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Iasi LNM, Chintalapati M, Skov L, Mesa AB, Hajdinjak M, Peter BM, Moorjani P. Neandertal ancestry through time: Insights from genomes of ancient and present-day humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593955. [PMID: 38798350 PMCID: PMC11118355 DOI: 10.1101/2024.05.13.593955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify the location and size of introgressed Neandertal ancestry segments in more than 300 genomes spanning the last 50,000 years. We study how Neandertal ancestry is shared among individuals to infer the time and duration of the Neandertal gene flow. We find the correlation of Neandertal segment locations across individuals and their divergence to sequenced Neandertals, both support a model of single major Neandertal gene flow. Our catalog of introgressed segments through time confirms that most natural selection-positive and negative-on Neandertal ancestry variants occurred immediately after the gene flow, and provides new insights into how the contact with Neandertals shaped human origins and adaptation.
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [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: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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3
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Arango-Isaza E, Capodiferro MR, Aninao MJ, Babiker H, Aeschbacher S, Achilli A, Posth C, Campbell R, Martínez FI, Heggarty P, Sadowsky S, Shimizu KK, Barbieri C. The genetic history of the Southern Andes from present-day Mapuche ancestry. Curr Biol 2023:S0960-9822(23)00607-3. [PMID: 37279753 DOI: 10.1016/j.cub.2023.05.013] [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: 11/03/2022] [Revised: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 06/08/2023]
Abstract
The southernmost regions of South America harbor some of the earliest evidence of human presence in the Americas. However, connections with the rest of the continent and the contextualization of present-day indigenous ancestries remain poorly resolved. In this study, we analyze the genetic ancestry of one of the largest indigenous groups in South America: the Mapuche. We generate genome-wide data from 64 participants from three Mapuche populations in Southern Chile: Pehuenche, Lafkenche, and Huilliche. Broadly, we describe three main ancestry blocks with a common origin, which characterize the Southern Cone, the Central Andes, and Amazonia. Within the Southern Cone, ancestors of the Mapuche lineages differentiated from those of the Far South during the Middle Holocene and did not experience further migration waves from the north. We find that the deep genetic split between the Central and Southern Andes is followed by instances of gene flow, which may have accompanied the southward spread of cultural traits from the Central Andes, including crops and loanwords from Quechua into Mapudungun (the language of the Mapuche). Finally, we report close genetic relatedness between the three populations analyzed, with the Huilliche characterized additionally by intense recent exchanges with the Far South. Our findings add new perspectives on the genetic (pre)history of South America, from the first settlement through to the present-day indigenous presence. Follow-up fieldwork took these results back to the indigenous communities to contextualize the genetic narrative alongside indigenous knowledge and perspectives.
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Affiliation(s)
- Epifanía Arango-Isaza
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland.
| | - Marco Rosario Capodiferro
- Trinity College Dublin, Dublin 2, Ireland; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | | | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Cosimo Posth
- Institute for Archaeological Sciences, Archaeo, and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen 72074, Germany
| | - Roberto Campbell
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago 6904411, Chile
| | - Felipe I Martínez
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago 6904411, Chile; Center for Intercultural and Indigenous Research, Santiago 7820436, Chile
| | - Paul Heggarty
- "Waves" ERC Group, Department of Human Behavior, Evolution and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Scott Sadowsky
- Department of Linguistics and Literature, Universidad de Cartagena, Cartagena 130001, Colombia
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
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4
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Aqil A, Gill S, Gokcumen O, Malhi RS, Reese EA, Smith JL, Heaton TT, Lindqvist C. A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska. iScience 2023; 26:106581. [PMID: 37138779 PMCID: PMC10149335 DOI: 10.1016/j.isci.2023.106581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.
