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Padilla-Iglesias C, Derkx I. Hunter-gatherer genetics research: Importance and avenues. EVOLUTIONARY HUMAN SCIENCES 2024; 6:e15. [PMID: 38516374 PMCID: PMC10955370 DOI: 10.1017/ehs.2024.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.
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Affiliation(s)
| | - Inez Derkx
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
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2
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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3
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Lopez Fang L, Peede D, Ortega-Del Vecchyo D, McTavish EJ, Huerta-Sánchez E. Leveraging shared ancestral variation to detect local introgression. PLoS Genet 2024; 20:e1010155. [PMID: 38190420 PMCID: PMC10798638 DOI: 10.1371/journal.pgen.1010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 01/19/2024] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson's D statistic can detect introgression by measuring an excess of shared derived alleles between populations. The D statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions. We propose a new statistic, D+, that leverages both shared ancestral and derived alleles to infer local introgressed regions. Incorporating both shared derived and ancestral alleles increases the number of informative sites per region, improving our ability to identify local introgression. We use a coalescent framework to derive the expected value of this statistic as a function of different demographic parameters under an instantaneous admixture model and use coalescent simulations to compute the power and precision of D+. While the power of D and D+ is comparable, D+ has better precision than D. We apply D+ to empirical data from the 1000 Genome Project and Heliconius butterflies to infer local targets of introgression in humans and in butterflies.
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Affiliation(s)
- Lesly Lopez Fang
- Department of Life & Environmental Sciences, University of California, Merced, Merced, California, United States of America
- Quantitative & Systems Biology Graduate Group, University of California, Merced, Merced, California, United States of America
| | - David Peede
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Biology, Brown University, Providence, Rhode Island, United States of America
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, United States of America
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Querétaro, México
| | - Emily Jane McTavish
- Department of Life & Environmental Sciences, University of California, Merced, Merced, California, United States of America
- Quantitative & Systems Biology Graduate Group, University of California, Merced, Merced, California, United States of America
| | - Emilia Huerta-Sánchez
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Biology, Brown University, Providence, Rhode Island, United States of America
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4
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Bacon AM, Bourgon N, Dufour E, Demeter F, Zanolli C, Westaway KE, Joannes-Boyau R, Duringer P, Ponche JL, Morley MW, Suzzoni E, Frangeul S, Boesch Q, Antoine PO, Boualaphane S, Sichanthongtip P, Sihanam D, Huong NTM, Tuan NA, Fiorillo D, Tombret O, Patole-Edoumba E, Zachwieja A, Luangkhoth T, Souksavatdy V, Dunn TE, Shackelford L, Hublin JJ. Palaeoenvironments and hominin evolutionary dynamics in southeast Asia. Sci Rep 2023; 13:16165. [PMID: 37758744 PMCID: PMC10533506 DOI: 10.1038/s41598-023-43011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Secure environmental contexts are crucial for hominin interpretation and comparison. The discovery of a Denisovan individual and associated fauna at Tam Ngu Hao 2 (Cobra) Cave, Laos, dating back to 164-131 ka, allows for environmental comparisons between this (sub)tropical site and the Palearctic Denisovan sites of Denisova Cave (Russia) and Baishiya Karst Cave (China). Denisovans from northern latitudes foraged in a mix of forested and open landscapes, including tundra and steppe. Using stable isotope values from the Cobra Cave assemblage, we demonstrate that, despite the presence of nearby canopy forests, the Denisovan individual from Cobra Cave primarily consumed plants and/or animals from open forests and savannah. Using faunal evidence and proxy indicators of climates, results herein highlight a local expansion of rainforest at ~ 130 ka, raising questions about how Denisovans responded to this local climate change. Comparing the diet and habitat of the archaic hominin from Cobra Cave with those of early Homo sapiens from Tam Pà Ling Cave (46-43 ka), Laos, it appears that only our species was able to exploit rainforest resources.
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Affiliation(s)
- Anne-Marie Bacon
- Université Paris Cité, CNRS, BABEL UMR 8045, 75012, Paris, France.
| | - Nicolas Bourgon
- IsoTROPIC Research Group, Max Planck Institute for Geoanthropology, 07745, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, 04103, Leipzig, Germany
| | - Elise Dufour
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), MNHN, CNRS, Université Paris Cité, Musée de l'Homme, 75016, Paris, France
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600, Pessac, France
| | - Kira E Westaway
- 'Traps' Luminescence Dating Facility, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group (GARG), Southern Cross University, Lismore, NSW, Australia
| | - Philippe Duringer
- Ecole et Observatoire des Sciences de la Terre, Institut de Physique du Globe de Strasbourg, UMR 7516 CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Luc Ponche
- Laboratoire Image, Ville Environnement, UMR 7362 UdS CNRS, Université de Strasbourg, Strasbourg, France
| | - Mike W Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Sturt Road, Bedford Park, Adelaide, SA, 5042, Australia
| | - Eric Suzzoni
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle en Vercors, France
| | - Sébastien Frangeul
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle en Vercors, France
| | - Quentin Boesch
- Ecole et Observatoire des Sciences de la Terre, Institut de Physique du Globe de Strasbourg, UMR 7516 CNRS, Université de Strasbourg, Strasbourg, France
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France
| | | | | | - Daovee Sihanam
- Ministry of Information, Culture and Tourism, Vientiane, Lao PDR
| | | | | | - Denis Fiorillo
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Olivier Tombret
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Elise Patole-Edoumba
- Muséum d'histoire naturelle de La Rochelle, UMRU 24140 Dynamiques, interactions, interculturalité asiatiques (UBM, LRUniv), La Rochelle, France
| | - Alexandra Zachwieja
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, USA
| | | | | | - Tyler E Dunn
- Anatomical Sciences Education Center, Oregon Health & Sciences University, Portland, OR, USA
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, 04103, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
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5
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Kou SH, Li J, Tam B, Lei H, Zhao B, Xiao F, Wang S. TP53 germline pathogenic variants in modern humans were likely originated during recent human history. NAR Cancer 2023; 5:zcad025. [PMID: 37304756 PMCID: PMC10251638 DOI: 10.1093/narcan/zcad025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
TP53 is crucial for maintaining genome stability and preventing oncogenesis. Germline pathogenic variation in TP53 damages its function, causing genome instability and increased cancer risk. Despite extensive study in TP53, the evolutionary origin of the human TP53 germline pathogenic variants remains largely unclear. In this study, we applied phylogenetic and archaeological approaches to identify the evolutionary origin of TP53 germline pathogenic variants in modern humans. In the phylogenic analysis, we searched 406 human TP53 germline pathogenic variants in 99 vertebrates distributed in eight clades of Primate, Euarchontoglires, Laurasiatheria, Afrotheria, Mammal, Aves, Sarcopterygii and Fish, but we observed no direct evidence for the cross-species conservation as the origin; in the archaeological analysis, we searched the variants in 5031 ancient human genomes dated between 45045 and 100 years before present, and identified 45 pathogenic variants in 62 ancient humans dated mostly within the last 8000 years; we also identified 6 pathogenic variants in 3 Neanderthals dated 44000 to 38515 years before present and 1 Denisovan dated 158 550 years before present. Our study reveals that TP53 germline pathogenic variants in modern humans were likely originated in recent human history and partially inherited from the extinct Neanderthals and Denisovans.
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Affiliation(s)
- Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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6
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Giesen A, Blanckenhorn WU, Schäfer MA, Shimizu KK, Shimizu-Inatsugi R, Misof B, Podsiadlowski L, Niehuis O, Lischer HEL, Aeschbacher S, Kapun M. Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evol Biol 2023; 50:395-412. [PMID: 37854269 PMCID: PMC10579158 DOI: 10.1007/s11692-023-09612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species. We investigate signals of admixture between allopatric and sympatric populations of the two closely related European dung fly species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). Based on microsatellite genotypes, we first inferred a baseline demographic history using Approximate Bayesian Computation. We then used genomic data from pooled DNA of natural and laboratory populations to test for past interspecific gene flow based on allelic configurations discordant with the inferred population tree (ABBA-BABA test with D-statistic). Comparing the detected signals of gene flow with the contemporary geographic relationship among interspecific pairs of populations (sympatric vs. allopatric), we made two contrasting observations. At one site in the French Cevennes, we detected an excess of past interspecific gene flow, while at two sites in Switzerland we observed lower signals of past microsatellite genotypes gene flow among populations in sympatry compared to allopatric populations. These results suggest that the species boundaries between these two species depend on the past and/or present eco-geographic context in Europe, which indicates that there is no uniform link between contemporary geographic proximity and past interspecific gene flow in natural populations. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-023-09612-5.
