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1. Demographic history and genetic structure in pre-Hispanic Central Mexico

Author

Viridiana Villa-Islas, Alan Izarraras-Gomez, Maximilian Larena, Elizabeth Mejía Perez Campos, Marcela Sandoval-Velasco, Juan Esteban Rodríguez-Rodríguez, Miriam Bravo-Lopez, Barbara Moguel, Rosa Fregel, Ernesto Garfias-Morales, Jazeps Medina Tretmanis, David Alberto Velázquez-Ramírez, Alberto Herrera-Muñóz, Karla Sandoval, Maria A. Nieves-Colón, Gabriela Zepeda García Moreno, Fernando A. Villanea, Eugenia Fernández Villanueva Medina, Ramiro Aguayo-Haro, Cristina Valdiosera, Alexander G. Ioannidis, Andrés Moreno-Estrada, Flora Jay, Emilia Huerta-Sanchez, J. Víctor Moreno-Mayar, Federico Sánchez-Quinto, and María C. Ávila-Arcos

Subjects
Multidisciplinary
Abstract

Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled “ghost” populations.

Published
2023
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2. Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull)

Author

Thorfinn Sand Korneliussen, J. Víctor Moreno-Mayar, Ernie LaPointe, Ida Moltke, William T. Billeck, Andaine Seguin-Orlando, Eske Willerslev, Moltke, Ida [0000-0001-7052-8554], Korneliussen, Thorfinn Sand [0000-0001-7576-5380], Seguin-Orlando, Andaine [0000-0002-8265-3229], Moreno-Mayar, J Víctor [0000-0002-7712-4496], Billeck, William [0000-0003-3219-9715], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
Multidisciplinary, History, IDENTIFICATION, Human Genome, GENOME SEQUENCE, SciAdv r-articles, Human Genetics, ANCESTRY, Sitting, Genealogy, 3105 Genetics, Social and Interdisciplinary Sciences, REMAINS, FOS: Biological sciences, PATTERNS, Genetics, LOUIS-XVI, Research Article, Great-grandson, 31 Biological Sciences
Abstract

Description, The identification of a living relative of Sitting Bull with a new method opens the door to future genealogical research., A great-grandson of the legendary Lakota Sioux leader Sitting Bull (Tatanka Iyotake), Ernie LaPointe, wished to have their familial relationship confirmed via genetic analysis, in part, to help settle concerns over Sitting Bull’s final resting place. To address Ernie LaPointe’s claim of family relationship, we obtained minor amounts of genomic data from a small piece of hair from Sitting Bull’s scalp lock, which was repatriated in 2007. We then compared these data to genome-wide data from LaPointe and other Lakota Sioux using a new probabilistic approach and concluded that Ernie LaPointe is Sitting Bull’s great-grandson. To our knowledge, this is the first published example of a familial relationship between contemporary and a historical individual that has been confirmed using such limited amounts of ancient DNA across such distant relatives. Hence, this study opens the possibility for broadening genealogical research, even when only minor amounts of ancient genetic material are accessible.

Published
2022
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3. Population genomics of the Viking world

Author

Inna Potekhina, Simon Rasmussen, Maeve Sikora, Sabine Sten, Gordon Turner-Walker, Jörgen Gustafsson, Jade Cheng, Per Holck, Pasquale Favia, Anders Albrechtsen, Julie Gibson, Monika Bajka, Mads Dengsø Jessen, Otto Uldum, Martin Sikora, Ceri Falys, Charlotte Hedenstierna Jonson, Mark Redknap, Tamara Pushkina, Rasmus Nielsen, Claude Bhérer, Enrico Cappellini, Helene Wilhelmson, Morten Søvsø, Wiesław Bogdanowicz, Fernando Racimo, Jan Bill, Ashot Margaryan, Vayacheslav Moiseyev, Marie Allen, Louise Loe, Tom Christensen, Raili Allmäe, Mark Collard, M. Thomas P. Gilbert, Thorfinn Sand Korneliussen, Eske Willerslev, Ida Moltke, Magdalena M. Buś, Ludovic Orlando, Inge Lundstrøm, Alexandra P. Buzhilova, Jette Arneborg, Marie Louise Jørkov, Daniel Lawson, Neil Price, Peter Pentz, Anne Pedersen, Gabriel Renaud, Jilong Ma, Morten E. Allentoft, Ole Kastholm, Ingrid Mainland, Jesper Stenderup, Hugh McColl, J. Víctor Moreno-Mayar, Anna K. Fotakis, Gabriele Scorrano, Allison M. Fox, Thomas Werge, Natalia Grigoreva, Italo M. Muntoni, Sturla Ellingvåg, Símun V. Arge, Niels Lynnerup, Denis Pezhemsky, Andres Ingason, Hildur Gestsdóttir, Linzi Simpson, Katrine Højholt Iversen, Peter de Barros Damgaard, Daniel G. Bradley, Yvonne Magnusson, Caroline Arcini, Jüri Peets, Rui Martiniano, Martyna Molak, Marek Florek, Søren M. Sindbæk, Mikkel Winther Pedersen, Lotte Hedeager, Kristian Kristiansen, Emil Jørsboe, Lara M. Cassidy, Maria Vretemark, Ingrid Gustin, Birgitte Skar, Lisa Strand, Dariusz Błaszczyk, Berit Schütz, Margaryan, Ashot [0000-0002-2576-2429], Lawson, Daniel J [0000-0002-5311-6213], Rasmussen, Simon [0000-0001-6323-9041], Moltke, Ida [0000-0001-7052-8554], Jørsboe, Emil [0000-0002-0593-7906], Korneliussen, Thorfinn [0000-0001-7576-5380], Wilhelmson, Helene [0000-0002-8422-2369], Renaud, Gabriel [0000-0002-0630-027X], Bhérer, Claude [0000-0002-2744-7246], Molak, Martyna [0000-0001-5068-8649], Buzhilova, Alexandra [0000-0001-6398-2177], Albrechtsen, Anders [0000-0001-7306-031X], Falys, Ceri [0000-0003-1903-9573], Strand, Lisa [0000-0002-4245-6298], Florek, Marek [0000-0002-9917-710X], Magnusson, Yvonne [0000-0002-7076-2583], Collard, Mark [0000-0002-2725-4989], Bradley, Daniel G [0000-0001-7335-7092], Nielsen, Rasmus [0000-0003-0513-6591], Werge, Thomas [0000-0003-1829-0766], Willerslev, Eske [0000-0002-7081-6748], Apollo - University of Cambridge Repository, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Gene Flow, Male, [SDV]Life Sciences [q-bio], Human Migration, Population, Greenland, Datasets as Topic, Scandinavian and Nordic Countries, Diaspora, Gene flow, Population genomics, Danish, Evolution, Molecular, 03 medical and health sciences, Young Adult, Spatio-Temporal Analysis, Humans, 0601 history and archaeology, Selection, Genetic, education, ComputingMilieux_MISCELLANEOUS, Alleles, 030304 developmental biology, Lactase, 0303 health sciences, education.field_of_study, Multidisciplinary, 060102 archaeology, Genome, Human, Immunity, 06 humanities and the arts, Genomics, language.human_language, History, Medieval, Geography, Ancient DNA, Genetics, Population, England, Genetic structure, Viking Age, language, Ethnology, Ireland
Abstract

