HUMAN EVOLUTION

Ancient human parallel lineageswithin North America contributedto a coastal expansionC. L. Scheib,1,2* Hongjie Li,3 Tariq Desai,4 Vivian Link,5 Christopher Kendall,6

Genevieve Dewar,6 Peter William Griffith,1 Alexander Mörseburg,1 John R. Johnson,7

Amiee Potter,8,9 Susan L. Kerr,10 Phillip Endicott,11 John Lindo,12 Marc Haber,13

Yali Xue,13 Chris Tyler-Smith,13 Manjinder S. Sandhu,13 Joseph G. Lorenz,14

Tori D. Randall,15 Zuzana Faltyskova,1 Luca Pagani,2,16 Petr Danecek,13

Tamsin C. O’Connell,1 Patricia Martz,17 Alan S. Boraas,18 Brian F. Byrd,19

Alan Leventhal,20,21 Rosemary Cambra,20 Ronald Williamson,22 Louis Lesage,23

Brian Holguin,24 Ernestine Ygnacio-De Soto,25 JohnTommy Rosas,26

Mait Metspalu,2 Jay T. Stock,1,27 Andrea Manica,28 Aylwyn Scally,4

Daniel Wegmann,5 Ripan S. Malhi,3* Toomas Kivisild1,2*

Little is known regarding the first people to enter the Americas and their genetic legacy.Genomic analysis of the oldest human remains from the Americas showed a directrelationship between a Clovis-related ancestral population and all modern Central andSouth Americans as well as a deep split separating them from North Americans in Canada.We present 91 ancient human genomes from California and Southwestern Ontario anddemonstrate the existence of two distinct ancestries in North America, which possibly splitsouth of the ice sheets. A contribution from both of these ancestral populations is found inall modern Central and South Americans. The proportions of these two ancestries inancient and modern populations are consistent with a coastal dispersal and multipleadmixture events.

An increasing body of archaeological (1–3)evidence shows that the initial peoplingof the Americas occurred at least a fewthousand years prior to the spread of theClovis cultural complex ~13,000 years ago

(all dates are calibrated) (4), with a majorityof well-supported Pre-Clovis sites clustered incoastal areas and around glacial edges (1, 3, 5).Studies of ancient and modern genomes haveuncovered four distinct ancestry componentswithin the Americas arriving in three hypothe-sizedwaves: themost recent Thule-relatedNeo-Eskimo ~2000 years ago, the Saqqaq/DorsetPaleo-Eskimo ~4500 years ago (both restrictedto the Arctic region), and a “First American” dis-persal prior to 13,000 years ago that split withinNorth America into a northern and a southernbranch (6–10). The northern branch is ancestralto populations including Algonquian, Na-Dené,Salishan, and Tsimshian speakers from Canada(NAM), whereas the southern branch includesthe ancestors of the Clovis individual (Anzick-1)

and allMexicans, Central Americans (CAM), andSouthAmericans (SAM) (9–12).Within the south-ern branch there is some localized evidence ofearly population structure, as a few modernAmazonian populations show an excess genet-ic affinity to Australasians (13, 14). The secondoldest North American genome, The Ancient One(Kennewick Man, 8700 to 8400 years ago), islikely to have derived from the ancestral north-ern branch but is a poor proxy for modeling thisancestry, given its low sequencing depth (10).Here, we investigated the ancestral relation-

ship between the northern (NAM) and southern(Mexico, CAM, and SAM)branch populations. Todo so, we sequenced 91 ancient whole genomesfromNorthAmerica,mainly from two geograph-ic areas: the California Channel Islands in thewestand Southwestern Ontario in the east, nearmod-ern Algonquian-speaking populations (Fig. 1Aand table S1) (15). Both of these areas show ev-idence of occupation from at least 13,000 yearsago (5, 16) and are geographically located south

of the known distribution of the ancient Neo- andPaleo-Eskimo dispersals (6). We radiocarbon-dated 27 individuals (table S2) (15) to between~4800 and ~200 years ago and sequenced allgenomes to an average depth of 0.007 to 13.6×(tables S1, S3, and S4) (15). Mitochondrial DNA(mtDNA) haplotypes were recovered from allsamples (tables S1 and S5) (15) andY chromosomehaplotypes from 34 of the male individuals (fig.S1 and data S1) (15). In addition, a set of mod-ern whole mitochondrial genomes (n = 45)were resequenced from a previous study to ex-plore sex-specific migration patterns on the westcoast of Southern California (tables S3 and S5)(15, 17).All ancient Native American individuals

