuropeanancestry.
exception of individuals who have a mix of African and Admixture date estimates for Latino admixture suggest
NativeAmericanancestrywithoutEuropeanancestry(see thatNativeAmericanandEuropeanmixtureoccurredfirst,
FiguresS4AandS1).Onaverage,weestimatethatLatinos about11generationsago,followedbyAfricanadmixture7
in the US carry 18.0% Native American ancestry, 65.1% generations ago. Consistent with previous studies that
European ancestry, and 6.2% African ancestry. We find show a sex bias in admixture in Latino populations,12–18
the highest levels of estimated Native American ancestry weestimate13%lessEuropeanancestryontheXchromo-
inself-reportedLatinosfromstatesintheSouthwest,espe- somethangenome-wide(Table1),showingproportionally
cially those bordering Mexico (Figure 2C). We find the greater European ancestry contributions from males. We
TheAmericanJournalofHumanGenetics96,37–53,January8,2015 43
A B
Mean Mean
African European
ancestry ancestry
0.20
0.85
0.15 0.80
0.10 0.75
0.70
0.05
0.65
C
Mean
Native
American
ancestry
0.20
0.15
0.10
0.05
Figure2. TheDistributionofAncestryofSelf-ReportedLatinosacrosstheUS
DifferencesinmeanlevelsofAfrican(A),European(B),andNativeAmerican(C)ancestryinLatinosfromeachstateisshownbyshadeof
blue,red,andorange,respectively.Stateswithfewerthantenindividualsareexcludedingray.
inferred elevated African and Native American ancestry instatesintheSouththaninotherpartsoftheUS:about5%
on the X chromosome, corresponding to higher female of self-reported European Americans living in South Car-
ancestry contributions from both Africans and Native olina and Louisiana have at least 2% African ancestry.
Americans. Lastly, Latinos show higher proportions of Lowering the threshold to at least 1% African ancestry
inferred Iberian ancestry than both European Americans (potentiallyarisingfromoneAfricangenealogicalancestor
andAfricanAmericans(FigureS6). withinthelast11generations),EuropeanAmericanswith
Patterns of Genetic Ancestry of Self-Reported European African ancestry comprise as much as 12% of European
Americans Americans from Louisiana and South Carolina and about
Wefindthatmanyself-reportedEuropeanAmericans,pre- 1in10individualsinotherpartsoftheSouth(FigureS8).
dominantlythoselivingwestoftheMississippiRiver,carry Mostindividualswhohavelessthan28%Africanancestry
NativeAmericanancestry(Figure3B).WeestimatethatEu- identifyasEuropeanAmerican,ratherthanasAfricanAmer-
ropeanAmericanswhocarryatleast2%NativeAmerican ican(Figures4and5A).Logisticregressionofself-identified
ancestry are found most frequently in Louisiana, North European Americans and African Americans reveals that
Dakota,andotherstatesintheWest.Usingalessstringent the proportion of African ancestry predicts self-reported
thresholdof1%,ourestimatessuggestthatasmanyas8% ancestry significantly, with a coefficient of 20.1 (95% CI:
of individuals from Louisiana and upward of 3% of indi- 18.0–22.2)(TableS6andFigureS9).Forafullcharacteriza-
vidualsfromsomestatesintheWestandSouthwestcarry tionoftermsandlogisticmodels,seeTableS6andFigureS9.
NativeAmericanancestry(FigureS7). Fitting a model of European and Native American
Consistent with previous anecdotal results,32 the fre- admixture followed later by African admixture, we find
quencyofEuropeanAmericanindividualswhocarryAfri- the best fit with initial Native American and European
canancestryvariesstronglybystateandregionoftheUS admixtureabout12generationsagoandsubsequentAfri-
(Figure3A).Weestimatethatasubstantialfraction,atleast cangeneflowabout4generationsago.
1.4%,ofself-reportedEuropeanAmericansintheUScarry Non-EuropeanancestryinEuropeanAmericansfollowsa
at least 2% African ancestry. Using a less conservative sexbiasinadmixturecontributionsfrommalesandfemales,
threshold, approximately 3.5% of European Americans asseeninAfricanAmericansandLatinos.Theratiobetween
have1%ormoreAfricanancestry(FigureS8).Individuals Xchromosomeandgenome-wideNativeAmericanancestry
withAfricanancestryarefoundatmuchhigherfrequencies estimates in European Americans shows greater Native
44 TheAmericanJournalofHumanGenetics96,37–53,January8,2015