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Affiliation(s)
- Athene Giesen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin A. Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
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7
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Ruan J, Timmermann A, Raia P, Yun KS, Zeller E, Mondanaro A, Di Febbraro M, Lemmon D, Castiglione S, Melchionna M. Climate shifts orchestrated hominin interbreeding events across Eurasia. Science 2023; 381:699-704. [PMID: 37561879 DOI: 10.1126/science.add4459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 04/19/2023] [Indexed: 08/12/2023]
Abstract
When, where, and how often hominin interbreeding happened is largely unknown. We study the potential for Neanderthal-Denisovan admixture using species distribution models that integrate extensive fossil, archaeological, and genetic data with transient coupled general circulation model simulations of global climate and biomes. Our Pleistocene hindcast of past hominins' habitat suitability reveals pronounced climate-driven zonal shifts in the main overlap region of Denisovans and Neanderthals in central Eurasia. These shifts, which influenced the timing and intensity of potential interbreeding events, can be attributed to the response of climate and vegetation to past variations in atmospheric carbon dioxide and Northern Hemisphere ice-sheet volume. Therefore, glacial-interglacial climate swings likely played an important role in favoring gene flow between archaic humans.
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Affiliation(s)
- Jiaoyang Ruan
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea
- Center for Climate Physics, Pusan National University, Busan, South Korea
| | - Axel Timmermann
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea
- Center for Climate Physics, Pusan National University, Busan, South Korea
| | - Pasquale Raia
- DiSTAR, Monte Sant'Angelo, Napoli Università di Napoli Federico II, Naples, Italy
| | - Kyung-Sook Yun
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea
- Center for Climate Physics, Pusan National University, Busan, South Korea
| | - Elke Zeller
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea
- Department of Climate System, Pusan National University, Busan, South Korea
| | | | - Mirko Di Febbraro
- Department of Biosciences and Territory, University of Molise, C. da Fonte Lappone, Pesche, Italy
| | - Danielle Lemmon
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea
- Center for Climate Physics, Pusan National University, Busan, South Korea
| | - Silvia Castiglione
- DiSTAR, Monte Sant'Angelo, Napoli Università di Napoli Federico II, Naples, Italy
| | - Marina Melchionna
- DiSTAR, Monte Sant'Angelo, Napoli Università di Napoli Federico II, Naples, Italy
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8
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Ferraz T, Suarez Villagran X, Nägele K, Radzevičiūtė R, Barbosa Lemes R, Salazar-García DC, Wesolowski V, Lopes Alves M, Bastos M, Rapp Py-Daniel A, Pinto Lima H, Mendes Cardoso J, Estevam R, Liryo A, Guimarães GM, Figuti L, Eggers S, Plens CR, Azevedo Erler DM, Valadares Costa HA, da Silva Erler I, Koole E, Henriques G, Solari A, Martin G, Serafim Monteiro da Silva SF, Kipnis R, Müller LM, Ferreira M, Carvalho Resende J, Chim E, da Silva CA, Borella AC, Tomé T, Müller Plumm Gomes L, Barros Fonseca D, Santos da Rosa C, de Moura Saldanha JD, Costa Leite L, Cunha CMS, Viana SA, Ozorio Almeida F, Klokler D, Fernandes HLA, Talamo S, DeBlasis P, Mendonça de Souza S, de Paula Moraes C, Elias Oliveira R, Hünemeier T, Strauss A, Posth C. Genomic history of coastal societies from eastern South America. Nat Ecol Evol 2023; 7:1315-1330. [PMID: 37524799 PMCID: PMC10406606 DOI: 10.1038/s41559-023-02114-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 06/08/2023] [Indexed: 08/02/2023]
Abstract
Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-colonial South America, extending from approximately 8,000 to 1,000 years before present (yr BP) across 3,000 km on the Atlantic coast. However, little is known about their connection to early Holocene hunter-gatherers, how this may have contributed to different historical pathways and the processes through which late Holocene ceramists came to rule the coast shortly before European contact. To contribute to our understanding of the population history of indigenous societies on the eastern coast of South America, we produced genome-wide data from 34 ancient individuals as early as 10,000 yr BP from four different regions in Brazil. Early Holocene hunter-gatherers were found to lack shared genetic drift among themselves and with later populations from eastern South America, suggesting that they derived from a common radiation and did not contribute substantially to later coastal groups. Our analyses show genetic heterogeneity among contemporaneous Sambaqui groups from the southeastern and southern Brazilian coast, contrary to the similarity expressed in the archaeological record. The complex history of intercultural contact between inland horticulturists and coastal populations becomes genetically evident during the final horizon of Sambaqui societies, from around 2,200 yr BP, corroborating evidence of cultural change.
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Affiliation(s)
- Tiago Ferraz
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Renan Barbosa Lemes
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Verônica Wesolowski
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Marcony Lopes Alves
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Murilo Bastos
- Departamento de Antropologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Jéssica Mendes Cardoso
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Géosciences Environnement Toulouse, Observatoire Midi Pyrénées, UMR 5563, CNRS, Toulouse, France
| | - Renata Estevam
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Andersen Liryo
- National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Geovan M Guimarães
- Grupo de Pesquisa em Educação Patrimonial e Arqueologia (Grupep), Universidade do Sul de Santa Catarina, Santa Catarina, Brazil
| | - Levy Figuti
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | - Cláudia R Plens
- Laboratory of Archaeological Studies, Department of History, Federal University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Ana Solari
- Fundação Museu do Homem Americano, Piauí, Brazil
| | | | | | | | - Letícia Morgana Müller
- Scientia Consultoria Científica, São Paulo, Brazil
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Mariane Ferreira
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Scientia Consultoria Científica, São Paulo, Brazil
| | - Janine Carvalho Resende
- Instituto Goiano de Pré-história e Arqueologia, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Eliane Chim
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | - Ana Claudia Borella
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Tiago Tomé
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lisiane Müller Plumm Gomes
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | | | - João Darcy de Moura Saldanha
- Universidade de Évora, Évora, Portugal
- Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Brazil
| | - Lúcio Costa Leite
- Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Brazil
| | - Claudia M S Cunha
- Federal University of Piauí, Piauí, Brazil
- Centro de Investigação em Antropologia e Saúde, Universidade de Coimbra, Coimbra, Portugal
| | - Sibeli Aparecida Viana
- Instituto Goiano de Pré-história e Arqueologia, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Fernando Ozorio Almeida
- Programa de Pós-Graduação em Arqueologia, Universidade Federal de Sergipe, Sergipe, Brazil
- Departamento de Arqueologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniela Klokler
- Programa de Pós-Graduação em Arqueologia, Universidade Federal de Sergipe, Sergipe, Brazil
- Departamento de Antropologia e Arqueologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henry Luydy Abraham Fernandes
- Programa de Pós-Graduação em Arqueologia e Patrimônio Cultural, Universidade Federal do Recôncavo da Bahia, Bahia, Brazil
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paulo DeBlasis
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | | | - Rodrigo Elias Oliveira
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
| | - Tábita Hünemeier
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil.
- Institut de Biologia Evolutiva, CSIC/Universitat Pompeu Fabra, Barcelona, Spain.
| | - André Strauss
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.
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9
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Kinneberg VB, Lü DS, Peris D, Ravinet M, Skrede I. Introgression between highly divergent fungal sister species. J Evol Biol 2023; 36:1133-1149. [PMID: 37363874 DOI: 10.1111/jeb.14190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA-BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations.
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Affiliation(s)
- Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Evolution and Paleobiology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Dabao Sun Lü
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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10
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Chian JS, Li J, Wang SM. Evolutionary Origin of Human PALB2 Germline Pathogenic Variants. Int J Mol Sci 2023; 24:11343. [PMID: 37511102 PMCID: PMC10379391 DOI: 10.3390/ijms241411343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
PALB2 (Partner and localizer of BRCA2) is crucial for repairing DNA double-stranded breaks (DSBs) through homologous recombination (HR). Germline pathogenic variation in PALB2 disrupts DNA damage repair and increases the risk of Fanconi Anemia, breast cancer, and ovarian cancer. Determination of the evolutionary origin of human PALB2 variants will promote a deeper understanding of the biological basis of PALB2 germline variation and its roles in human diseases. We tested the evolution origin for 1444 human PALB2 germline variants, including 484 pathogenic and 960 benign variants. We performed a phylogenic analysis by tracing the variants in 100 vertebrates. However, we found no evidence to show that cross-species conservation was the origin of PALB2 germline pathogenic variants, but it is indeed a rich source for PALB2 germline benign variants. We performed a paleoanthropological analysis by tracing the variants in over 5000 ancient humans. We identified 50 pathogenic in 71 ancient humans dated from 32,895 to 689 before the present, of which 90.1% were dated within the recent 10,000 years. PALB2 benign variants were also highly shared with ancient humans. Data from our study reveal that human PALB2 pathogenic variants mostly arose in recent human history.