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

Published
2020
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4. Native American gene flow into Polynesia predating Easter Island settlement

Author

Alexander J. Mentzer, Juan Esteban Rodríguez-Rodríguez, Kathryn Auckland, Genevieve L. Wojcik, Ricardo A. Verdugo, Carlos Bustamante, Javier Blanco-Portillo, J. Víctor Moreno-Mayar, Mauricio Moraga, Soledad Berríos, M. Acuña, Scott Huntsman, Julian R. Homburger, Juan Francisco Miquel-Poblete, Christopher R. Gignoux, Lucía Cifuentes, Adrian V. S. Hill, Elena Llop, Andrés Moreno-Estrada, Esteban G. Burchard, Kathryn J. H. Robson, Alexandra Sockell, Consuelo D. Quinto-Cortés, Alexander G. Ioannidis, Luisa Herrera, Celeste Eng, Tom Parks, María C. Ávila-Arcos, Karla Sandoval, Kathleen C. Barnes, and Erika Hagelberg

Subjects
Gene Flow, Native Hawaiian or Other Pacific Islander, Time Factors, General Science & Technology, Human Migration, Population, Archaeological record, ANCESTRY, Colombia, SWEET-POTATO, Polymorphism, Single Nucleotide, Indigenous, Polynesia, Gene flow, COLONIZATION, MEXICO, Prehistory, 03 medical and health sciences, 0302 clinical medicine, OCEANIA, HISPANIC/LATINO, Humans, POPULATION-STRUCTURE, RAPANUI, education, 030304 developmental biology, Islands, 0303 health sciences, education.field_of_study, Multidisciplinary, Science & Technology, Native american, Genome, Human, Indians, South American, Biological anthropology, Central America, South America, Indians, Central American, History, Medieval, Multidisciplinary Sciences, ADMIXTURE, Europe, Geography, Genetics, Population, PATTERNS, Ethnology, Science & Technology - Other Topics, Settlement (litigation), 030217 neurology & neurosurgery
Abstract

The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas1–6, while critics have argued that these botanical dispersals need not have been human mediated7. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South American populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui)2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested8–12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian individuals with Native American individuals (around ad 1200) contemporaneous with the settlement of remote Oceania13–15. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia. Genomic analyses of DNA from modern individuals show that, about 800 years ago, pre-European contact occurred between Polynesian individuals and Native American individuals from near present-day Colombia, while remote Pacific islands were still being settled.

Published
2020

5. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Author

M. Thomas P. Gilbert, Ralf Dietrich Kahlke, Senthilvel K. S. S. Nathan, Yoshan Moodley, Bienvenido Martínez-Navarro, Lorenzo Rook, Luca Pandolfi, Jesper V. Olsen, Marc R. Dickinson, Reid Ferring, Jordi Agustí, Beth Shapiro, David Lyon, Christian D. Kelstrup, Jazmín Ramos-Madrigal, Morten E. Allentoft, Patrick Rüther, Mikkel-Holger S. Sinding, Anna K. Fotakis, David Lordkipanidze, Meaghan Mackie, Rosa Rakownikow Jersie-Christensen, Love Dalén, Eske Willerslev, Marcela Sandoval Velasco, Joshua D. Kapp, Gocha Kiladze, Aurélien Ginolhac, Frido Welker, Irina V. Kirillova, Peter D. Heintzman, J. Víctor Moreno-Mayar, Kirsty Penkman, Maia Bukhsianidze, Thomas W. Stafford, Ludovic Orlando, Diana Samodova, Enrico Cappellini, Martha Tappen, Shanlin Liu, Yvonne L. Chan, Anders Götherström, Eleftheria Palkopoulou, University of Copenhagen = Københavns Universitet (KU), The National Museum of Georgia, LibraGen, industriel, Stockholm Univ, Dept Biochem & Biophys, S-10691 Stockholm, Sweden, Department of Zoology, University of Venda [South Africa], University of Venda, Institució Catalana de Recerca i Estudis Avançats (ICREA), Área de Prehistoria, URV-IPHES, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Georgian State Museum, Geology Paleontology and Paleoanthropology, and Musée de Géorgie