clustered with modern Native Americans on aworldwide principal components analysis (PCA)(Fig. 1B) (15, 18). In a regional plot that includesSiberians, the northern and southern branchesshow clear distinction (Fig. 1B, inset). AncientCalifornians cluster alongside southern branchpopulations near to Anzick-1, whereas the an-cient Southwestern Ontario (ASO) populationclusters with modern Algonquian speaking pop-ulations and The Ancient One (Fig. 1B). Modernand ancient Athabaskans map between ASOand Northeast Siberian populations (Chukchi/Koryak) (Fig. 1B). The Upper Sun River individ-uals (USR1 and USR2) map near to Shuká Káa,between Central Siberians and the northernbranch populations (Fig. 1B).Both PCA and ADMIXTURE (19) analysis of

the ancient genomes within the context of aworldwide panel (Fig. 1, B and C, fig. S2, anddata S2) (15) indicate that, relative to the ASO,extant NAM as well as ancient Pacific NorthwestCoast (PNWC) and ancient Northern Athabas-kans have up to 50%moreArctic-related ancestry,prominent in Greenland Inuits and also found inSiberian Eskimos (Fig. 1C) (15). These differencesare further confirmed by significant Z (Z > 3)scores forD-statisticsD(Mbuti,SiberianPop;Mixe,TestPop) (20) and f3-statistics f(ASO,TestPop;Mbuti) (21, 22) (table S6 and data S3) (15). Wefound no significant evidence of gene flow intothe ASO from any non-American population(table S7 and data S3) (15).All ancient Californian genomes clustered to-

gether with southern branch (Anzick-1, Mexico,CAM, SAM) populations on the regional PCA(Fig. 1B) (15). As suggested by the archaeologicaland osteological evidence (23–25), radiocarbon-dated individuals from San Nicolas Island fromearly (ESN) and late (LSN) periods (Fig. 1D)

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1Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK. 2Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. 3Department of Anthropologyand Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. 4Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.5Department of Biology, Université de Fribourg, Fribourg, Switzerland. 6Department of Anthropology, University of Toronto, Toronto, Ontario M5S 2S2, Canada. 7Santa Barbara Museum of NaturalHistory, Santa Barbara, CA 93105, USA. 8Department of Anthropology, Portland State University, Portland, OR 97232, USA. 9Knight Diagnostics Laboratory, Oregon Health & Science University,Portland, OR 97239, USA. 10Department of Anthropology, Modesto Junior College, Modesto, CA 95350, USA. 11Department Hommes Natures Societies, Musée de l’Homme, Paris 75016, France.12Department of Anthropology, Emory University, Atlanta, GA 30322, USA. 13Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. 14Department of Anthropology andMuseum Studies, Central Washington University, Ellensburg, WA 98926, USA. 15Department of Anthropology, San Diego City College, San Diego, CA 92101, USA. 16APE Lab, Department ofBiology, University of Padova, Padova, Italy. 17Department of Anthropology, California State University, Los Angeles, CA 90032, USA. 18Kenai Peninsula College, Soldotna, AK 99669, USA. 19FarWestern Anthropological Research Group Inc., Davis, CA 95618, USA. 20Muwekma Ohlone Tribe of the San Francisco Bay Area, P.O. Box 360791, Milpitas, CA 95036, USA. 21Department ofAnthropology, San Jose State University, San Jose, CA 95192, USA. 22Archaeological Services Inc., Toronto, Canada. 23Huron-Wendat Nation, Canada. 24Department of Anthropology, Universityof California, Los Angeles, CA 90095, USA. 25Barbareño Chumash, California Indian Advisory Committee, Santa Barbara Museum of Natural History, Santa Barbara, CA 93105, USA. 26TongvaNation, CA, USA. 27Department of Anthropology, University of Western Ontario, London, Ontario N6A 3K7, Canada. 28Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.*Corresponding author. Email: cls83@ut.ee (C.L.S.); tk331@cam.ac.uk (T.K.); malhi@illinois.edu (R.S.M.)

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clustered into two distinct genetic populationsin both the autosomal and uniparental markerswith evidence of 11% autosomal continuity be-tween the early and late populations (Fig. 1E) (15).The genome-wide diversity estimates (26) of the

earliest-dated LSN individuals are greater thanthose of the ESN individuals (fig. S3) (15), whichis consistent with higher effective populationsizes in the LSN source population and/or re-cent admixture. Outgroup f3(Test,X;Mbuti) and

D(Mbuti,Test;Mixe,X) tests show that the ESNshares more drift with SAM (Z > 3) than withgeographically proximal populations (data S3)(15), which suggests that the ESN is related to apopulation that expanded into South America.