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Affiliation(s)
- Jia Sheng Chian
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
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11
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Vaill M, Kawanishi K, Varki N, Gagneux P, Varki A. Comparative physiological anthropogeny: exploring molecular underpinnings of distinctly human phenotypes. Physiol Rev 2023; 103:2171-2229. [PMID: 36603157 PMCID: PMC10151058 DOI: 10.1152/physrev.00040.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Anthropogeny is a classic term encompassing transdisciplinary investigations of the origins of the human species. Comparative anthropogeny is a systematic comparison of humans and other living nonhuman hominids (so-called "great apes"), aiming to identify distinctly human features in health and disease, with the overall goal of explaining human origins. We begin with a historical perspective, briefly describing how the field progressed from the earliest evolutionary insights to the current emphasis on in-depth molecular and genomic investigations of "human-specific" biology and an increased appreciation for cultural impacts on human biology. While many such genetic differences between humans and other hominids have been revealed over the last two decades, this information remains insufficient to explain the most distinctive phenotypic traits distinguishing humans from other living hominids. Here we undertake a complementary approach of "comparative physiological anthropogeny," along the lines of the preclinical medical curriculum, i.e., beginning with anatomy and considering each physiological system and in each case considering genetic and molecular components that are relevant. What is ultimately needed is a systematic comparative approach at all levels from molecular to physiological to sociocultural, building networks of related information, drawing inferences, and generating testable hypotheses. The concluding section will touch on distinctive considerations in the study of human evolution, including the importance of gene-culture interactions.
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Affiliation(s)
- Michael Vaill
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
| | - Kunio Kawanishi
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nissi Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Pascal Gagneux
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Ajit Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
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12
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Rigaud S, Rybin EP, Khatsenovich AM, Queffelec A, Paine CH, Gunchinsuren B, Talamo S, Marchenko DV, Bolorbat T, Odsuren D, Gillam JC, Izuho M, Fedorchenko AY, Odgerel D, Shelepaev R, Hublin JJ, Zwyns N. Symbolic innovation at the onset of the Upper Paleolithic in Eurasia shown by the personal ornaments from Tolbor-21 (Mongolia). Sci Rep 2023; 13:9545. [PMID: 37308668 DOI: 10.1038/s41598-023-36140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
Figurative depictions in art first occur ca. 50,000 years ago in Europe, Africa, and Southeast Asia. Considered by most as an advanced form of symbolic behavior, they are restricted to our species. Here, we report a piece of ornament interpreted as a phallus-like representation. It was found in a 42,000 ca.-year-old Upper Paleolithic archaeological layer at the open-air archaeological site of Tolbor-21, in Mongolia. Mineralogical, microscopic, and rugosimetric analyses points toward the allochthonous origin of the pendant and a complex functional history. Three-dimensional phallic pendants are unknown in the Paleolithic record, and this discovery predates the earliest known sexed anthropomorphic representation. It attests that hunter-gatherer communities used sex anatomical attributes as symbols at a very early stage of their dispersal in the region. The pendant was produced during a period that overlaps with age estimates for early introgression events between Homo sapiens and Denisovans, and in a region where such encounters are plausible.
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Affiliation(s)
- Solange Rigaud
- CNRS, Université de Bordeaux, UMR5199 PACEA Bâtiment B2 Allée Geoffroy Saint Hilaire, 33615, Pessac, France.
| | - Evgeny P Rybin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, 17 Lavrentiev Ave., Novosibirsk, Russia, 630090.
| | - Arina M Khatsenovich
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, 17 Lavrentiev Ave., Novosibirsk, Russia, 630090
| | - Alain Queffelec
- CNRS, Université de Bordeaux, UMR5199 PACEA Bâtiment B2 Allée Geoffroy Saint Hilaire, 33615, Pessac, France
| | - Clea H Paine
- Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Byambaa Gunchinsuren
- Institute of Archaeology, Mongolian Academy of Sciences, Peace Avenue, Ulaanbaatar, 13330, Mongolia
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi, 2, 40126, Bologna, Italy
| | - Daria V Marchenko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, 17 Lavrentiev Ave., Novosibirsk, Russia, 630090
| | - Tsedendorj Bolorbat
- Institute of Archaeology, Mongolian Academy of Sciences, Peace Avenue, Ulaanbaatar, 13330, Mongolia
| | - Davaakhuu Odsuren
- Institute of Archaeology, Mongolian Academy of Sciences, Peace Avenue, Ulaanbaatar, 13330, Mongolia
| | | | - Masami Izuho
- Faculty of Social Sciences and Humanities, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan
| | - Alexander Yu Fedorchenko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, 17 Lavrentiev Ave., Novosibirsk, Russia, 630090
| | | | - Roman Shelepaev
- V.S. Sobolev's Institute of Geology and Mineralogy, Siberian Branch of Russian Academy of Science, Ak. Koptyug Avenue 3, Novosibirsk, Russia, 630090
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, 75005, Paris, France
| | - Nicolas Zwyns
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- Department of Anthropology, University of California-Davis, 1 Shields Avenue, Davis, CA, 95616, USA
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13
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Witt KE, Funk A, Añorve-Garibay V, Fang LL, Huerta-Sánchez E. The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations. Genome Biol Evol 2023; 15:evad066. [PMID: 37103242 PMCID: PMC10194819 DOI: 10.1093/gbe/evad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 03/07/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, which have shaped genetic ancestry in modern humans. For example, populations in the Americas are often mosaics of different ancestries due to recent admixture events as part of European colonization. Admixed individuals also often have introgressed DNA from Neanderthals and Denisovans that may have come from multiple ancestral populations, which may affect how archaic ancestry is distributed across an admixed genome. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual's archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight increase of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
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Affiliation(s)
- Kelsey E Witt
- Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Alyssa Funk
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island
| | - Valeria Añorve-Garibay
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Licenciatura en Ciencias Genómicas, Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Querétaro, Mexico
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Lesly Lopez Fang
- Department of Life & Environmental Sciences, University of California, Merced, California, United States of America
| | - Emilia Huerta-Sánchez
- Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
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14
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Pop E, Hilgen S, Adhityatama S, Berghuis H, Veldkamp T, Vonhof H, Sutisna I, Alink G, Noerwidi S, Roebroeks W, Joordens J. Reconstructing the provenance of the hominin fossils from Trinil (Java, Indonesia) through an integrated analysis of the historical and recent excavations. J Hum Evol 2023; 176:103312. [PMID: 36745959 DOI: 10.1016/j.jhevol.2022.103312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 12/17/2022] [Accepted: 12/17/2022] [Indexed: 02/06/2023]
Abstract
In the early 1890s at Trinil, Eugène Dubois found a hominin skullcap (Trinil 2) and femur (Trinil 3, Femur I), situated at the same level ca. 10-15 m apart. He interpreted them as representing one species, Pithecanthropus erectus (now Homo erectus) which he inferred to be a transitional form between apes and humans. Ever since, this interpretation has been questioned-as the skullcap looked archaic and the femur surprisingly modern. From the 1950s onward, chemical and morphological analyses rekindled the debate. Concurrently, (bio)stratigraphic arguments gained importance, raising the stakes by extrapolating the consequences of potential mixing of hominin remains to the homogeneity of the complete Trinil fossil assemblage. However, conclusive evidence on the provenance and age of the hominin fossils remains absent. New Trinil fieldwork yielded unmanned aerial vehicle imagery, digital elevation models, and stratigraphic observations that have been integrated here with an analysis of the historical excavation documentation. Using a geographic information system and sightline analysis, the position of the historical excavation pits and the hominin fossils therein were reconstructed, and the historical stratigraphy was connected to that of new sections and test pits. This study documents five strata situated at low water level at the excavation site. Cutting into a lahar breccia are two similarly oriented, but asynchronous pre-terrace fluvial channels whose highly fossiliferous infills are identified as the primary targets of the historical excavations (Bone-Bearing Channel 1, 830-773 ka; Bone-Bearing Channel 2, 560-380 ka), providing evidence for a mixed faunal assemblage and yielding most of the hominin fossils. These channels were incised by younger terrace-related fluvial channels (terminal Middle or Late Pleistocene) that directly intersect the historical excavations and the reconstructed discovery location of Femur I, thereby providing an explanation for the relatively modern morphology of this 'bone of contention'. The paleoanthropological implications are discussed in light of the current framework of human evolution in Southeast Asia.