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Affiliation(s)
- Alber Aqil
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Ripan S. Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Jane L. Smith
- USDA-Forest Service, Tongass National Forest, Petersburg, AK 99833, USA
| | - Timothy T. Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, SD 57069, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Corresponding author
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5
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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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6
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Prentiss AM, Laue C, Gjesfjeld E, Walsh MJ, Denis M, Foor TA. Evolution of the Okvik/Old Bering Sea culture of the Bering Strait as a major transition. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210415. [PMID: 36688384 PMCID: PMC9869439 DOI: 10.1098/rstb.2021.0415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Great transitions are thought to embody major shifts in locus of selection, labour diversification and communication systems. Such expectations are relevant for biological and cultural systems as decades of research has demonstrated similar dynamics within the evolution of culture. The evolution of the Neo-Inuit cultural tradition in the Bering Strait provides an ideal context for examination of cultural transitions. The Okvik/Old Bering Sea (Okvik/OBS) culture of Bering Strait is the first representative of the Neo-Inuit tradition. Archaeological evidence drawn for settlement and subsistence data, technological traditions and mortuary contexts suggests that Okvik/OBS fits the definition of a major transition given change in the nature of group membership (from families to political groups with social ranking), task organization (emergent labour specialization) and communication (advent of complex art forms conveying social and ideological information). This permits us to develop a number of implications about the evolutionary process recognizing that transitions may occur on three scales: (1) ephemeral variants, as for example, simple technological entities; (2) integrated systems, spanning modular technology to socio-economic strategies; and (3) simultaneous change across all scales with emergent properties. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
| | - Cheyenne Laue
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
| | - Erik Gjesfjeld
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, England
| | - Matthew J. Walsh
- Modern History and World Cultures Section, The National Museum of Denmark, Ny Vestergade 10 Prinsens Palæ 1471, Copenhagen, Denmark
| | - Megan Denis
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
| | - Thomas A. Foor
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
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7
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Nielsen SV, Vaughn AH, Leppälä K, Landis MJ, Mailund T, Nielsen R. Bayesian inference of admixture graphs on Native American and Arctic populations. PLoS Genet 2023; 19:e1010410. [PMID: 36780565 PMCID: PMC9956672 DOI: 10.1371/journal.pgen.1010410] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/24/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023] Open
Abstract
Admixture graphs are mathematical structures that describe the ancestry of populations in terms of divergence and merging (admixing) of ancestral populations as a graph. An admixture graph consists of a graph topology, branch lengths, and admixture proportions. The branch lengths and admixture proportions can be estimated using numerous numerical optimization methods, but inferring the topology involves a combinatorial search for which no polynomial algorithm is known. In this paper, we present a reversible jump MCMC algorithm for sampling high-probability admixture graphs and show that this approach works well both as a heuristic search for a single best-fitting graph and for summarizing shared features extracted from posterior samples of graphs. We apply the method to 11 Native American and Siberian populations and exploit the shared structure of high-probability graphs to characterize the relationship between Saqqaq, Inuit, Koryaks, and Athabascans. Our analyses show that the Saqqaq is not a good proxy for the previously identified gene flow from Arctic people into the Na-Dene speaking Athabascans.