Subjects
0106 biological sciences, 0301 basic medicine, Male, Proteomics, History, Early Pleistocene, Proteome, Lineage (evolution), [SDV]Life Sciences [q-bio], Amino Acid Motifs, 01 natural sciences, Woolly rhinoceros, Naturvetenskap, Phosphorylation, ComputingMilieux_MISCELLANEOUS, History, Ancient, Phylogeny, Paleoproteomics, Stephanorhinus, Phylogeny, Dmanisi, Early Pleistocene, Stephanorhinus, Multidisciplinary, Fossils, Coelodonta, DNA, Ancient/analysis, Sister group, VDP::Mathematics and natural science: 400::Geosciences: 450::Stratigraphy and paleontology: 461, Natural Sciences, Biotechnology, General Science & Technology, Dental Enamel/metabolism, Perissodactyla/classification, Biology, 010603 evolutionary biology, Article, Ancient, 03 medical and health sciences, stomatognathic system, Phylogenetics, Genetics, Proteome/analysis, Animals, Humans, Amino Acid Sequence, DNA, Ancient, Dental Enamel, Perissodactyla, VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Stratigrafi og paleontologi: 461, Bayes Theorem, DNA, 15. Life on land, biology.organism_classification, 030104 developmental biology, Ancient DNA, Evolutionary biology, Phosphorylation/genetics
Abstract

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5—although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7–9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck’s rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel—which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record—can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation. Palaeoproteomic analysis of dental enamel from an Early Pleistocene Stephanorhinus resolves the phylogeny of Eurasian Rhinocerotidae, by enabling the reconstruction of molecular evolution beyond the limits of ancient DNA preservation.

Published
2019
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6. Author Correction: Population genomics of the Viking world

Author

Jilong Ma, Italo M. Muntoni, Símun V. Arge, Niels Lynnerup, Hildur Gestsdóttir, Linzi Simpson, Daniel G. Bradley, Ingrid Gustin, Alexandra P. Buzhilova, Morten Søvsø, Peter Pentz, Anne Pedersen, Dariusz Błaszczyk, Ingrid Mainland, Birgitte Skar, Berit Schütz, Denis Pezhemsky, Thomas Højlund Christensen, Marie Louise Jørkov, Jesper Stenderup, Mark Collard, Ida Moltke, Jette Arneborg, Daniel Lawson, Gordon Turner-Walker, Ludovic Orlando, Charlotte Hedenstierna Jonson, Raili Allmäe, Otto Uldum, Enrico Cappellini, Lara M. Cassidy, Mark Redknap, M. Thomas P. Gilbert, Emil Jørsboe, Rui Martiniano, Martin Sikora, Thorfinn Sand Korneliussen, Marie Allen, Tamara Pushkina, Ceri Falys, Maria Vretemark, Inge Lundstrøm, Louise Loe, Ole Kastholm, Inna Potekhina, Simon Rasmussen, Anna K. Fotakis, Helene Wilhelmson, Andres Ingason, Allison M. Fox, Claude Bhérer, Maeve Sikora, Sabine Sten, Lisa Strand, Sturla Ellingvåg, Yvonne Magnusson, Vayacheslav Moiseyev, Jörgen Gustafsson, Lotte Hedeager, Jade Cheng, Neil Price, Eske Willerslev, Katrine Højholt Iversen, Morten E. Allentoft, Anders Albrechtsen, Peter de Barros Damgaard, Mads Dengsø Jessen, Julie Gibson, Wiesław Bogdanowicz, Caroline Arcini, Per Holck, Gabriel Renaud, Monika Bajka, Kristian Kristiansen, Fernando Racimo, J. Víctor Moreno-Mayar, Hugh McColl, Thomas Werge, Natalia Grigoreva, Jan Bill, Ashot Margaryan, Søren M. Sindbæk, Rasmus Nielsen, Magdalena M. Buś, Martyna Molak, Gabriele Scorrano, Pasquale Favia, Mikkel Winther Pedersen, Jüri Peets, and Marek Florek

Subjects
Population genomics, Multidisciplinary, History, Published Erratum, MEDLINE, Genealogy
Published
2021
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7. Origins and genetic legacies of the Caribbean Taino

Author

Hannes Schroeder, Menno L. P. Hoogland, Eske Willerslev, Jane S. Day, Martin Sikora, Shyam Gopalakrishnan, Carlos Bustamante, Julian R. Homburger, William C. Schaffer, Gabriel Renaud, Rachel J A Hopkins, J. Víctor Moreno-Mayar, Robert S. Carr, Corinne L. Hofman, Pierpaolo Maisano Delser, Antonio Salas, Alberto Gómez-Carballa, Morten E. Allentoft, Daniel G. Bradley, Jason E. Laffoon, Rasmus Nielsen, Joshua G. Schraiber, Marcela Sandoval Velasco, María C. Ávila-Arcos, Simon Rasmussen, Lara M. Cassidy, Thomas Higham, Geology and Geochemistry, and CLUE+