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Affiliation(s)
- Eduard Pop
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, the Netherlands; Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands.
| | - Sander Hilgen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, the Netherlands; Faculty of Science, Vrije Universiteit, de Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Shinatria Adhityatama
- Griffith Centre for Social and Cultural Research, Griffith University, Gold Coast Campus, 58 Parklands Drive, Southport, Qld, 4222, Australia
| | - Harold Berghuis
- Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands
| | - Tom Veldkamp
- Faculty ITC, University of Twente, P.O. Box 217, 7500 AE, Enschede, the Netherlands
| | - Hubert Vonhof
- Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany
| | - Indra Sutisna
- Geological Museum, Jl. Diponegoro 57, Bandung, Jawa Barat, 40122, Bandung, Indonesia
| | - Gerrit Alink
- Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands
| | - Sofwan Noerwidi
- Pusat Riset Arkeometri, Organisasi Riset Arkeologi, Bahasa, dan Sastra, Badan Riset dan Inovasi Nasional (OR ARBASTRA - BRIN), Jl. Condet Pejaten 4, Ps. Minggu, Jakarta Selatan, DKI Jakarta, 12510, Indonesia
| | - Wil Roebroeks
- Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands
| | - Josephine Joordens
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, the Netherlands; Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands; Faculty of Science, Vrije Universiteit, de Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands; Faculty of Science and Engineering, Maastricht University, Paul-Henri Spaaklaan 1, 6229 EN, Maastricht, the Netherlands
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15
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Syukriani Y, Wulandari AS, Wanranto B, Hidayat Y. Thousands of years of Malay and Chinese population history in Indonesia and its implication on Paternity Index in DNA paternity testing. Sci Justice 2023; 63:229-237. [PMID: 36870702 DOI: 10.1016/j.scijus.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
The existence of the Chinese population in the predominantly Malay population in Indonesia can be traced back thousands of years, and it has been suspected that it played an essential role in the history of the Malay population origin in Maritime South East Asia. With the fact that the Malay-Indonesian population is currently predominant compared to the Chinese population in Indonesia (Chinese-Indonesian), the selection of the origin of the STRs allele frequency panel population becomes an issue in DNA profiling, including in paternity testing. This study analyses the genetic relationship between the Chinese-Indonesian and Malay-Indonesian populations and how this affects the Paternity Index (PI) calculation in paternity test cases. The study of the relationship between populations was carried out using neighbour-joining (NJ) tree analysis and multidimensional scaling (MDS) on the allele frequency panel of 19 autosomal STRs loci of Malay-Indonesian (n = 210) and Chinese-Indonesian (n = 78) populations. Four population groups were used as references: Malay-Malaysian, Filipino, Chinese, and Caucasian. An MDS analysis was also performed based on the pairwise FST calculation. The combined Paternity Index (CPI) calculation was carried out on 132 paternity cases from the Malay-Indonesian population with inclusive results using a panel of allele frequencies from the six populations. The pairwise FST MDS indicates a closer relationship between the Chinese-Indonesian and Malay-Indonesian compared to the Chinese population, which is in line with the CPIs comparison test. The outcome suggests that the alternative use of allele frequency database between Malay-Indonesian and Chinese-Indonesian for CPI calculations is not very influential. These results can also be considered in studying the extent of genetic assimilation between the two populations. In addition, these results support the robustness claim of multivariate analysis to represent phenomena that phylogenetic analyses may not be able to demonstrate, especially for massive panel data.
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Affiliation(s)
- Yoni Syukriani
- Department of Forensic and Legal Medicine, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.
| | - Ari Sri Wulandari
- Department of Forensic and Legal Medicine, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Busyra Wanranto
- Department of Forensic and Legal Medicine, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia; Faculty of Medicine, Syiah Kuala University, Banda Aceh, Indonesia
| | - Yuyun Hidayat
- Department of Statistics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
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16
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Min-Shan Ko A. The 2022 nobel prize in physiology or medicine awarded for the decoding of the complete ancient human genome. Biomed J 2023; 46:100584. [PMID: 36796758 DOI: 10.1016/j.bj.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Since the publication of the first ancient DNA sequence in 1984, experimental methods used to recover ancient DNA have advanced greatly, illuminating previously unknown branches of the human family tree and opening up several promising new avenues for future studies of human evolution. The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his work on ancient DNA and human evolution. On his first day back at work, he was thrown in the pond as part of his institute's tradition of celebrating award winners.
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Affiliation(s)
- Albert Min-Shan Ko
- Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan; Cardiovascular Department, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Healthy Aging Research Center, Chang Gung University, Taoyuan, Taiwan.
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17
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Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise. Commun Biol 2023; 6:150. [PMID: 36739308 PMCID: PMC9899273 DOI: 10.1038/s42003-023-04510-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/20/2023] [Indexed: 02/06/2023] Open
Abstract
Rapid sea-level rise between the Last Glacial Maximum (LGM) and the mid-Holocene transformed the Southeast Asian coastal landscape, but the impact on human demography remains unclear. Here, we create a paleogeographic map, focusing on sea-level changes during the period spanning the LGM to the present-day and infer the human population history in Southeast and South Asia using 763 high-coverage whole-genome sequencing datasets from 59 ethnic groups. We show that sea-level rise, in particular meltwater pulses 1 A (MWP1A, ~14,500-14,000 years ago) and 1B (MWP1B, ~11,500-11,000 years ago), reduced land area by over 50% since the LGM, resulting in segregation of local human populations. Following periods of rapid sea-level rises, population pressure drove the migration of Malaysian Negritos into South Asia. Integrated paleogeographic and population genomic analysis demonstrates the earliest documented instance of forced human migration driven by sea-level rise.
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18
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The impact of modern admixture on archaic human ancestry in human populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524232. [PMID: 36711776 PMCID: PMC9882123 DOI: 10.1101/2023.01.16.524232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, as well as introgression between humans and archaic humans, Neanderthals and Denisovans. One example are genomes from populations in the Americas, as these are often mosaics of different ancestries due to recent admixture events as part of European colonization. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual’s archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight enrichment of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
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19
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Zhang X, Kim B, Singh A, Sankararaman S, Durvasula A, Lohmueller KE. MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations. Mol Biol Evol 2023; 40:msad001. [PMID: 36617238 PMCID: PMC9887621 DOI: 10.1093/molbev/msad001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/25/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023] Open
Abstract
Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Furthermore, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and the validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.
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Affiliation(s)
- Xinjun Zhang
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA
| | - Armaan Singh
- Department of Computer Science, UCLA, Los Angeles, CA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA
- Department of Computational Medicine, UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Arun Durvasula
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
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20
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Profile of Svante Pääbo: 2022 Nobel laureate in physiology or medicine. Proc Natl Acad Sci U S A 2023; 120:e2217025119. [PMID: 36580591 PMCID: PMC9910432 DOI: 10.1073/pnas.2217025119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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21
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Taufik L, Teixeira JC, Llamas B, Sudoyo H, Tobler R, Purnomo GA. Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects. Genes (Basel) 2022; 13:genes13122373. [PMID: 36553640 PMCID: PMC9778601 DOI: 10.3390/genes13122373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.
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Affiliation(s)
- Leonard Taufik
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
- Correspondence: (L.T.); (G.A.P.)
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
- Centre for Interdisciplinary Studies, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2601, Australia
- Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, SA 5001, Australia
| | - Herawati Sudoyo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
| | - Gludhug A. Purnomo
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (L.T.); (G.A.P.)
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22
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Vespasiani DM, Jacobs GS, Cook LE, Brucato N, Leavesley M, Kinipi C, Ricaut FX, Cox MP, Gallego Romero I. Denisovan introgression has shaped the immune system of present-day Papuans. PLoS Genet 2022; 18:e1010470. [PMID: 36480515 PMCID: PMC9731433 DOI: 10.1371/journal.pgen.1010470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/10/2022] [Indexed: 12/13/2022] Open
Abstract
Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.