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Affiliation(s)
- Svend V. Nielsen
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Andrew H. Vaughn
- Center for Computational Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Kalle Leppälä
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
| | - Michael J. Landis
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California Berkeley, Berkeley, California, United States of America
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
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8
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Luis JR, Palencia-Madrid L, Garcia-Bertrand R, Herrera RJ. Bidirectional dispersals during the peopling of the North American Arctic. Sci Rep 2023; 13:1268. [PMID: 36690673 PMCID: PMC9871004 DOI: 10.1038/s41598-023-28384-8] [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: 08/27/2022] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
It is thought that Paleo-Inuit were the first people that settled the American Arctic about 5000 BP (before the present) from a migration that crossed Beringia from Northeast Asia. It is theorized that this group initially migrated to the North Slopes of Alaska and subsequently expanded eastward, eventually reaching Greenland. A second circumpolar dispersal of Neo-Inuit from the North Slopes associated with the Thule-Inuk culture has been postulated to have extended eastward around 800 BP, totally replacing the original Paleo-Inuit without admixing. Although generally accepted, this migration scenario is incompatible with previously reported indications of east to west gene flow across the American Arctic. Here we report on the Y-chromosome haplogroup and Y-STR diversity of the four circumpolar populations of the Tuva Republic (N = 24), Northeast Siberia (N = 9), Bethel, Alaska (N = 40), and Barrow, Alaska (N = 31). Four haplogroup lineages (Q-NWT01, Q-M3, Q-M346, and Q-M120) were detected, Q-NWT01 and Q-M3 being the most abundant at 11.11 and 66.67% in Northeast Siberia, 32.50 and 65.00% in Bethel, and 67.74 and 32.26% in Barrow, respectively. The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STYR loci using the AmpFlSTR Yfiler system. Age estimates and diversity values for the Q-NWT01 and Q-M3 mutations suggest extensive movement of male individuals along the entire longitudinal stretch of the American circumpolar region. Throughout the entire region, Q-M3 exhibits a west to east decreasing gradient in age and diversity while Q-NWT01 indicates the opposite with older TMRCA and higher diversity values running from east to west with the most recent estimates in Canada and Alaska. The high age and diversity values in Greenland are congruent with an origin of the Q-NWT01 mutation in the east of the circumpolar range about 2000-3000 ya. This scenario is incompatible with a complete biological replacement starting about 700 BP of Paleo-Inuit like the Dorset by the Thule-Inuit (Neo-Inuit), as is currently thought, and more parsimonious with gene flow carrying the NWT01 mutation from a pre-Thule population to the ancestors of the present-day Inuit.
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Affiliation(s)
- Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA.
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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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10
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A novel splice-affecting HNF1A variant with large population impact on diabetes in Greenland. THE LANCET REGIONAL HEALTH. EUROPE 2022; 24:100529. [PMID: 36649380 PMCID: PMC9832271 DOI: 10.1016/j.lanepe.2022.100529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/15/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022]
Abstract
Background The genetic disease architecture of Inuit includes a large number of common high-impact variants. Identification of such variants contributes to our understanding of the genetic aetiology of diseases and improves global equity in genomic personalised medicine. We aimed to identify and characterise novel variants in genes associated with Maturity Onset Diabetes of the Young (MODY) in the Greenlandic population. Methods Using combined data from Greenlandic population cohorts of 4497 individuals, including 448 whole genome sequenced individuals, we screened 14 known MODY genes for previously identified and novel variants. We functionally characterised an identified novel variant and assessed its association with diabetes prevalence and cardiometabolic traits and population impact. Findings We identified a novel variant in the known MODY gene HNF1A with an allele frequency of 1.9% in the Greenlandic Inuit and absent elsewhere. Functional assays indicate that it prevents normal splicing of the gene. The variant caused lower 30-min insulin (β = -232 pmol/L, βSD = -0.695, P = 4.43 × 10-4) and higher 30-min glucose (β = 1.20 mmol/L, βSD = 0.441, P = 0.0271) during an oral glucose tolerance test. Furthermore, the variant was associated with type 2 diabetes (OR 4.35, P = 7.24 × 10-6) and HbA1c (β = 0.113 HbA1c%, βSD = 0.205, P = 7.84 × 10-3). The variant explained 2.5% of diabetes variance in Greenland. Interpretation The reported variant has the largest population impact of any previously reported variant within a MODY gene. Together with the recessive TBC1D4 variant, we show that close to 1 in 5 cases of diabetes (18%) in Greenland are associated with high-impact genetic variants compared to 1-3% in large populations. Funding Novo Nordisk Foundation, Independent Research Fund Denmark, and Karen Elise Jensen's Foundation.
