Genomic insights into the origin and diversification PNAS PLUS of late maritime hunter-gatherers from the Chilean Patagonia Constanza de la Fuentea,b, María C. Ávila-Arcosc, Jacqueline Galimanya, Meredith L. Carpenterd,e, Julian R. Homburgerf, Alejandro Blancoa,PalomaContrerasa, Diana Cruz Dávalosg,OmarReyesh, Manuel San Romanh, Andrés Moreno-Estradai, Paula F. Camposb,j, Celeste Engk, Scott Huntsmank, Esteban G. Burchardl, Anna-Sapfo Malaspinasm, Carlos D. Bustamanted,f, Eske Willerslevb,n,o, Elena Llopa, Ricardo A. Verdugoa,1, and Mauricio Moragaa,1 aHuman Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago 8380453, Chile; bCentre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark; cInternational Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla 76230, Santiago de Querétaro, Mexico; dCenter for Computational, Evolutionary and Human Genomics, Stanford University, Stanford, CA 94305; eArc Bio, LLC, Menlo Park, CA 94025; fDepartment of Genetics, Stanford University, Stanford, CA 94305; gInstitute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; hCentro de Estudios del Hombre Austral, Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas 6213029, Chile; iNational Laboratory of Genomics for Biodiversity, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36821 Guanajuato, Mexico; jInterdisciplinary Centre of Marine and Environmental Research, University of Porto, Novo Edificio do Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; kDepartment of Medicine, University of California, San Francisco, CA 94131; lDepartment of Bioengineering and Therapeutic Science, University of California, San Francisco, CA 94158; mDepartment of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; nDepartment of Zoology, University of Cambridge, Cambridge CB2 1TN, United Kingdom; and oWellcome Genome Campus, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom Edited by Tony Tosi, Kent State, and accepted by Editorial Board Member C. O. Lovejoy February 5, 2018 (received for review September 30, 2017) Patagonia was the last region of the Americas reached by humans resources. A systematic and specialized exploitation of the who entered the continent from Siberia ∼15,000–20,000 y ago. De- marine environment began only ∼6,000 YBP (3). Evidence of this adaptation is found in three areas: (i) Chiloé (north of the spite recent genomic approaches to reconstruct the continental evo- GENETICS lutionary history, regional characterization of ancient and modern Patagonian archipelago), (ii)StraitofMagellan–Otway Sound iii genomes remains understudied. Exploring the genomic diversity (western shore), and ( ) the Beagle Channel (4, 5). The latter within Patagonia is not just a valuable strategy to gain a better un- two areas are located south of the Patagonian archipelago (Fig. 1) derstanding of the history and diversification of human populations and show the earliest evidence of a maritime tradition, although it is in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases Significance of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and Recent genomic studies of ancient and modern humans from four ancient maritime individuals from Patagonia (∼1,000 y old). Both the Americas have given a comprehensive view of the peopling ANTHROPOLOGY the modern and ancient individuals studied in this work have a of the continent. However, regional characterization of ancient greater genetic affinity with other modern Native Americans than and modern individuals is lacking, being key to unveiling fine- to any non-American population, showing within South America a scale differences within the continent. We present genome- clear structure between major geographical regions. Native Patago- wide analyses of ancient and modern individuals from South nian Kawéskar and Yámana showed the highest genetic affinity with America from Western Patagonia. We found a strong affinity the ancient individuals, indicating genetic continuity in the region between modern and ancient individuals from the region, during the past 1,000 y before present, together with an important providing evidence of continuity in the region for the last agreement between the ethnic affiliation and historical distribution of ∼1,000 years and regional genetic structure within Southern both groups. Lastly, the ancient maritime individuals were genetically South America. In particular, the analysis of these ancient ge- equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del nomes helps address questions related to the maritime tradi- Fuego, which supports a model with an initial separation of a common tion in the region and its diversification posterior to the split ancestral group to both maritime populations from a terrestrial popu- from terrestrial hunter-gatherers. lation, with a later diversification of the maritime groups. Author contributions: C.d.l.F., R.A.V., and M.M. designed research; C.d.l.F., M.C.