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Affiliation(s)
- Davide M. Vespasiani
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
| | - Guy S. Jacobs
- Department of Archaeology, University of Cambridge, Cambridge, Uniteed Kingdom
| | - Laura E. Cook
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
| | - Nicolas Brucato
- Laboratoire de Evolution et Diversite Biologique, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Matthew Leavesley
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
- College of Arts, Society and Education, James Cook University, Cairns, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, Australia
| | - Christopher Kinipi
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - François-Xavier Ricaut
- Laboratoire de Evolution et Diversite Biologique, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Murray P. Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
- Center for Stem Cell Systems, University of Melbourne, Parkville, Australia
- Center for Genomics, Evolution and Medicine, University of Tartu, Tartu, Estonia
- * E-mail:
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23
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Reilly PF, Tjahjadi A, Miller SL, Akey JM, Tucci S. The contribution of Neanderthal introgression to modern human traits. Curr Biol 2022; 32:R970-R983. [PMID: 36167050 PMCID: PMC9741939 DOI: 10.1016/j.cub.2022.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.
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Affiliation(s)
| | - Audrey Tjahjadi
- Department of Anthropology, Yale University, New Haven, CT, USA
| | | | - Joshua M Akey
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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24
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Phylogeographic analysis of the Bantu language expansion supports a rainforest route. Proc Natl Acad Sci U S A 2022; 119:e2112853119. [PMID: 35914165 PMCID: PMC9372543 DOI: 10.1073/pnas.2112853119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Southern Africa has been shaped by the large-scale expansion of Bantu populations fueled by agriculture: Currently, 240 million people speak one of the more than 500 Bantu languages. However, the timing and geographic routes undergone by the Bantu populations remain largely unknown. We use cutting-edge phylogeographic techniques to show that Bantu populations migrated through the Central African tropical rainforest around 4,400 y ago. This adds to the growing evidence that agricultural expansions can successfully overcome ecological challenges as they unfold. The Bantu expansion transformed the linguistic, economic, and cultural composition of sub-Saharan Africa. However, the exact dates and routes taken by the ancestors of the speakers of the more than 500 current Bantu languages remain uncertain. Here, we use the recently developed “break-away” geographical diffusion model, specially designed for modeling migrations, with “augmented” geographic information, to reconstruct the Bantu language family expansion. This Bayesian phylogeographic approach with augmented geographical data provides a powerful way of linking linguistic, archaeological, and genetic data to test hypotheses about large language family expansions. We compare four hypotheses: an early major split north of the rainforest; a migration through the Sangha River Interval corridor around 2,500 BP; a coastal migration around 4,000 BP; and a migration through the rainforest before the corridor opening, at 4,000 BP. Our results produce a topology and timeline for the Bantu language family, which supports the hypothesis of an expansion through Central African tropical forests at 4,420 BP (4,040 to 5,000 95% highest posterior density interval), well before the Sangha River Interval was open.
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25
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Churchill SE, Keys K, Ross AH. Midfacial Morphology and Neandertal-Modern Human Interbreeding. BIOLOGY 2022; 11:1163. [PMID: 36009790 PMCID: PMC9404802 DOI: 10.3390/biology11081163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages.
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Affiliation(s)
- Steven E. Churchill
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA;
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Kamryn Keys
- Human Identification & Forensic Analysis Laboratory, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Ann H. Ross
- Human Identification & Forensic Analysis Laboratory, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA;
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26
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Brucato N, André M, Hudjashov G, Mondal M, Cox MP, Leavesley M, Ricaut FX. Chronology of natural selection in Oceanian genomes. iScience 2022; 25:104583. [PMID: 35880026 PMCID: PMC9308150 DOI: 10.1016/j.isci.2022.104583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul. 239 human genomes from both sides of the Wallacean ecogeographical barriers Signals of selection are dated between -54,000 to -52,000 in modern Oceanian genomes Genes related to immunity and diet were under strong selection Denisovan introgressions participated to the genetic adaptations present in Oceanians
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Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
| | - Mathilde André
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France.,Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Georgi Hudjashov
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, National Capital District 134, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, QLD 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
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27
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Ancient genomes from the last three millennia support multiple human dispersals into Wallacea. Nat Ecol Evol 2022; 6:1024-1034. [PMID: 35681000 PMCID: PMC9262713 DOI: 10.1038/s41559-022-01775-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/13/2022] [Indexed: 12/27/2022]
Abstract
Previous research indicates that human genetic diversity in Wallacea-islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves-has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region's demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600-250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.
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28
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Roberts P, Douka K, Tromp M, Bedford S, Hawkins S, Bouffandeau L, Ilgner J, Lucas M, Marzo S, Hamilton R, Ambrose W, Bulbeck D, Luu S, Shing R, Gosden C, Summerhayes G, Spriggs M. Fossils, fish and tropical forests: prehistoric human adaptations on the island frontiers of Oceania. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200495. [PMID: 35249390 PMCID: PMC8899615 DOI: 10.1098/rstb.2020.0495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Oceania is a key region for studying human dispersals, adaptations and interactions with other hominin populations. Although archaeological evidence now reveals occupation of the region by approximately 65–45 000 years ago, its human fossil record, which has the best potential to provide direct insights into ecological adaptations and population relationships, has remained much more elusive. Here, we apply radiocarbon dating and stable isotope approaches to the earliest human remains so far excavated on the islands of Near and Remote Oceania to explore the chronology and diets of the first preserved human individuals to step across these Pacific frontiers. We demonstrate that the oldest human (or indeed hominin) fossil outside of the mainland New Guinea-Aru area dates to approximately 11 800 years ago. Furthermore, although these early sea-faring populations have been associated with a specialized coastal adaptation, we show that Late Pleistocene–Holocene humans living on islands in the Bismarck Archipelago and in Vanuatu display a persistent reliance on interior tropical forest resources. We argue that local tropical habitats, rather than purely coasts or, later, arriving domesticates, should be emphasized in discussions of human diets and cultural practices from the onset of our species' arrival in this part of the world. This article is part of the theme issue ‘Tropical forests in the deep human past’.
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Affiliation(s)
- Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Germany.,School of Social Science, The University of Queensland, Brisbane, Australia
| | - Katerina Douka
- Department of Archaeology, Max Planck Institute for the Science of Human History, Germany.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Monica Tromp
- Department of Archaeology, Max Planck Institute for the Science of Human History, Germany.,Southern Pacific Archaeological Research, Archaeology Programme, University of Otago, Dunedin, New Zealand.,Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Stuart Bedford
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Germany.,College of Asia and the Pacific, The Australian National University, Canberra, Australia
| | - Stuart Hawkins
- College of Asia and the Pacific, The Australian National University, Canberra, Australia
| | - Laurie Bouffandeau
- UMR 7209 AASPE, CNRS, Muséum National d'Histoire Naturelle, Paris, France.,CIRAP, Université de la Polynésie française, Tahiti, French Polynesia
| | - Jana Ilgner
- Department of Archaeology, Max Planck Institute for the Science of Human History, Germany
| | - Mary Lucas
- Department of Archaeology, Max Planck Institute for the Science of Human History, Germany
| | - Sara Marzo
- Department of Archaeology, Max Planck Institute for the Science of Human History, Germany
| | - Rebecca Hamilton
- Department of Archaeology, Max Planck Institute for the Science of Human History, Germany.,College of Asia and the Pacific, The Australian National University, Canberra, Australia
| | - Wallace Ambrose
- College of Asia and the Pacific, The Australian National University, Canberra, Australia
| | - David Bulbeck
- College of Asia and the Pacific, The Australian National University, Canberra, Australia
| | - Sindy Luu
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Archaeology Programme, University of Otago, Dunedin, New Zealand
| | | | - Chris Gosden
- School of Archaeology, University of Oxford, Oxford, UK
| | - Glenn Summerhayes
- School of Social Science, The University of Queensland, Brisbane, Australia.,Archaeology Programme, University of Otago, Dunedin, New Zealand.,College of Asia and the Pacific, The Australian National University, Canberra, Australia
| | - Matthew Spriggs
- School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, Australia.,Vanuatu Cultural Centre, Port Vila, Vanuatu
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29
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Rodríguez-Rodríguez JE, Ioannidis AG, Medina-Muñoz SG, Barberena-Jonas C, Blanco-Portillo J, Quinto-Cortés CD, Moreno-Estrada A. The genetic legacy of the Manila galleon trade in Mexico. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200419. [PMID: 35430879 PMCID: PMC9014187 DOI: 10.1098/rstb.2020.0419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The population of Mexico has a considerable genetic substructure due to both its pre-Columbian diversity and due to genetic admixture from post-Columbian trans-oceanic migrations. The latter primarily originated in Europe and Africa, but also, to a lesser extent, in Asia. We analyze previously understudied genetic connections between Asia and Mexico to infer the timing and source of this genetic ancestry in Mexico. We identify the predominant origin within Southeast Asia—specifically western Indonesian and non-Negrito Filipino sources—and we date its arrival in Mexico to approximately 13 generations ago (1620 CE). This points to a genetic legacy from the seventeenth century Manila galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco. Indeed, within Mexico we observe the highest level of this trans-Pacific ancestry in Acapulco, located in the state of Guerrero. This colonial Spanish trade route from East Asia to Europe was centred on Mexico and appears in historical records, but its legacy has been largely ignored. Identities and stories were suppressed due to slavery, assimilation of the immigrants as ‘Indios’ and incomplete historical records. Here we characterize this understudied Mexican ancestry. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Santiago G. Medina-Muñoz
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
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30
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Zhang P, Zhang X, Zhang X, Gao X, Huerta-Sanchez E, Zwyns N. Denisovans and Homo sapiens on the Tibetan Plateau: dispersals and adaptations. Trends Ecol Evol 2022; 37:257-267. [PMID: 34863581 PMCID: PMC9140327 DOI: 10.1016/j.tree.2021.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
Recent archaeological discoveries suggest that both archaic Denisovans and Homo sapiens occupied the Tibetan Plateau earlier than expected. Genetic studies show that a pulse of Denisovan introgression was involved in the adaptation of Tibetan populations to high-altitude hypoxia. These findings challenge the traditional view that the plateau was one of the last places on earth colonized by H. sapiens and warrant a reappraisal of the population history of this highland. Here, we integrate archaeological and genomic evidence relevant to human dispersal, settlement, and adaptation in the region. We propose two testable models to address the peopling of the plateau in the broader context of H. sapiens dispersal and their encounters with Denisovans in Asia.