Subjects
Male, 0301 basic medicine, History, Bahamas, Social Sciences, Genome, 0302 clinical medicine, Effective population size, History, Ancient, Phylogeny, Migration, education.field_of_study, Multidisciplinary, Ancient DNA, Human migration, Genomics, Hispanic or Latino, Biological Sciences, Mitochondrial, Geography, Archaeology, SDG 1 - No Poverty, Female, Hispanic Americans, Human, Adult, American Native Continental Ancestry Group, Human Migration, Population, DNA, Mitochondrial, Ancient, Young Adult, 03 medical and health sciences, Genetics, Humans, DNA, Ancient, education, American Indian or Alaska Native, Whole genome sequencing, Ancestry, Genome, Human, business.industry, Paleontology, DNA, Genetics, Population, 030104 developmental biology, Paleogenomics, Evolutionary biology, Anthropology, Human genome, business, 030217 neurology & neurosurgery
Abstract

Significance Ancient DNA has revolutionized the field of archaeology, but in the Caribbean and other tropical regions of the world, the work has been hampered by poor DNA preservation. We present an ancient human genome from the Caribbean and use it to shed light on the early peopling of the islands. We demonstrate that the ancestors of the so-called “Taino” who inhabited large parts of the Caribbean in pre-Columbian times originated in northern South America, and we find evidence that they had a comparatively large effective population size. We also show that the native components in some modern Caribbean genomes are closely related to the ancient Taino, suggesting that indigenous ancestry in the region has survived through the present day., The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Published
2018
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8. The prehistoric peopling of Southeast Asia

Author

Hsiao-chun Hung, Tadayuki Masuyama, Christophe Pottier, Farhang Aghakhanian, Thi Minh Tran, Anne-Marie Bacon, Lasse Vinner, Andaine Seguin-Orlando, Laura L. Shackelford, Thi Mai Huong Nguyen, Tsunehiko Hanihara, Anh Nguyen, Hajime Ishida, Ashot Margaryan, Yasuhiro Yamada, Thongsa Sayavongkhamdy, Hiroki Shibata, Constanza de la Fuente Castro, Rasmi Shoocongdej, Eske Willerslev, Silas Anselm Rasmussen, Peter de Barros Damgaard, Patcharee Lertrit, Nobuo Shigehara, Marta Mirazón Lahr, Jean Christophe Galipaud, Jean Luc Ponche, Thomas Higham, Shigeki Nakagome, Sally Wasef, Uffe Gram Wilken, David M. Lambert, Thibaut Devièse, Takashi Gakuhari, Robert Foley, George van Driem, Atsushi Tajima, Ludovic Orlando, Bérénice Bellina-Pryce, Morten E. Allentoft, Charles Higham, Hiroki Oota, J. Víctor Moreno-Mayar, Anna-Sapfo Malaspinas, Huu Nghia Truong, Giang Hai Nguyen, Maude E. Phipps, Fernando Racimo, Rebecca Kinaston, Elise Patole-Edoumba, Supannee Kaewsutthi, Ketut Wiradnyana, Ana Prohaska, Fabrice Demeter, Viengkeo Souksavatdy, Shaiful Shahidan, Hugh McColl, Mokhtar Saidin, Hallie R. Buckley, Thorfinn Sand Korneliussen, Minoru Yoneda, Atsushi Toyoda, Takehiro Sato, Hiromi Matsumae, Philippe Duringer, Martin Sikora, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Préhistoire et Technologie (PréTech), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Université Silpakorn, Department of Museums, Historic Buildings and Archaeology, Ministry of Information and Culture, Département des musées et de l'archéologie, Ministère de la Culture et de l?Information, Kyoto University [Kyoto], Dynamique de l'évolution humaine : individus, populations, espèces [Paris] (DEHIPE), Centre National de la Recherche Scientifique (CNRS), Centre de géochimie de la surface (CGS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de chimie et procédés pour l'énergie, l'environnement et la santé (ICPEES), Université de Strasbourg (UNISTRA)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Illinois at Urbana Champaign (UIUC), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Museum d'Histoire Naturelle de La Rochelle, Service d'Anatomo-Cyto-Pathologie et de NeuroPathologie [Hôpital de la Timone - APHM] (ACPNP), Aix Marseille Université (AMU)- Hôpital de la Timone [CHU - APHM] (TIMONE), Patrimoines Locaux et Gouvernance (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Anatomy, University of Otago, Dunedin, University of Otago [Dunedin, Nouvelle-Zélande], École française d'Extrême-Orient (EFEO), Ctr Biol Sequence Anal, Technical University of Denmark [Lyngby] (DTU), Research Laboratory for Archaeology and the History of Art, University of Oxford [Oxford], Institut de Biologia Evolutiva (UPF-CSIC), Max-Planck-Institut für evolutionäre Anthropologie (MPI-EVA), Max-Planck-Gesellschaft, Silpakorn University [Bangkok, Thaïlande], Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Analyse et de Mathématiques Appliquées (LAMA), Université Paris-Est Marne-la-Vallée (UPEM)-Fédération de Recherche Bézout-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Illinois System, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Oxford, Kyoto University, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), McColl, Hugh [0000-0002-7568-4270], Racimo, Fernando [0000-0002-5025-2607], Demeter, Fabrice [0000-0002-1288-5534], Gakuhari, Takashi [0000-0003-1855-8371], Gram Wilken, Uffe [0000-0003-3434-7312], Seguin-Orlando, Andaine [0000-0002-8265-3229], de la Fuente Castro, Constanza [0000-0002-2857-3615], Wasef, Sally [0000-0002-7207-7395], Sayavongkhamdy, Thongsa [0000-0001-9467-0811], Korneliussen, Thorfinn [0000-0001-7576-5380], Prohaska, Ana [0000-0001-5459-6186], Margaryan, Ashot [0000-0002-2576-2429], Kaewsutthi, Supannee [0000-0002-3959-8420], Lertrit, Patcharee [0000-0002-4801-3834], Hung, Hsiao-Chun [0000-0001-5794-3040], Minh Tran, Thi [0000-0001-8833-693X], Nghia Truong, Huu [0000-0003-3291-5646], Shahidan, Shaiful [0000-0002-8367-3539], Matsumae, Hiromi [0000-0003-1858-3833], Ishida, Hajime [0000-0002-5781-7914], Tajima, Atsushi [0000-0001-6808-5491], Toyoda, Atsushi [0000-0002-0728-7548], Nakagome, Shigeki [0000-0001-9613-975X], Deviese, Thibaut [0000-0003-0495-7398], Duringer, Philippe [0000-0001-6213-5726], Patole-Edoumba, Elise [0000-0002-9378-2202], Bellina-Pryce, Bérénice [0000-0001-8790-1394], Galipaud, Jean-Christophe [0000-0003-3546-5265], Kinaston, Rebecca [0000-0001-7697-4950], Higham, Tom [0000-0002-5949-598X], Foley, Robert A [0000-0003-0479-3039], Lahr, Marta Mirazón [0000-0001-5752-5770], Orlando, Ludovic [0000-0003-3936-1850], Sikora, Martin [0000-0003-2818-8319], Lambert, David M [0000-0002-5821-3637], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Human Migration, Population, Southeast asian, Indigenous, Prehistory, 03 medical and health sciences, 0302 clinical medicine, Asian People, Humans, East Asia, 14. Life underwater, DNA, Ancient, education, Asia, Southeastern, History, Ancient, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Genome, Human, business.industry, Human migration, Genetic Variation, Sequence Analysis, DNA, Hoabinhian, 030104 developmental biology, Agriculture, Ethnology, [SHS.HIST]Humanities and Social Sciences/History, business, 030217 neurology & neurosurgery
Abstract