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11
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Duncan CJ, Skouboe MK, Howarth S, Hollensen AK, Chen R, Børresen ML, Thompson BJ, Stremenova Spegarova J, Hatton CF, Stæger FF, Andersen MK, Whittaker J, Paludan SR, Jørgensen SE, Thomsen MK, Mikkelsen JG, Heilmann C, Buhas D, Øbro NF, Bay JT, Marquart HV, de la Morena MT, Klejka JA, Hirschfeld M, Borgwardt L, Forss I, Masmas T, Poulsen A, Noya F, Rouleau G, Hansen T, Zhou S, Albrechtsen A, Alizadehfar R, Allenspach EJ, Hambleton S, Mogensen TH. Life-threatening viral disease in a novel form of autosomal recessive IFNAR2 deficiency in the Arctic. J Exp Med 2022; 219:e20212427. [PMID: 35442417 PMCID: PMC9026249 DOI: 10.1084/jem.20212427] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Type I interferons (IFN-I) play a critical role in human antiviral immunity, as demonstrated by the exceptionally rare deleterious variants of IFNAR1 or IFNAR2. We investigated five children from Greenland, Canada, and Alaska presenting with viral diseases, including life-threatening COVID-19 or influenza, in addition to meningoencephalitis and/or hemophagocytic lymphohistiocytosis following live-attenuated viral vaccination. The affected individuals bore the same homozygous IFNAR2 c.157T>C, p.Ser53Pro missense variant. Although absent from reference databases, p.Ser53Pro occurred with a minor allele frequency of 0.034 in their Inuit ancestry. The serine to proline substitution prevented cell surface expression of IFNAR2 protein, small amounts of which persisted intracellularly in an aberrantly glycosylated state. Cells exclusively expressing the p.Ser53Pro variant lacked responses to recombinant IFN-I and displayed heightened vulnerability to multiple viruses in vitro-a phenotype rescued by wild-type IFNAR2 complementation. This novel form of autosomal recessive IFNAR2 deficiency reinforces the essential role of IFN-I in viral immunity. Further studies are warranted to assess the need for population screening.
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Affiliation(s)
- Christopher J.A. Duncan
- Clinical and Translational Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Morten K. Skouboe
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Sophie Howarth
- Clinical and Translational Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Anne K. Hollensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Rui Chen
- Clinical and Translational Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Malene L. Børresen
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Benjamin J. Thompson
- Clinical and Translational Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Jarmila Stremenova Spegarova
- Clinical and Translational Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Catherine F. Hatton
- Clinical and Translational Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Frederik F. Stæger
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mette K. Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - John Whittaker
- Clinical and Translational Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | | | - Sofie E. Jørgensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Carsten Heilmann
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Medical Department, Pediatric Section, Dronning Ingrid Hospital, Nuuk, Greenland
| | - Daniela Buhas
- Division of Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Nina F. Øbro
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jakob T. Bay
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hanne V. Marquart
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - M. Teresa de la Morena
- Seattle Children’s Hospital, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
| | | | | | - Line Borgwardt
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Isabel Forss
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Tania Masmas
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anja Poulsen
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Francisco Noya
- Division of Allergy & Clinical Immunology, Montreal Children’s Hospital, Montreal General Hospital, McGill University, Montreal, Quebec, Canada
| | - Guy Rouleau
- The Neuro, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Reza Alizadehfar
- Division of Allergy & Clinical Immunology, Montreal Children’s Hospital, Montreal General Hospital, McGill University, Montreal, Quebec, Canada
| | - Eric J. Allenspach
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
- Seattle Children’s Hospital, Seattle, WA
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Sophie Hambleton
- Clinical and Translational Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Trine H. Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
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12
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Gelabert P, Schmidt RW, Fernandes DM, Karsten JK, Harper TK, Madden GD, Ledogar SH, Sokhatsky M, Oota H, Kennett DJ, Pinhasi R. Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine. Sci Rep 2022; 12:7242. [PMID: 35508651 PMCID: PMC9068698 DOI: 10.1038/s41598-022-11117-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000–3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935–825 cal BCE). Results reveal that the CTCC individuals’ ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980–825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
| | - Ryan W Schmidt
- University of Porto, CIBIO-InBIO, Rua Padre Armando Quintas, nº 7, 4485-661, Vairão, Portugal. .,School of Archaeology & Earth Institute, University College, Dublin, Belfield, Dublin 4, Ireland.