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Affiliation(s)
- Peiqi Zhang
- Department of Anthropology, University of California, Davis, CA 95616, USA.
| | - Xinjun Zhang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Xiaoling Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 10044, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 10044, China
| | - Emilia Huerta-Sanchez
- Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Nicolas Zwyns
- Department of Anthropology, University of California, Davis, CA 95616, USA; Department of Human Evolution, Max Planck Insititute for Evolutionary Anthropology, Leipzig 04103, Germany
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31
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Wohns AW, Wong Y, Jeffery B, Akbari A, Mallick S, Pinhasi R, Patterson N, Reich D, Kelleher J, McVean G. A unified genealogy of modern and ancient genomes. Science 2022; 375:eabi8264. [PMID: 35201891 PMCID: PMC10027547 DOI: 10.1126/science.abi8264] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
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Affiliation(s)
- Anthony Wilder Wohns
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ali Akbari
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Swapan Mallick
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; 1090 Vienna, Austria
| | - Nick Patterson
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - David Reich
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
- Corresponding author.
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32
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Göllner T, Larena M, Kutanan W, Lukas H, Fieder M, Schaschl H. Unveiling the Genetic History of the Maniq, a primary hunter-gatherer society. Genome Biol Evol 2022; 14:6526392. [PMID: 35143674 PMCID: PMC9005329 DOI: 10.1093/gbe/evac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
The Maniq of southern Thailand is one of the last remaining practicing hunter-gatherer communities in the world. However, our knowledge on their genetic origins and demographic history is still largely limited. We present here the genotype data covering ∼2.3 million single nucleotide polymorphisms of 11 unrelated Maniq individuals. Our analyses reveal the Maniq to be closely related to the Semang populations of Malaysia (Malay Negritos), who altogether carry an Andamanese-related ancestry linked to the ancient Hòabìnhian hunter-gatherers of Mainland Southeast Asia (MSEA). Moreover, the Maniq possess ∼35% East Asian-related ancestry, likely brought about by recent admixture with surrounding agriculturist communities in the region. In addition, the Maniq exhibit one of the highest levels of genetic differentiation found among living human populations, indicative of their small population size and historical practice of endogamy. Similar to other hunter-gatherer populations of MSEA, we also find the Maniq to possess low levels of Neanderthal ancestry and undetectable levels of Denisovan ancestry. Altogether, we reveal the Maniq to be a Semang group that experienced intense genetic drift and exhibits signs of ancient Hòabìnhian ancestry.
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Affiliation(s)
- Tobias Göllner
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Maximilian Larena
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen, Uppsala, 18C, 75236, Sweden
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Helmut Lukas
- Institute for Social Anthropology, Austrian Academy of Sciences, Vienna, Austria
| | - Martin Fieder
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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33
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Hoh BP, Deng L, Xu S. The Peopling and Migration History of the Natives in Peninsular Malaysia and Borneo: A Glimpse on the Studies Over the Past 100 years. Front Genet 2022; 13:767018. [PMID: 35154269 PMCID: PMC8829068 DOI: 10.3389/fgene.2022.767018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/07/2022] [Indexed: 12/05/2022] Open
Abstract
Southeast Asia (SEA) has one of the longest records of modern human habitation out-of-Africa. Located at the crossroad of the mainland and islands of SEA, Peninsular Malaysia is an important piece of puzzle to the map of peopling and migration history in Asia, a question that is of interest to many anthropologists, archeologists, and population geneticists. This review aims to revisit our understanding to the population genetics of the natives from Peninsular Malaysia and Borneo over the past century based on the chronology of the technology advancement: 1) Anthropological and Physical Characterization; 2) Blood Group Markers; 3) Protein Markers; 4) Mitochondrial and Autosomal DNA Markers; and 5) Whole Genome Analysis. Subsequently some missing gaps of the study are identified. In the later part of this review, challenges of studying the population genetics of natives will be elaborated. Finally, we conclude our review by reiterating the importance of unveiling migration history and genetic diversity of the indigenous populations as a steppingstone towards comprehending disease evolution and etiology.
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Affiliation(s)
- Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, UCSI Hospital, Port Dickson, Malaysia
- *Correspondence: Boon-Peng Hoh,
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Vallini L, Marciani G, Aneli S, Bortolini E, Benazzi S, Pievani T, Pagani L. OUP accepted manuscript. Genome Biol Evol 2022; 14:6563828. [PMID: 35445261 PMCID: PMC9021735 DOI: 10.1093/gbe/evac045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 11/14/2022] Open
Abstract
The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust’Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal’ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.
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Affiliation(s)
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Department of Physical Sciences, Earth and Environment, University of Siena, Italy
| | - Serena Aneli
- Department of Biology, University of Padova, Italy
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Luca Pagani
- Department of Biology, University of Padova, Italy
- Institute of Genomics, University of Tartu, Estonia
- Corresponding author: E-mail:
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Brown S, Massilani D, Kozlikin MB, Shunkov MV, Derevianko AP, Stoessel A, Jope-Street B, Meyer M, Kelso J, Pääbo S, Higham T, Douka K. The earliest Denisovans and their cultural adaptation. Nat Ecol Evol 2022; 6:28-35. [PMID: 34824388 PMCID: PMC7612221 DOI: 10.1038/s41559-021-01581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 09/23/2021] [Indexed: 11/15/2022]
Abstract
Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave's sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205-192 ka at 68.2% or 217-187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.
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Affiliation(s)
- Samantha Brown
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Scientific Archaeology, University of Tübingen, Tübingen, Germany.
| | - Diyendo Massilani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Maxim B. Kozlikin
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V. Shunkov
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P. Derevianko
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Stoessel
- Max Planck Institute for the Science of Human History, Jena, Germany,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany,Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany
| | - Blair Jope-Street
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, UK,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Austria
| | - Katerina Douka
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
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36
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Deng L, Pan Y, Wang Y, Chen H, Yuan K, Chen S, Lu D, Lu Y, Mokhtar SS, Rahman TA, Hoh BP, Xu S. Genetic connections and convergent evolution of tropical indigenous peoples in Asia. Mol Biol Evol 2021; 39:6481554. [PMID: 34940850 PMCID: PMC8826522 DOI: 10.1093/molbev/msab361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
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Affiliation(s)
- Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Yinan Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Sihan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Siti Shuhada Mokhtar
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia
| | - Thuhairah Abdul Rahman
- Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia
| | - Boon-Peng Hoh
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, UCSI Heights 56000 Cheras, Kuala Lumpur, Malaysia
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. Nat Commun 2021; 12:6232. [PMID: 34716342 PMCID: PMC8556419 DOI: 10.1038/s41467-021-26503-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/06/2021] [Indexed: 12/30/2022] Open
Abstract
We developed a method, ArchaicSeeker 2.0, to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8-94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g., ZNF169), cardiovascular and lung function (e.g., HHAT), UV response and carbohydrate metabolism (e.g., HYAL1/HYAL2/HYAL3), while "archaic deserts" are enriched with genes associated with skin development and keratinization.