Ancient migrations in Southeast AsiaThe past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipsonet al.generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McCollet al.sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations.Science, this issue p.92, p.88; see also p.31

Published
2018
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9. 137 ancient human genomes from across the Eurasian steppes

Author

Karl-Göran Sjögren, Nina Lau, Nikolay N. Kradin, Igor Kukushkin, Arman Beisenov, Kadicha Tashbaeva, Andrey Logvin, Peter de Barros Damgaard, Irina Shevnina, Viktor K. Mertz, Ilya V. Mertz, Alexander Tkachev, Amy Goldberg, Zaruhi Khachatryan, Vyacheslav Moiyesev, Nina Marchi, Valeriy Evdokimov, Gabit Baimbetov, Valeriy Loman, Turaly Tulegenov, Evgeniy Dmitriev, Kasper Nielsen, Diimaajav Erdenebaatar, Lotte Hedeager, Levon Yepiskoposyan, Almaz Aldashev, Egor Kitov, Evelyne Heyer, Kristian Kristiansen, Victor Varfolomeev, Nurbol Baimukhanov, Enkhbayar Mijiddorj, Tereza Štolcová, Melissa A. Wilson Sayres, Sturla Ellingvåg, Dmitriy Voyakin, Gennady Afanasiev, Simon Rasmussen, Anders Gorm Pedersen, Ashyk Alpaslan, Mikkel Winther Pedersen, Ashot Margaryan, Sainbileg Undrakhbold, Z. Orozbekova, Bekmukhanbet Nurmukhanbetov, Tabaldiev Kubatbek, Eske Willerslev, Andrey Gromov, Ruslan Khaskhanov, Hakon Hakonarson, Alina Kolbina, Václav Smrčka, Rasmus Nielsen, Morten E. Allentoft, Gulmira Mukhtarova, Martin Sikora, Gabriel Renaud, J. Víctor Moreno-Mayar, Bazartseren Boldgiv, Angela M. Taravella, Tatyana Hegay, Choduraa Dorzhu, Emma Usmanova, Karol Pieta, Inga Merkyte, Alexey Kukushkin, Michaël Peyrot, Kunbolot Akmatov, Karin Margarita Frei, Vladimir I. Bazaliiskii, Thorfinn Sand Korneliussen, Alexander Goryachev, Ludovic Orlando, Andrzej W. Weber, Irina P. Panyushkina, Rana Dajani, Bazartseren Boldbaatar, Eco-Anthropologie et Ethnobiologie (EAE), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Muséum national d'Histoire naturelle (MNHN), Ctr Biol Sequence Anal, Technical University of Denmark [Lyngby] (DTU), Max Planck Institute for Evolutionary Anthropology, Max-Planck-Gesellschaft, Institute of Molecular Biology and Medicine, Irkutsk State University (ISU), The Center for Applied Genomics, Children’s Hospital of Philadelphia (CHOP ), Institute of Immunology, Uzbekistan Academy of Sciences, Laboratory for Tree-Ring Research, University of Arizona, University of Copenhagen = Københavns Universitet (KU), Dept Integrat Biol, Institut de Biologia Evolutiva (UPF-CSIC), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Max Planck Institute for Evolutionary Anthropology [Leipzig], Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7), Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Asia, Steppe, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Ancient history, Plague (disease), White People, 03 medical and health sciences, Asian People, Bronze Age, Humans, Middle Ages, East Asia, education, History, Ancient, Phylogeny, geography, education.field_of_study, Farmers, Multidisciplinary, geography.geographical_feature_category, Genome, Human, Human migration, business.industry, Grassland, Europe, 030104 developmental biology, Iron Age, business
Abstract

