Genomic evidence for the Pleistocene and recent population history of Native Americans


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Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan Maanasa (co-first), Steinrücken Matthias (co-first), Harris Kelley (co-first), Schiffels Stephan (co-first), Rasmussen Simon (co-first), DeGiorgio Michael (co-first), Albrechtsen Anders (co-first), Valdiosera Cristina (co-first), Ávila-Arcos María C. (co-first), Malaspinas Anna-Sapfo (co-first), Eriksson Anders, Moltke Ida, Metspalu Mait, Homburger Julian R., Wall Jeff, Cornejo Omar E., Moreno-Mayar J. Víctor, Korneliussen Thorfinn S., Pierre Tracey, Rasmussen Morten, Campos Paula F., Damgaard Peter de Barros, Allentoft Morten E., Lindo John, Metspalu Ene, Rodríguez-Varela Ricardo, Mansilla Josefina, Henrickson Celeste, Seguin-Orlando Andaine, Malmström Helena, Stafford Thomas, Shringarpure Suyash S., Moreno-Estrada Andrés, Karmin Monika, Tambets Kristiina, Bergström Anders, Xue Yali, Warmuth Vera, Friend Andrew D., Singarayer Joy, Valdes Paul, Balloux Francois, Leboreiro Ilán, Vera Jose Luis, Rangel-Villalobos Hector, Pettener Davide, Luiselli Donata, Davis Loren G., Heyer Evelyne, Zollikofer Christoph P. E., León Marcia S. Ponce de, Smith Colin I., Grimes Vaughan, Pike Kelly-Anne, Deal Michael, Fuller Benjamin T., Arriaza Bernardo, Standen Vivien, Luz Maria F., Ricaut Francois, Guidon Niede, Osipova Ludmila, Voevoda Mikhail I., Posukh Olga L., Balanovsky Oleg, Lavryashina Maria, Bogunov Yuri, Khusnutdinova Elza, Gubina Marina, Balanovska Elena, Fedorova Sardana, Litvinov Sergey, Malyarchuk Boris, Derenko Miroslava, Mosher M. J., Archer David, Cybulski Jerome, Petzelt Barbara, Mitchell Joycelynn, Worl Rosita, Norman Paul J., Parham Peter, Kemp Brian M., Kivisild Toomas, Tyler-Smith Chris, Sandhu Manjinder S., Crawford Michael, Villems Richard, Smith David Glenn, Waters Michael R., Goebel Ted, Johnson John R., Malhi Ripan S., Jakobsson Mattias, Meltzer David J., Manica Andrea, Durbin Richard, Bustamante Carlos D., Song Yun S., Nielsen Rasmus, Willerslev Eske
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Genetic history of Native Americans
Several theories have been put forth as to the origin and timing of when Native American ancestors entered the Americas. To clarify this controversy, Raghavan et al. examined the genomic variation among ancient and modern individuals from Asia and the Americas. There is no evidence for multiple waves of entry or recurrent gene flow with Asians in northern populations. The earliest migrations occurred no earlier than 23,000 years ago from Siberian ancestors. Amerindians and Athabascans originated from a single population, splitting approximately 13,000 years ago.
Science, this issue 10.1126/science.aab3884
Structured Abstract
INTRODUCTIONThe consensus view on the peopling of the Americas is that ancestors of modern Native Americans entered the Americas from Siberia via the Bering Land Bridge and that this occurred at least {\textasciitilde}14.6 thousand years ago (ka). However, the number and timing of migrations into the Americas remain controversial, with conflicting interpretations based on anatomical and genetic evidence.
RATIONALEIn this study, we address four major unresolved issues regarding the Pleistocene and recent population history of Native Americans: (i) the timing of their divergence from their ancestral group, (ii) the number of migrations into the Americas, (iii) whether there was {\textasciitilde}15,000 years of isolation of ancestral Native Americans in Beringia (Beringian Incubation Model), and (iv) whether there was post-Pleistocene survival of relict populations in the Americas related to Australo-Melanesians, as suggested by apparent differences in cranial morphologies between some early (“Paleoamerican”) remains and those of more recent Native Americans. We generated 31 high-coverage modern genomes from the Americas, Siberia, and Oceania; 23 ancient genomic sequences from the Americas dating between {\textasciitilde}0.2 and 6 ka; and SNP chip genotype data from 79 present-day individuals belonging to 28 populations from the Americas and Siberia. The above data sets were analyzed together with published modern and ancient genomic data from worldwide populations, after masking some present-day Native Americans for recent European admixture.
RESULTSUsing three different methods, we determined the divergence time for all Native Americans (Athabascans and Amerindians) from their Siberian ancestors to be {\textasciitilde}20 ka, and no earlier than {\textasciitilde}23 ka. Furthermore, we dated the divergence between Athabascans (northern Native American branch, together with northern North American Amerindians) and southern North Americans and South and Central Americans (southern Native American branch) to be {\textasciitilde}13 ka. Similar divergence times from East Asian populations and a divergence time between the two branches that is close in age to the earliest well-established archaeological sites in the Americas suggest that the split between the branches occurred within the Americas. We additionally found that several sequenced Holocene individuals from the Americas are related to present-day populations from the same geographical regions, implying genetic continuity of ancient and modern populations in some parts of the Americas over at least the past 8500 years. Moreover, our results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo-Melanesians, the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders. Last, using both genomic and morphometric analyses, we found that historical Native American groups such as the Pericúes and Fuego-Patagonians were not “relicts” of Paleoamericans, and hence, our results do not support an early migration of populations directly related to Australo-Melanesians into the Americas.
CONCLUSIONOur results provide an upper bound of {\textasciitilde}23 ka on the initial divergence of ancestral Native Americans from their East Asian ancestors, followed by a short isolation period of no more than {\textasciitilde}8000 years, and subsequent entrance and spread across the Americas. The data presented are consistent with a single-migration model for all Native Americans, with later gene flow from sources related to East Asians and, indirectly, Australo-Melanesians. The single wave diversified {\textasciitilde}13 ka, likely within the Americas, giving rise to the northern and southern branches of present-day Native Americans. {\textless}img class="fragment-image" src=""/{\textgreater} Download high-res image Open in new tab Download Powerpoint Population history of present-day Native Americans.The ancestors of all Native Americans entered the Americas as a single migration wave from Siberia (purple) no earlier than {\textasciitilde}23 ka, separate from the Inuit (green), and diversified into “northern” and “southern” Native American branches {\textasciitilde}13 ka. There is evidence of post-divergence gene flow between some Native Americans and groups related to East Asians/Inuit and Australo-Melanesians (yellow).
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
Genetic variation within ancient and extant Native American populations informs on their migration into the Americas.
Genetic variation within ancient and extant Native American populations informs on their migration into the Americas.
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