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38
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Jinam TA, Hosomichi K, Nakaoka H, Phipps ME, Saitou N, Inoue I. Allelic and haplotypic HLA diversity in indigenous Malaysian populations explored using Next Generation Sequencing. Hum Immunol 2021; 83:17-26. [PMID: 34615609 DOI: 10.1016/j.humimm.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/04/2022]
Abstract
The heterogenous population of Malaysia includes more than 50 indigenous groups, and characterizing their HLA diversity would not only provide insights to their ancestry, but also on the effects of natural selection on their genome. We utilized hybridization-based sequence capture and short-read sequencing on the HLA region of 172 individuals representing seven indigenous groups in Malaysia (Jehai, Kintaq, Temiar, Mah Meri, Seletar, Temuan, Bidayuh). Allele and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DQA1, -DQB1, -DPA1, and -DPB1 revealed several ancestry-informative markers. Using SNP-based heterozygosity and pairwise Fst, we observed signals of natural selection, particularly in HLA-A, -C and -DPB1 genes. Consequently, we showed the impact of natural selection on phylogenetic inference using HLA and non-HLA SNPs. We demonstrate the utility of Next Generation Sequencing for generating unambiguous, high-throughput, high-resolution HLA data that adds to our knowledge of HLA diversity and natural selection in indigenous minority groups.
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Affiliation(s)
- Timothy A Jinam
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, Tokyo, Japan
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
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39
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Ashraf B, Lawson DJ. Genetic drift from the out-of-Africa bottleneck leads to biased estimation of genetic architecture and selection. Eur J Hum Genet 2021; 29:1549-1556. [PMID: 33846580 PMCID: PMC8484570 DOI: 10.1038/s41431-021-00873-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
Most complex traits evolved in the ancestors of all modern humans and have been under negative or balancing selection to maintain the distribution of phenotypes observed today. Yet all large studies mapping genomes to complex traits occur in populations that have experienced the Out-of-Africa bottleneck. Does this bottleneck affect the way we characterise complex traits? We demonstrate using the 1000 Genomes dataset and hypothetical complex traits that genetic drift can strongly affect the joint distribution of effect size and SNP frequency, and that the bias can be positive or negative depending on subtle details. Characterisations that rely on this distribution therefore conflate genetic drift and selection. We provide a model to identify the underlying selection parameter in the presence of drift, and demonstrate that a simple sensitivity analysis may be enough to validate existing characterisations. We conclude that biobanks characterising more worldwide diversity would benefit studies of complex traits.
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Affiliation(s)
- Bilal Ashraf
- Department of Statistical Sciences, School of Mathematics, University of Bristol, Fry Building, Bristol, BS8 1UG, UK
- Department of Anthropology, Durham Research Methods Centre, University of Durham, Dawson Building, Durham, DH13LE, UK
| | - Daniel John Lawson
- Department of Statistical Sciences, School of Mathematics, University of Bristol, Fry Building, Bristol, BS8 1UG, UK.
- Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Oakfield House, Bristol, BS8 2BN, UK.
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40
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An etiology of human modernity. ANTHROPOLOGICAL REVIEW 2021. [DOI: 10.2478/anre-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Following the refutation of the replacement hypothesis, which had proposed that a ‘superior’ hominin species arose in Africa and replaced all other humans existing at the time, the auto-domestication hypothesis remains the only viable explanation for the relatively abrupt change from robust to gracile humans in the Late Pleistocene. It invokes the incidental institution of the domestication syndrome in humans, most probably by newly introduced cultural practices. It also postulates that the induction of exograms compensated for the atrophy of the brain caused by domestication. This new explanation of the origins of modernity in humans elucidates practically all its many aspects, in stark contrast to the superseded replacement hypothesis, which explained virtually nothing. The first results of the domestication syndrome’s genetic exploration have become available in recent years, and they endorse the human self-domestication hypothesis.
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41
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Brucato N, André M, Tsang R, Saag L, Kariwiga J, Sesuki K, Beni T, Pomat W, Muke J, Meyer V, Boland A, Deleuze JF, Sudoyo H, Mondal M, Pagani L, Romero IG, Metspalu M, Cox MP, Leavesley M, Ricaut FX. Papua New Guinean genomes reveal the complex settlement of north Sahul. Mol Biol Evol 2021; 38:5107-5121. [PMID: 34383935 PMCID: PMC8557464 DOI: 10.1093/molbev/msab238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our dataset, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.
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Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Mathilde André
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France.,Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Roxanne Tsang
- School of Humanities, Languages and Social Science and Place, Evolution and Rock Art Heritage Unit, Griffith University Centre for Social and Cultural Research, Griffith University, Australia.,Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Jason Kariwiga
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea.,School of Social Science, University of Queensland, Australia, St Lucia, QLD 4072, Australia
| | - Kylie Sesuki
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Teppsy Beni
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - John Muke
- Social Research Institute, Papua New Guinea
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Luca Pagani
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia.,Department of Biology, University of Padua, Italy
| | | | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Murray P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, Queensland, 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New south Wales, 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
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42
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Larena M, McKenna J, Sanchez-Quinto F, Bernhardsson C, Ebeo C, Reyes R, Casel O, Huang JY, Hagada KP, Guilay D, Reyes J, Allian FP, Mori V, Azarcon LS, Manera A, Terando C, Jamero L, Sireg G, Manginsay-Tremedal R, Labos MS, Vilar RD, Latiph A, Saway RL, Marte E, Magbanua P, Morales A, Java I, Reveche R, Barrios B, Burton E, Salon JC, Kels MJT, Albano A, Cruz-Angeles RB, Molanida E, Granehäll L, Vicente M, Edlund H, Loo JH, Trejaut J, Ho SYW, Reid L, Lambeck K, Malmström H, Schlebusch C, Endicott P, Jakobsson M. Philippine Ayta possess the highest level of Denisovan ancestry in the world. Curr Biol 2021; 31:4219-4230.e10. [PMID: 34388371 PMCID: PMC8596304 DOI: 10.1016/j.cub.2021.07.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/04/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world-∼30%-40% greater than that of Australians and Papuans-consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.