For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century bc, forming the Hun traditions in the fourth–fifth century ad, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry. Sequences of 137 ancient and 502 modern human genomes illuminate the population history of the Eurasian steppes after the Bronze Age and document the replacement of Indo-European speakers of West Eurasian ancestry by Turkic-speaking groups of East Asian ancestry.

Published
2018
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10. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

Author

Ben A. Potter, Yun S. Song, Joel D. Irish, Matthias Steinrücken, Anders Albrechtsen, Martin Sikora, J. Víctor Moreno-Mayar, Jack Kamm, Joshua D. Reuther, Anna-Sapfo Malaspinas, Ludovic Orlando, Ripan S. Malhi, Jonathan Terhorst, Eske Willerslev, Lasse Vinner, Rasmus Nielsen, Simon Rasmussen, and David J. Meltzer

Subjects
Gene Flow, 0301 basic medicine, Time Factors, Pleistocene, Human Migration, Population, Beringia, Gene flow, QH301, 03 medical and health sciences, 0302 clinical medicine, Rivers, Humans, education, QH426, History, Ancient, Phylogeny, education.field_of_study, Multidisciplinary, Models, Genetic, Asia, Eastern, Genome, Human, Land bridge, Infant, Founder Effect, Siberia, Genetics, Population, 030104 developmental biology, Geography, GN, Genetic structure, Indians, North American, Biological dispersal, Ethnology, Alaska, 030217 neurology & neurosurgery, Founder effect
Abstract

An Ancient Beringian population from Late Pleistocene Alaska and the ancestors of other Native American groups descended from a single founding population that diversified around twenty thousand years ago. Studies of human remains from Late Pleistocene Alaska are important for resolving theories on the early population of the Americas. Eske Willerslev and colleagues report the sequencing of the genome of an individual (USR1, from Upward Sun River) who lived in Alaska around 11,500 years ago. Their demographic modelling suggests that USR1 represents a distinct Ancient Beringian population, which together with ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36,000 years ago, but with gene flow persisting until around 25,000 years ago. Their findings agree with the Beringian standstill model, and provide genomic evidence that Native American ancestry can be traced back to the same source population from a single Late Pleistocene founding event. Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved1,2,3,4,5. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka)6. Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans1,7,8. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. Gene flow from ancient north Eurasians into all Native Americans took place 25–20 ka, with Ancient Beringians branching off around 22–18.1 ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian ‘standstill model’9. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5–14.6 ka, and that this probably occurred south of the North American ice sheets. We also show that after 11.5 ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos1, Inuits or Kets10, and that Native American gene flow into Inuits was through northern and not southern Native American groups1. Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.

Published
2017
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11. Author Correction: 137 ancient human genomes from across the Eurasian steppes

Author

Karin Margarita Frei, Vyacheslav Moiyesev, Vladimir I. Bazaliiskii, Thorfinn Sand Korneliussen, Ashyk Alpaslan, Alexander Goryachev, Ruslan Khaskhanov, Andrey Gromov, Nikolay N. Kradin, Amy Goldberg, Bazartseren Boldgiv, Melissa A. Wilson Sayres, Emma Usmanova, Dmitriy Voyakin, Enkhbayar Mijiddorj, Kunbolot Akmatov, Alina Kolbina, Kadicha Tashbaeva, Tereza Štolcová, Zaruhi Khachatryan, Bazartseren Boldbaatar, Karol Pieta, Anders Gorm Pedersen, Nina Lau, Egor Kitov, Levon Yepiskoposyan, Karl-Göran Sjögren, Alexander Tkachev, Simon Rasmussen, Sturla Ellingvåg, Z. Orozbekova, Andrzej W. Weber, Tatyana Hegay, Martin Sikora, Choduraa Dorzhu, Nina Marchi, Valeriy Evdokimov, Gabriel Renaud, Peter de Barros Damgaard, Diimaajav Erdenebaatar, Irina P. Panyushkina, Sainbileg Undrakhbold, Morten E. Allentoft, Gabit Baimbetov, Eske Willerslev, J. Víctor Moreno-Mayar, Viktor K. Mertz, Evgeniy Dmitriev, Ashot Margaryan, Hakon Hakonarson, Bekmukhanbet Nurmukhanbetov, Inga Merkyte, Gulmira Mukhtarova, Irina Shevnina, Kasper Nielsen, Victor Varfolomeev, Nurbol Baimukhanov, Gennady Afanasiev, Arman Beisenov, Evelyne Heyer, Ludovic Orlando, Rasmus Nielsen, Angela M. Taravella, Tabaldiev Kubatbek, Valeriy Loman, Turaly Tulegenov, Václav Smrčka, Lotte Hedeager, Alexey Kukushkin, Michaël Peyrot, Almaz Aldashev, Kristian Kristiansen, Mikkel Winther Pedersen, Rana Dajani, Igor Kukushkin, Andrey Logvin, and Ilya V. Mertz

Subjects
0301 basic medicine, 03 medical and health sciences, 030104 developmental biology, Multidisciplinary, Geography, Published Erratum, Section (typography), Center (algebra and category theory), Classics
Abstract

In this Article, Angela M. Taravella and Melissa A. Wilson Sayres have been added to the author list (associated with: School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ, USA). The author list and Author Information section have been corrected online.