Á.-A., paleogenomics | Patagonia | maritime hunter-gatherers M.L.C., A.M.-E., P.F.C., R.A.V., and M.M. performed research; O.R., M.S.R., A.M.-E., C.E., S.H., E.G.B., C.D.B., E.W., and E.L. contributed new reagents/analytic tools; C.d.l.F., M.C.Á-A., J.G., J.R.H., A.B., P.C., D.C.D., and A.-S.M. analyzed data; and C.d.l.F., M.C.Á.-A., O.R., M.S.R., he Southern part of South America, known as Patagonia, is a P.F.C., R.A.V., and M.M. wrote the paper. Thighly diverse territory with two contrasting environments: the The authors declare no conflict of interest. Andean mountains to the Southwest—encompassing an irregular This article is a PNAS Direct Submission. T.T. is a guest editor invited by the Editorial Board. coast, numerous islands and archipelagos, and plateaus—and low- Published under the PNAS license. lands in the Northeast. The earliest evidence of human occupation is Data deposition: All the modern data from this paper can be accessed through request to found in North Patagonia in the Monte Verde site, dated to 14,500 y the authors. Researchers interested in accessing individual-level data must send a signed letter stating: “With regards to the non-public samples from the PatagoniaDNA Project, I before present (YBP) (1). During this time, Tierra del Fuego island agree that: (a) I will not secondarily distribute the data to anyone, (b) I will not post it was still connected to the mainland, and it was not until ∼8,000 YBP publicly, (c) I will make no attempt to connect the genetic data to personal identifiers for that the Strait of Magellan was formed, isolating some human groups the samples, (d) I will not use the data for any commercial purposes.” The ancient data are available for download through the European Nucleotide Archive (ENA) (accession no. on the island (2). Different disciplines have contributed to unraveling PRJEB24629). the first human occupation and dispersion in Patagonia. However, 1To whom correspondence may be addressed. Email: [email protected] or mmoraga@ from a genetic point of view, little is known about their affinities at med.uchile.cl. a regional scale. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. The first inhabitants of Patagonia were broad-spectrum 1073/pnas.1715688115/-/DCSupplemental. hunter-gatherers with a nonspecialized exploitation of marine www.pnas.org/cgi/doi/10.1073/pnas.1715688115 PNAS Latest Articles | 1of7 Downloaded by guest on September 27, 2021 After the arrival of Europeans in the 16th century, six major ethnic groups were recognized in the area: three maritime hunter- gatherer groups (from north to south): Chono, Kawéskar or Alacalufe, and Yámana or Yaghan; and three terrestrial hunter- gatherer groups, known as Tehuelche or Aonikenk, Selk’nam or Ona, and Haush (Fig. 1). In addition to different subsistence strategies, these groups were identified based on their language, physical appearance, and geographical location. The maritime groups occupied the archipelagos to the west of the Andes, from Reloncaví Sea to the Cape Horn (∼40°S to 56°S), while the ter- restrial groups inhabited the plateaus and lowlands from the Argentinean Patagonia (Tehuelches) to Tierra del Fuego (Selk’nam and Haush) (8–11). The biological variation of the native populations from Patagonia has been described by using morphological and genetic data. Only a few human remains have been found dating to between 12,000 and 3,000 YBP. Consequently, most of the morphological and genetic studies have focused on modern populations and late historical groups, such as Selk’nam, Kawéskar, and Yámana. Both approaches have suggested a close relationship between these groups (12–18). Studies based on mitochondrial DNA (mtDNA) variation have identified only two main lineages (C and D) in the ancient Patagonian populations (12, 14). A more recent study showed a high differentiation at the D-loop region of the mtDNA between ancient Kawéskar and Yámana, with a high frequency of D lineages, particularly D4h3a5, in the former and a higher frequency of C in the latter (17). Furthermore, lineages B2i2, C1b13, and D1g have been identified in present-day individuals from Southern Chile and Argentina. The coalescent time and distribution of these line- ages suggest a rapid coastal migration through America and, sub- sequently, extensive trans-Andean migration in Southern South America (18–20). Genome-wide data of modern individuals from Patagonia have been analyzed in the context of the peopling of the Americas, strongly suggesting that the populations from the area descend from a single major migration wave into the continent (21, 22). Fig. 1. Approximate distribution of Native populations from Patagonia. Additionally, the study of complete genomes from ancient Pata- The distribution of the maritime groups is shown in gray, and the associ- gonian individuals shows no closer affinity between these and ated labels are adjacent to each area.