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Affiliation(s)
- Maximilian Larena
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Federico Sanchez-Quinto
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
| | - Carolina Bernhardsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Carlo Ebeo
- National Committee on Cultural Education, National Commission for Culture and the Arts, Intramuros, Manila, Philippines; National Museum of the Philippines, Padre Burgos Avenue, Rizal Park, Ermita, Manila, Philippines
| | - Rebecca Reyes
- Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines; National Commission on Indigenous Peoples, Philippines
| | - Ophelia Casel
- Mindanao Doctors Hospital and Cancer Center, Kabacan, Cotabato, Philippines
| | - Jin-Yuan Huang
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Kim Pullupul Hagada
- National Commission on Indigenous Peoples, Philippines; Young Indigenous Peoples Empowered to Act in Community Engagement, Diffun, Quirino
| | - Dennis Guilay
- Balangao Indigenous Cultural Community, Paracelis, Mountain Province, Cordillera Administrative Region, Philippines
| | - Jennelyn Reyes
- Department of Education - Bataan Division, Bataan, Philippines
| | - Fatima Pir Allian
- Nisa Ul Haqq fi Bangsamoro, Zamboanga City, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines; Tarbilang Foundation, Inc., Bongao, Tawi-Tawi, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | - Virgilio Mori
- Tarbilang Foundation, Inc., Bongao, Tawi-Tawi, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | - Lahaina Sue Azarcon
- Center for Language and Culture, Quirino State University, Barangay Andres Bonifacio, Diffun, Quirino, Philippines
| | - Alma Manera
- Center for Language and Culture, Cagayan State University - Andrews Campus, Caritan Highway, Tuguegarao, Cagayan, Philippines
| | - Celito Terando
- Tagakaulo Indigenous Cultural Community, Malungon, Sarangani, Philippines; Sulong Tribu Program, Provincial Government of Sarangani, Glan, Sarangani, Philippines
| | - Lucio Jamero
- Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines
| | - Gauden Sireg
- Subanen Indigenous Cultural Community, Lakewood, Zamboanga del Sur, Philippines; Dumendingan Arts Guild Inc., Pagadian City, Zamboanga del Sur, Philippines
| | | | - Maria Shiela Labos
- Ateneo Institute of Anthropology, Ateneo de Davao University, Roxas Avenue, 8016 Davao City, Philippines; Museo Dabawenyo, Andres Bonifacio Rotunda, Poblacion District, Davao City, Philippines
| | - Richard Dian Vilar
- Cultural Outreach Program, Kaliwat Performing Artists Collective, Gumamela St., Lanang, Davao City, Philippines; Culture, Heritage, and Arts Office, Local Government Unit of Butuan, Butuan City, Philippines
| | - Acram Latiph
- Institute for Peace and Development in Mindanao, Mindanao State University - Marawi Campus, Marawi City, Lanao del Sur, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | | | - Erwin Marte
- Legal Affairs Office, Indigenous People's Mandatory Representative - Sangguniang Panlalawigan, Bukidnon, Northern Mindanao, Philippines
| | - Pablito Magbanua
- National Commission on Indigenous Peoples, Philippines; Cuyonon Indigenous Cultural Community, Cuyo Island, Palawan, Philippines
| | - Amor Morales
- Surigaonon Heritage Center, Surigao City, Surigao del Norte, Philippines
| | - Ismael Java
- Kabankalan City Cultural and Tourism Foundation, Inc., Kabankalan City, Negros Occidental, Philippines; Cultural Research and Documentation, Negros Museum, Gatuslao St., Bacolod, Negros Occidental, Philippines
| | - Rudy Reveche
- Cultural Research and Documentation, Negros Museum, Gatuslao St., Bacolod, Negros Occidental, Philippines; Culture and Arts Program, Colegio San Agustin, BS Aquino Drive, Bacolod, Negros Occidental, Philippines
| | - Becky Barrios
- Panaghiusa Alang Sa Kaugalingnan Ug Kalingkawasan, Inc., Bunawan, Agusan del Sur, Philippines; Agusan Manobo Indigenous Cultural Community, La Paz, Agusan del Sur, Philippines
| | - Erlinda Burton
- Museo de Oro, Xavier University - Ateneo de Cagayan, Corrales Avenue, Cagayan de Oro City, Philippines
| | - Jesus Christopher Salon
- Museo de Oro, Xavier University - Ateneo de Cagayan, Corrales Avenue, Cagayan de Oro City, Philippines; City Museum of Cagayan de Oro, Fernandez St., Cagayan de Oro City, Philippines
| | - Ma Junaliah Tuazon Kels
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Adrian Albano
- Kalanguya Indigenous Cultural Community, Tinoc, Ifugao, Cordillera Administrative Region, Philippines; Office of Tinoc Campus Administrator, Ifugao State University, Tinoc, Ifugao, Cordillera Administrative Region, Philippines
| | | | - Edison Molanida
- Heritage Office, National Commission for Culture and the Arts, Intramuros, Manila, Philippines; Office of the Executive Director, National Commission for Culture and the Arts, Intramuros, Manila, Philippines
| | - Lena Granehäll
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Mário Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Jean Trejaut
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Lawrence Reid
- Department of Linguistics, University of Hawai'i at Mānoa, Mānoa, HI, USA; National Museum of the Philippines, Padre Burgos Avenue, Rizal Park, Ermita, Manila, Philippines
| | - Kurt Lambeck
- Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa; SciLifeLab, Stockholm and Uppsala, Sweden
| | - Phillip Endicott
- Department Hommes Natures Societies, Musée de l'Homme, 75016 Paris, Ile de France, France
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa; SciLifeLab, Stockholm and Uppsala, Sweden.
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43
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Khan N, de Manuel M, Peyregne S, Do R, Prufer K, Marques-Bonet T, Varki N, Gagneux P, Varki A. Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins. Genome Biol Evol 2021; 12:1040-1050. [PMID: 32556248 PMCID: PMC7379906 DOI: 10.1093/gbe/evaa125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface “self-associated molecular patterns” that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2–3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a “hotspot” in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human–Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal–human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.
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Affiliation(s)
- Naazneen Khan
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Stephane Peyregne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Raymond Do
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Kay Prufer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain
| | - Nissi Varki
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Pascal Gagneux
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Ajit Varki
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
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44
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Storz JF, Signore AV. Introgressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates. Front Genet 2021; 12:696484. [PMID: 34239546 PMCID: PMC8258166 DOI: 10.3389/fgene.2021.696484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
In natural populations of animals, a growing body of evidence suggests that introgressive hybridization may often serve as an important source of adaptive genetic variation. Population genomic studies of high-altitude vertebrates have provided strong evidence of positive selection on introgressed allelic variants, typically involving a long-term highland species as the donor and a more recently arrived colonizing species as the recipient. In high-altitude humans and canids from the Tibetan Plateau, case studies of adaptive introgression involving the HIF transcription factor, EPAS1, have provided insights into complex histories of ancient introgression, including examples of admixture from now-extinct source populations. In Tibetan canids and Andean waterfowl, directed mutagenesis experiments involving introgressed hemoglobin variants successfully identified causative amino acid mutations and characterized their phenotypic effects, thereby providing insights into the functional properties of selectively introgressed alleles. We review case studies of adaptive introgression in high-altitude vertebrates and we highlight findings that may be of general significance for understanding mechanisms of environmental adaptation involving different sources of genetic variation.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Anthony V Signore
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
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45
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Abstract
Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000-59,500) y ago, and selection started around 9,000 (2,500-42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.
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46
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The deep population history of northern East Asia from the Late Pleistocene to the Holocene. Cell 2021; 184:3256-3266.e13. [PMID: 34048699 DOI: 10.1016/j.cell.2021.04.040] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/20/2021] [Accepted: 04/23/2021] [Indexed: 11/22/2022]
Abstract
Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6-3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia.
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47
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Locarnini SA, Littlejohn M, Yuen LKW. Origins and Evolution of the Primate Hepatitis B Virus. Front Microbiol 2021; 12:653684. [PMID: 34108947 PMCID: PMC8180572 DOI: 10.3389/fmicb.2021.653684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
Recent interest in the origins and subsequent evolution of the hepatitis B virus (HBV) has strengthened with the discovery of ancient HBV sequences in fossilized remains of humans dating back to the Neolithic period around 7,000 years ago. Metagenomic analysis identified a number of African non-human primate HBV sequences in the oldest samples collected, indicating that human HBV may have at some stage, evolved in Africa following zoonotic transmissions from higher primates. Ancestral genotype A and D isolates were also discovered from the Bronze Age, not in Africa but rather Eurasia, implying a more complex evolutionary and migratory history for HBV than previously recognized. Most full-length ancient HBV sequences exhibited features of inter genotypic recombination, confirming the importance of recombination and the mutation rate of the error-prone viral replicase as drivers for successful HBV evolution. A model for the origin and evolution of HBV is proposed, which includes multiple cross-species transmissions and favors subsequent recombination events that result in a pathogen and can successfully transmit and cause persistent infection in the primate host.
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Affiliation(s)
- Stephen A Locarnini
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Lilly K W Yuen
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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48
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Gopalan S, Atkinson EG, Buck LT, Weaver TD, Henn BM. Inferring archaic introgression from hominin genetic data. Evol Anthropol 2021; 30:199-220. [PMID: 33951239 PMCID: PMC8360192 DOI: 10.1002/evan.21895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/03/2020] [Accepted: 03/29/2021] [Indexed: 01/05/2023]
Abstract
Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Elizabeth G Atkinson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Stanley Center for Psychiatric Research, Broad Institute, Boston, Massachusetts, USA
| | - Laura T Buck
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, California, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, University of California, Davis, California, USA.,UC Davis Genome Center, University of California, Davis, California, USA
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49
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Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture. Nat Ecol Evol 2021; 5:616-624. [PMID: 33753899 DOI: 10.1038/s41559-021-01408-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.
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50
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Liu D, Duong NT, Ton ND, Van Phong N, Pakendorf B, Van Hai N, Stoneking M. Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity. Mol Biol Evol 2021; 37:2503-2519. [PMID: 32344428 PMCID: PMC7475039 DOI: 10.1093/molbev/msaa099] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Vietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia. Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here, we analyze newly generated genome-wide single-nucleotide polymorphism data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in Mainland Southeast Asia. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. In contrast to previous studies that suggested a largely indigenous origin for Vietnamese genetic diversity, we find that Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that likely reflect different sources for the ancestry associated with each language family. However, linguistic diversity does not completely match genetic diversity: There have been extensive interactions between the Hmong-Mien and Tai-Kadai groups; different Austro-Asiatic groups show different affinities with other ethnolinguistic groups; and we identified a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages during the past 2,500 years. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically diverse region, such as Vietnam.
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Affiliation(s)
- Dang Liu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nguyen Thuy Duong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Van Phong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Brigitte Pakendorf
- Laboratoire Dynamique du Langage, UMR5596, CNRS & Université de Lyon, Lyon, France
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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