Published
2018
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12. The ancestry and affiliations of Kennewick Man

Author

Ripan S. Malhi, Eske Willerslev, Marcia S. Ponce de León, Ida Moltke, Ludovic Orlando, Morten Rasmussen, Cristina Valdiosera, J. Víctor Moreno-Mayar, Carlos Bustamante, Rasmus Nielsen, Thomas W. Stafford, Morten E. Allentoft, Thorfinn Sand Korneliussen, Hakon Jonsson, Christoph P. E. Zollikofer, David J. Meltzer, Martin Sikora, G. David Poznik, Anders Albrechtsen, University of Zurich, and Willerslev, Eske

Subjects
Cranial morphology, Male, Washington, 10207 Department of Anthropology, common, Genomic data, Population, Biology, Article, Polynesians, HISTORY, Humans, Scientific debate, AMERICA, education, POPULATION, Phylogeny, Skeleton, education.field_of_study, 1000 Multidisciplinary, Multidisciplinary, Native american, Genome, Human, 300 Social sciences, sociology & anthropology, Skull, DNA, Genomics, humanities, GORDON CREEK WOMAN, GENOME, common.group, Indians, North American, Ethnology, Americas, Native American Graves Protection and Repatriation Act, Repatriation
Abstract

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.

Published
2015
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13. A genomic history of Aboriginal Australia

Author

Sankar Subramanian, David M. Lambert, Pascale Gerbault, Joe Dortch, Stephan Peischl, Marta Mirazón Lahr, Sturla Ellingvåg, Nicolas Brucato, Anna-Sapfo Malaspinas, Gudjugudju Fourmile, François-Xavier Ricaut, William Pomat, Simon Rasmussen, Mark Stoneking, Tim H. Heupink, Mait Metspalu, Michael C. Westaway, J. Víctor Moreno-Mayar, Shengyu Ni, Aubrey Lynch, Elizabeth Matisoo-Smith, Fernando Racimo, Joanne L. Wright, Anders Albrechtsen, Farhang Aghakhanian, Andrea Manica, Warren Clark, Ivan P. Levkivskyi, Yali Xue, Thomas Wales, Rasmus Nielsen, Andrea Bamberg Migliano, Alexander J. Mentzer, Craig Muller, Laurent Excoffier, Anders Bergström, Irina Pugach, Thomas Mailund, Søren Brunak, Jacob E. Crawford, Richard Durbin, Paula F. Campos, Anders Eriksson, Claire Bowern, George Koki, Enrico Macholdt, Manjinder S. Sandhu, Ashot Margaryan, Les Murgha, Betty Logan, Vitor C. Sousa, Thorfinn Sand Korneliussen, Maude E. Phipps, Jade Yu Cheng, Isabel Alves, Stephan Schiffels, Eske Willerslev, Colleen Ma Run Wall, Robert Foley, Georgios Athanasiadis, Chris Tyler-Smith, Stephen Oppenheimer, Oscar Lao, Mark G. Thomas, Ida Moltke, Darren Injie, Jeffrey D. Wall, Mikkel H. Schierup, Chiara Barbieri, Doc Reynolds, Peter McAllister, Peter Siba, Martin Sikora, Matthew Leavesley, Isabelle Dupanloup, Institut de Neurobiologie de la Méditerranée [Aix-Marseille Université] (INMED - INSERM U901), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Forensic Molecular Biology, ErasmusMC, Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Evolutionary Genetics, Environmental Futures Centre, Griffith University [Brisbane], Section of Biostatistics [Copenhagen], Department of Public Health [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institute of Ecology and Evolution, University of Berne, Swedish Institute of Space Physics [Uppsala] (IRF), Institut de Biologia Evolutiva (UPF-CSIC), Human Evolution, The Wellcome Trust Sanger Institute [Cambridge], Human Genetics, Technical University of Denmark [Lyngby] (DTU), Allan Wilson Center for Molecular Ecology and Evolution, University of Auckland [Auckland], Wellcome Trust Ctr Human Genet, University of Oxford [Oxford], University of Tartu, Papua New Guinea Institute of Medical Research, Papua New Guinea of Medical Research, Wellcome Trust Genome Campus, Yale University [New Haven], Bioinformatics Research Center (BiRC), Dept Integrat Biol, Strangeways Research Laboratory, MRC, Zoological Institute - Conservation Biology, University of Bern, Section for GeoGenetics, Globe Institute, Center for Biological Sequence Analysis, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), University of Auckland [Auckland]-Massey University-University of Canterbury [Christchurch]-University of Otago [Dunedin, Nouvelle-Zélande], Papua New Guinea Institute of Medical Research (PNG-IMR), Université Nice Sophia Antipolis (1965 - 2019) (UNS), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Universität Bern [Bern] (UNIBE), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Oxford, Eriksson, Anders [0000-0003-3436-3726], Durbin, Richard [0000-0002-9130-1006], Manica, Andrea [0000-0003-1895-450X], Foley, Robert [0000-0003-0479-3039], Mirazon Lahr, Marta [0000-0001-5752-5770], Sandhu, Manjinder [0000-0002-2725-142X], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
Gene Flow, 0301 basic medicine, Native Hawaiian or Other Pacific Islander, Neanderthal, Population genetics, Human Migration, Population Dynamics, Population, Population structure, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Datasets as Topic, Tasmania, 03 medical and health sciences, 0302 clinical medicine, biology.animal, Humans, education, Denisovan, History, Ancient, Phylogeny, Language, New Guinea, education.field_of_study, Multidisciplinary, biology, Genome, Human, Human migration, business.industry, Racial Groups, Australia, New guinea, Genomics, biology.organism_classification, Data processing, Genetics, Population, 030104 developmental biology, Geography, Anthropology, Africa, Ethnology, Biological dispersal, Desert Climate, business, 030217 neurology & neurosurgery
Abstract