Scheib et al., Science 360, 1024–1027 (2018) 1 June 2018 2 of 4

Fig. 1. Ancient individuals, population genetic analyses and modeling.(A) Sites of newly sequenced ancient individuals are designated bycolored triangles. Comparative modern populations and ancient individualsare designated by blackcircles and triangles, respectively. (B) PCAwith ancientindividuals projected onto modern Native American and Siberian variation.Inset: Ancient genomes projected onto modern worldwide data. (C) Visualiza-tion of model-based ancestry analysis at fivefold cross-validation–supported

K = 9 ancestral components (15). Underlines denote new and ancientgenomes; italics, published ancient genomes; single asterisks, masked data;double asterisks, Oceanian populations including Onge, Aeta, and Agta (15).(D) Probability area of radiocarbon dates grouped by population and calibratedwith IntCal13 (colored area) and Marine13 (light gray area) (28) whereappropriate (15). (E) A model that explains genetic diversity in the LateSouthern Channel Island populations through three-way admixture.

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By contrast, the LSN population shares moredrift and alleles with geographically proximalpopulations (Z > 3) (data S3) (15).We modeled the population history of the

Americas using qpGraph (15, 21) and found thatthe ASO and Mexican (Pima) populations wereconsistently outgroups to sets of clades formedbyAnzick-1, SAM (Surui), andESNpopulations inanalyses that did not involve admixture (fig. S4)(15, 21). Fit between the data and the tree couldbe significantly improvedwhenmodeling ancientCalifornian,modern Pima, and Surui populationsthrough admixture of two basal ancestries thatwe call ANC-A andANC-B (Fig. 2A) (15). The ESN,

Northern Channel Islands and Santa Barbara(NCI/SB), and Surui populations share similarproportions of both components, while the Pimahave a higher ANC-B component (Fig. 2A) (15).We used qpGraph to estimate the ANC-B con-tribution inmodern CAM and SAM populationsand found it to vary within a range of 42 to 71%(average 53%; table S8) (15). In SAMpopulations,the lower end of the spectrum of contributionsof ANC-B are found in the Amazonian EquatorialTucanoan-speaking groups (including Surui)(40 to 53%) and the highest in the Andeans (50to 71%) (Fig. 2B and table S8) (15), particularly inthe Chilote andHuilliche (~70%) from locations

overlapping the Monte Verde site (~18,500 to14,500 years ago) (Fig. 2B).The clear separation of ANC-A and ANC-B an-

cestries is further supported by the sharing ofunambiguous, derived haplotype segments inmodern Surui and Pima populations (27) withboth the ASO (CK-13) and Anzick-1 individuals(fig. S5) (15). The results of this analysis are con-sistent with ancient substructure and a separa-tion of at least a few thousand years between theANC-A and ANC-B populations prior tomerging(fig. S6) (15). The summary of evidence presentedhere allows us to reject models of a panmictic“first wave” population from which the ASO

Scheib et al., Science 360, 1024–1027 (2018) 1 June 2018 3 of 4

Fig. 2. Visual model of ancestry components and distribution of proportions in the Americas. (A) A model with four admixture events that offers agood fit to the data (Z = 0.888) (15). (B) Scale of ANC-B ancestry from 0% in Anzick-1 to 100% in the ASO and modern Algonquian-speaking populations.

Fig. 3. Dispersal models that are consistent with the results of this study. Red and blue indicate ANC-A and ANC-B, respectively; symbols denoteadmixture event(s). Locations of admixture events are hypothetical. (A) A model with one admixture event in North America. (B) A model in whichan ANC-B population first reached South America, followed by an ANC-A population with multiple admixture events. (C) The same model as (B), butreversing the populations. (D) A model with multiple admixture events and dispersals.