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Jordan K Karsten
- Department of Anthropology, Global Religions, and Cultures, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI, 54901, USA
| | - Thomas K Harper
- Institute for European and Mediterranean Archaeology, State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Gwyn D Madden
- Department of Anthropology, Grand Valley State University, 1 Campus Dr., Allendale, MI, 49401, USA
| | - Sarah H Ledogar
- Department of Archaeology, Classics, and History, University of New England, Armidale, NSW, 2351, Australia
| | - Mykhailo Sokhatsky
- Borschiv Regional Museum of Local Lore, Borschiv, Ternopil Oblast, Ukraine
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
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13
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Andersen MK, Skotte L, Jørsboe E, Polito R, Stæger FF, Aldiss P, Hanghøj K, Waples RK, Santander CG, Grarup N, Dahl-Petersen IK, Diaz LJ, Overvad M, Senftleber NK, Søborg B, Larsen CVL, Lemoine C, Pedersen O, Feenstra B, Bjerregaard P, Melbye M, Jørgensen ME, Færgeman NJ, Koch A, Moritz T, Gillum MP, Moltke I, Hansen T, Albrechtsen A. Loss of Sucrase-Isomaltase Function Increases Acetate Levels and Improves Metabolic Health in Greenlandic Cohorts. Gastroenterology 2022; 162:1171-1182.e3. [PMID: 34914943 DOI: 10.1053/j.gastro.2021.12.236] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS The sucrase-isomaltase (SI) c.273_274delAG loss-of-function variant is common in Arctic populations and causes congenital sucrase-isomaltase deficiency, which is an inability to break down and absorb sucrose and isomaltose. Children with this condition experience gastrointestinal symptoms when dietary sucrose is introduced. We aimed to describe the health of adults with sucrase-isomaltase deficiency. METHODS The association between c.273_274delAG and phenotypes related to metabolic health was assessed in 2 cohorts of Greenlandic adults (n = 4922 and n = 1629). A sucrase-isomaltase knockout (Sis-KO) mouse model was used to further elucidate the findings. RESULTS Homozygous carriers of the variant had a markedly healthier metabolic profile than the remaining population, including lower body mass index (β [standard error], -2.0 [0.5] kg/m2; P = 3.1 × 10-5), body weight (-4.8 [1.4] kg; P = 5.1 × 10-4), fat percentage (-3.3% [1.0%]; P = 3.7 × 10-4), fasting triglyceride (-0.27 [0.07] mmol/L; P = 2.3 × 10-6), and remnant cholesterol (-0.11 [0.03] mmol/L; P = 4.2 × 10-5). Further analyses suggested that this was likely mediated partly by higher circulating levels of acetate observed in homozygous carriers (β [standard error], 0.056 [0.002] mmol/L; P = 2.1 × 10-26), and partly by reduced sucrose uptake, but not lower caloric intake. These findings were verified in Sis-KO mice, which, compared with wild-type mice, were leaner on a sucrose-containing diet, despite similar caloric intake, had significantly higher plasma acetate levels in response to a sucrose gavage, and had lower plasma glucose level in response to a sucrose-tolerance test. CONCLUSIONS These results suggest that sucrase-isomaltase constitutes a promising drug target for improvement of metabolic health, and that the health benefits are mediated by reduced dietary sucrose uptake and possibly also by higher levels of circulating acetate.