The population history of Aboriginal Australians remains largely uncharacterised, not least because of a lack of extensive genomic data. We generated high-coverage genomes for 83 geographically diverse Aboriginal Australians (all speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified from each other 25-40 thousand years ago (kya), suggesting early population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all contemporary Aboriginal Australians studied descend from a single founding population that differentiated around 10-32 kya. We infer a population expansion in northeast Australia during the Holocene (past c.10 kya) associated with limited gene flow from this region to the rest of Australia. This is broadly consistent with the spread of the Pama-Nyungan languages and cultural changes taking place across the continent in the mid-Holocene. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 60-100 kya, following a single out of Africa dispersal and subsequent admixture with different archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

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14. The first horse herders and the impact of early Bronze Age steppe expansions into Asia

Author

Catriona McKenzie, Vyacheslav Moiseyev, Alan K. Outram, Rui Martiniano, Karl-Göran Sjögren, Ilja Merz, J. Víctor Moreno-Mayar, Olga I. Goriunova, Eske Willerslev, Andrey Gromov, Victor Zaibert, Nazish Gul, Brian E. Hemphill, Vladimir I. Bazaliiskii, Valeriy Loman, Valeriy Evdokimov, Katrine Højholt Iversen, Peter de Barros Damgaard, Abdul Hameed, Ashot Margaryan, Abdul Samad, Süleyman Yücel Senyurt, Martin Sikora, Emma Usmanova, Habib Ahmad, Kristian Kristiansen, Muhammad Hassan Khokhar, John Novembre, Arjun Biddanda, Andrzej W. Weber, Nurbol Baimukhanov, Rasmus Nielsen, Guus Kroonen, Andaine Seguin-Orlando, Hannes Schroeder, Simon Rasmussen, Fulya Eylem Yediay, Gojko Barjamovic, Jack Kamm, Richard Durbin, Michaël Peyrot, Melissa Ilardo, Morten E. Allentoft, Andrei V. Polyakov, Constanza de la Fuente, Jeremy Choin, Inam Ullah, Victor Merz, Sachihiro Omura, Ludovic Orlando, Claus M. Zacho, Martiniano, Rui [0000-0003-0216-778X], Kamm, Jack [0000-0003-2412-756X], Kroonen, Guus [0000-0002-3708-0476], Peyrot, Michaël [0000-0002-5983-9690], Barjamovic, Gojko [0000-0002-7455-946X], Zacho, Claus [0000-0002-6217-4220], Baimukhanov, Nurbol [0000-0003-3617-1007], Biddanda, Arjun [0000-0003-1861-1523], Merz, Ilja [0000-0001-9066-9629], Loman, Valeriy [0000-0001-6951-0509], Seguin-Orlando, Andaine [0000-0002-8265-3229], Yediay, Fulya Eylem [0000-0003-3722-3091], Sjögren, Karl-Göran [0000-0003-1791-3175], de la Fuente, Constanza [0000-0002-2857-3615], Polyakov, Andrei [0000-0002-3418-2469], Omura, Sachihiro [0000-0002-2600-9703], McKenzie, Catriona [0000-0001-7288-1319], Margaryan, Ashot [0000-0002-2576-2429], Novembre, John [0000-0001-5345-0214], Orlando, Ludovic [0000-0003-3936-1850], Nielsen, Rasmus [0000-0003-0513-6591], Sikora, Martin [0000-0003-2818-8319], Outram, Alan K [0000-0003-3360-089X], Durbin, Richard [0000-0002-9130-1006], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Asia, South asia, Steppe, Human Migration, Population, Ancient history, Inner Asia, DNA, Mitochondrial, Article, Domestication, 03 medical and health sciences, Asian People, Bronze Age, Animals, Humans, Horses, DNA, Ancient, education, History, Ancient, Language, 2. Zero hunger, geography, education.field_of_study, Chromosomes, Human, Y, Multidisciplinary, geography.geographical_feature_category, Whole Genome Sequencing, Genome, Human, Extramural, Genetic Drift, Grassland, Europe, 030104 developmental biology
Abstract

Ancient steppes for human equestrians The Eurasian steppes reach from the Ukraine in Europe to Mongolia and China. Over the past 5000 years, these flat grasslands were thought to be the route for the ebb and flow of migrant humans, their horses, and their languages. de Barros Damgaard et al. probed whole-genome sequences from the remains of 74 individuals found across this region. Although there is evidence for migration into Europe from the steppes, the details of human movements are complex and involve independent acquisitions of horse cultures. Furthermore, it appears that the Indo-European Hittite language derived from Anatolia, not the steppes. The steppe people seem not to have penetrated South Asia. Genetic evidence indicates an independent history involving western Eurasian admixture into ancient South Asian peoples. Science , this issue p. eaar7711

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