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diverged after the peopling of South America orinwhich solely theANC-Apopulation contributedto modern southern branch populations. Be-cause populations vary in ANC-A and ANC-B pro-portions but do not differ significantly in theiraffinity to non-American populations (table S7)(15), it is possible that ANC-A and ANC-B splitwithin America as opposed to Beringia wherethere would have been ongoing gene flow withSiberia.Four possible models can explain the contri-

bution of both branches to CAM and SAM popu-lations: (i) an admixture event inNorth Americaprior to the peopling of South America (Fig. 3A);(ii) ANC-B–related ancestral population(s) dis-persing into South America first, followed by adispersal of ANC-A–related population(s) and ad-mixture of the two branches occurring in SouthAmerica (Fig. 3B); (iii) ANC-A–related ancestralpopulation(s) dispersing into SouthAmerica first,followed by a dispersal of ANC-B–related pop-ulation(s) and admixture of the two branchesoccurring in South America (Fig. 3C); and (iv)multiple admixture events occurring in NorthAmerica, with multiple dispersals into SouthAmerica (Fig. 3D). Additional ancient DNA fromterminal Pleistocene human remains within theAmericas is needed to determine which modelbest describes the sequence of events con-stituting the complex population history ofthe Americas.

REFERENCES AND NOTES

1. T. Goebel, M. R. Waters, D. H. O’Rourke, Science 319,1497–1502 (2008).

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12. P. Verdu et al., PLOS Genet. 10, e1004530 (2014).13. M. Raghavan et al., Science 349, aab3884 (2015).14. P. Skoglund et al., Nature 525, 104–108 (2015).15. See supplementary materials.16. J. R. Johnson, T. W. Stafford Jr., H. O. Ajie, D. P. Morris,

in Proceedings of the Fifth California Islands Symposium(Santa Barbara Museum of Natural History, 2002),pp. 541–545.

17. J. R. Johnson, J. G. Lorenz, J. Calif. Gt. Basin Anthropol. 26,33–64 (2006).

18. N. Patterson, A. L. Price, D. Reich, PLOS Genet. 2, e190(2006).

19. D. H. Alexander, J. Novembre, K. Lange, Genome Res. 19,1655–1664 (2009).

20. R. E. Green et al., Science 328, 710–722 (2010).21. N. Patterson et al., Genetics 192, 1065–1093 (2012).22. D. Reich, K. Thangaraj, N. Patterson, A. L. Price, L. Singh,

Nature 461, 489–494 (2009).23. J. A. Ezzo, “The Ancient Mariners of San Nicolas Island:

A Bioarchaeological Analysis of the Burial Collections” (Tech.Rep. 01-64, Statistical Research Inc., Tucson, 2002).

24. S. L. Kerr, G. M. Hawley, in Fifth California Islands Symposium,D. R. Browne, K. L. Mitchell, H. W. Chaney, Eds. (SantaBarbara Museum of Natural History, 1999), pp. 546–554.

25. P. Martz, in Proceedings of the Sixth California IslandsSymposium (Santa Barbara Museum of Natural History, 2008),pp. 65–82.

26. A. Kousathanas et al., Genetics 205, 317–332 (2017).27. S. Mallick et al., Nature 538, 201–206 (2016).28. P. Reimer et al., Radiocarbon 55, 1869–1887 (2013).

ACKNOWLEDGMENTS

We thank T. Biers, D. Bolnick, and M. Schillaci for providingNAGPRA-related counsel and tribal contacts; the MostLikely Descendant (MLD) appointed by the CaliforniaNative American Heritage Commission for grantingpermission to test the tooth from the Carpinteria burial;A. (S.) Lindgren for her support and facilitating the partnershipwith the Kenaitze Tribe; and H. Schroeder for providingreagents and guidance for mtDNA target capture. Funding:Supported by European Research Council Starting Investigatorgrant FP7-261213 (T.K.); Natural Environment ResearchCouncil (NERC) Radiocarbon Facility grant NF/2016/1/6(T.K. and C.L.S.); the Economic and Social Research CouncilImpact Accelerator Award RG76702 (C.L.S.); NSF grantsBCS-1518026 and SMA-1620239 (R.S.M.); EuropeanResearch Council Consolidator Grant FP7-617627 (J.T.S.);Wellcome grant 098051 (M.H., Y.X., C.T.-S., M.S.S., andP.D.); the European Union through European RegionalDevelopment Fund project no. 2014-2020.4.01.16-0024,MOBTT53 (L.P.); and European Research Council Consolidator