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Affiliation(s)
- Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Emil Jørsboe
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ryan Polito
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frederik F Stæger
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Aldiss
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ryan K Waples
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Cindy G Santander
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Inger K Dahl-Petersen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark; Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Lars J Diaz
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | | | - Ninna K Senftleber
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Bolette Søborg
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Christina V L Larsen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark; Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Clara Lemoine
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Bjerregaard
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Marit E Jørgensen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark; Steno Diabetes Center Copenhagen, Gentofte, Denmark; Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Anders Koch
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark; Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland; Department of Infectious Diseases, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Thomas Moritz
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew P Gillum
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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14
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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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15
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Balanovsky O, Petrushenko V, Mirzaev K, Abdullaev S, Gorin I, Chernevskiy D, Agdzhoyan A, Balanovska E, Kryukov A, Temirbulatov I, Sychev D. Variation of Genomic Sites Associated with Severe Covid-19 Across Populations: Global and National Patterns. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:1391-1402. [PMID: 34764675 PMCID: PMC8575442 DOI: 10.2147/pgpm.s320609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/04/2021] [Indexed: 01/10/2023]
Abstract
Background Information about the distribution of clinically significant genetic markers in different populations may be helpful in elaborating personalized approaches to the clinical management of COVID-19 in the absence of consensus guidelines. Aim Analyze frequencies and distribution patterns of two markers associated with severe COVID-19 (rs11385942 and rs657152) and look for potential correlations between these markers and deaths from COVID-19 among populations in Russia and across the world. Methods We genotyped 1883 samples from 91 ethnic groups pooled into 28 populations representing Russia and its neighbor states. We also compiled a dataset on 32 populations from other regions using genotypes extracted or imputed from the available databases. Geographic maps showing the frequency distribution of the analyzed markers were constructed using the obtained data. Results The cartographic analysis revealed that rs11385942 distribution follows the West Eurasian pattern: the marker is frequent among the populations of Europe, West Asia and South Asia but rare or absent in all other parts of the globe. Notably, the transition from high to low rs11385942 frequencies across Eurasia is not abrupt but follows the clinal variation pattern instead. The distribution of rs657152 is more homogeneous. The analysis of correlations between the frequencies of the studied markers and the epidemiological characteristics of COVID-19 in a population revealed that higher frequencies of both risk alleles correlated positively with mortality from this disease. For rs657152, the correlation was especially strong (r = 0.59, p = 0.02). These reasonable correlations were observed for the "Russian" dataset only: no such correlations were established for the "world" dataset. This could be attributed to the differences in methodology used to collect COVID-19 statistics in different countries. Conclusion Our findings suggest that genetic differences between populations make a small yet tangible contribution to the heterogeneity of the pandemic worldwide.
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Affiliation(s)
- Oleg Balanovsky
- Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia.,Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Valeria Petrushenko
- Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia.,Department of Bioinformatics Moscow Institute of Physics and Technology, Moscow, Russia
| | - Karin Mirzaev
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia.,Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Sherzod Abdullaev
- Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Igor Gorin
- Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia.,Department of Bioinformatics Moscow Institute of Physics and Technology, Moscow, Russia
| | - Denis Chernevskiy
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Anastasiya Agdzhoyan
- Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia.,Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Elena Balanovska
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Alexander Kryukov
- Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Ilyas Temirbulatov
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia.,Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Dmitriy Sychev
- Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
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16
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Viehberg FA, Medeiros AS, Plessen B, Wang X, Muir D, Pienitz R. The influence of a lost society, the Sadlermiut, on the environment in the Canadian Arctic. Sci Rep 2021; 11:18504. [PMID: 34531423 PMCID: PMC8446097 DOI: 10.1038/s41598-021-97631-7] [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] [Received: 04/05/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
High latitude freshwater ecosystems are sentinels of human activity and environmental change. The lakes and ponds that characterize Arctic landscapes have a low resilience to buffer variability in climate, especially with increasing global anthropogenic stressors in recent decades. Here, we show that a small freshwater pond in proximity of the archaeological site “Native Point” on Southampton Island (Nunavut, Arctic Canada) is a highly sensitive environmental recorder. The sediment analyses allowed for pinpointing the first arrival of Sadlermiut culture at Native Point to ~ 1250 CE, followed by a dietary shift likely in response to the onset of cooling in the region ~ 1400 CE. The influence of the Sadlermiut on the environment persisted long after the last of their population perished in 1903. Presently, the pond remains a distorted ecosystem that has experienced fundamental shifts in the benthic invertebrate assemblages and accumulated anthropogenic metals in the sediment. Our multi-proxy paleolimnological investigation using geochemical and biological indicators emphasizes that direct and indirect anthropogenic impacts have long-term environmental implications on high latitude ecosystems.