Grant 647787 “Local Adaptation” (A.Ma.). Authorcontributions: C.L.S., T.K., and J.S. conceived the study;Z.F. contributed to the conception of the study and providedprotocols/reagents/training necessary for extractionand analysis; T.R., P.E., S.L.K., J.R.J., A.P., and G.D. providedsamples; R.S.M. provided data processed by H.L. and J.L.;C.L.S. and C.K. extracted the Lucier samples; C.L.S. extractedother samples; C.L.S., T.K., V.L., L.P., A.Mö., P.D., D.W.,T.O.C., T.D., and G.D. analyzed data; J.R.J. and R.S.M.facilitated communication with indigenous representatives;A.S.B., A.S.L., B.F.B., A.L., R.C., R.W., L.L., J.R., B.E.H.,and E.Y.-D.S. facilitated discussions with indigenouscommunity members and tribal governments; P.W.G. madethe figures; M.M. provided access to data; C.L.S., D.W.,C.T.-S., Y.X., M.H., B.E.H., P.M., L.P., T.K., A.S., and A.Ma.contributed to interpretation of results; and C.L.S. and T.K.wrote the manuscript. Competing interests: The authorsdeclare no competing financial interests. Data and materialsavailability: All data needed to evaluate the conclusions arepresent in the manuscript or supplementary materials.Genomic data used in this paper are publicly available. Scriptsfor calculating haplotype matching segments were writtenby T.D. and are available at https://github.com/td329/NA-hapmatch-2018. Accession numbers: Sequence datawere deposited in the European Nucleotide Archive underaccession PRJEB25445. Ethics statement: Human remainsanalyzed for this study from the Palm Site, Sii Túupentak,and the Teston Road and Turnbull Ossuaries were transferredto R.S.M. for destructive analysis by representatives of theKenaitze, Muwekma Ohlone, and Huron-Wendat tribes,respectively. R.S.M. has visited the Kenaitze and the MuwekmaOhlone regularly and has formed mutually beneficialpartnerships on genomics research with them. With supportof First Nations, remains from the Lucier site were provided toG.D. with permission from the University of Toronto Office ofResearch Ethics. All other remains were housed in museums, andpermission for destructive analysis was granted by the curatoror loan committee. C.L.S. has visited and shared results of thisstudy with representatives of Chumash and other SouthernCalifornia communities. Some members of these communitieshave consented to collaborate on this work and have seen andcontributed to the final version of this manuscript (15).

SUPPLEMENTARY MATERIALS

www.sciencemag.org/content/360/6392/1024/suppl/DC1Supplementary TextFigs. S1 to S14Tables S1 to S12Data S1 to S4References (29–99)

10 December 2017; accepted 20 April 201810.1126/science.aar6851

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Ancient human parallel lineages within North America contributed to a coastal expansion

Aylwyn Scally, Daniel Wegmann, Ripan S. Malhi and Toomas KivisildLouis Lesage, Brian Holguin, Ernestine Ygnacio-De Soto, JohnTommy Rosas, Mait Metspalu, Jay T. Stock, Andrea Manica,Tamsin C. O'Connell, Patricia Martz, Alan S. Boraas, Brian F. Byrd, Alan Leventhal, Rosemary Cambra, Ronald Williamson, Tyler-Smith, Manjinder S. Sandhu, Joseph G. Lorenz, Tori D. Randall, Zuzana Faltyskova, Luca Pagani, Petr Danecek,Mörseburg, John R. Johnson, Amiee Potter, Susan L. Kerr, Phillip Endicott, John Lindo, Marc Haber, Yali Xue, Chris C. L. Scheib, Hongjie Li, Tariq Desai, Vivian Link, Christopher Kendall, Genevieve Dewar, Peter William Griffith, Alexander

DOI: 10.1126/science.aar6851 (6392), 1024-1027.360Science 

, this issue p. 1028, p. 1024; see also p. 964Sciencethe Ice Age, but the peoples remixed at a later date.that now live in Mexico and South America. It appears that a genetic split and population isolation likely occurred during well as to modern Algonquian-speaking Native Americans. In contrast, the California individuals were more like groupsCalifornia, USA, and Ontario, Canada. The ancient Ontario population was similar to other ancient North Americans, as

sequenced ancient genomes from the Channel Islands ofet al.still skewed toward those of their Norse founders. Scheib Genetic drift since the initial settlement has left modern Icelanders with allele frequencies that are distinctive, althoughwith modernday Icelandic populations. The ancient DNA revealed that the founders had Gaelic and Norse origins.

examined the genomes of ancient Icelandic people, dating to near the colonization of Iceland, and compared themet al.1100 years ago). Ebenesersdóttir∼). Iceland has a genetically distinct population, despite relatively recent settlement (al.

etThe genomes of ancient humans can reveal patterns of early human migration (see the Perspective by Achilli Founder effects in modern populations

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