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Affiliation(s)
- Finn A Viehberg
- Laboratoire de Paléoécologie Aquatique, Centre d'Études Nordiques, Pavillon Abitibi-Price, Université Laval, Québec, G1V 0A6, Canada. .,Institut Für Geographie Und Geologie, University of Greifswald, Friedrich-Ludwig-Jahn Str. 16, 17487, Greifswald, Germany.
| | - Andrew S Medeiros
- School for Resource and Environmental Studies, Dalhousie University, Halifax, B3H 4R2, Canada
| | - Birgit Plessen
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Climate Dynamics and Landscape Evolution, 14473, Potsdam, Germany
| | - Xiaowa Wang
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, L7S 1A1, Canada
| | - Derek Muir
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, L7S 1A1, Canada
| | - Reinhard Pienitz
- Laboratoire de Paléoécologie Aquatique, Centre d'Études Nordiques, Pavillon Abitibi-Price, Université Laval, Québec, G1V 0A6, Canada
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17
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Ribeiro S, Limoges A, Massé G, Johansen KL, Colgan W, Weckström K, Jackson R, Georgiadis E, Mikkelsen N, Kuijpers A, Olsen J, Olsen SM, Nissen M, Andersen TJ, Strunk A, Wetterich S, Syväranta J, Henderson ACG, Mackay H, Taipale S, Jeppesen E, Larsen NK, Crosta X, Giraudeau J, Wengrat S, Nuttall M, Grønnow B, Mosbech A, Davidson TA. Vulnerability of the North Water ecosystem to climate change. Nat Commun 2021; 12:4475. [PMID: 34294719 PMCID: PMC8298575 DOI: 10.1038/s41467-021-24742-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/01/2021] [Indexed: 11/18/2022] Open
Abstract
High Arctic ecosystems and Indigenous livelihoods are tightly linked and exposed to climate change, yet assessing their sensitivity requires a long-term perspective. Here, we assess the vulnerability of the North Water polynya, a unique seaice ecosystem that sustains the world’s northernmost Inuit communities and several keystone Arctic species. We reconstruct mid-to-late Holocene changes in sea ice, marine primary production, and little auk colony dynamics through multi-proxy analysis of marine and lake sediment cores. Our results suggest a productive ecosystem by 4400–4200 cal yrs b2k coincident with the arrival of the first humans in Greenland. Climate forcing during the late Holocene, leading to periods of polynya instability and marine productivity decline, is strikingly coeval with the human abandonment of Greenland from c. 2200–1200 cal yrs b2k. Our long-term perspective highlights the future decline of the North Water ecosystem, due to climate warming and changing sea-ice conditions, as an important climate change risk. The North Water polynya is a unique but vulnerable ecosystem, home to Indigenous people and Arctic keystone species. New palaeoecological records from Greenland suggest human abandonment c. 2200–1200 cal yrs BP occurred during climate-forced polynya instability, foreshadowing future ecosystem declines.
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Affiliation(s)
- Sofia Ribeiro
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark.
| | - Audrey Limoges
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark.,Department of Earth Sciences, University of New Brunswick, Fredericton, NB, Canada
| | - Guillaume Massé
- Université Laval, CNRS, UMI 3376 TAKUVIK, Québec City, QC, Canada.,Station Marine de Concarneau, CNRS, UMR7159 LOCEAN, Concarneau, France
| | - Kasper L Johansen
- Department of Bioscience, Arctic Research Center, Aarhus University, Roskilde, Denmark
| | - William Colgan
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Kaarina Weckström
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark.,Ecosystems and Environment Research Programme (ECRU), and Helsinki Institute of Sustainability Science, Helsinki University, Helsinki, Finland
| | - Rebecca Jackson
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Eleanor Georgiadis
- Université Laval, CNRS, UMI 3376 TAKUVIK, Québec City, QC, Canada.,Université de Bordeaux, CNRS, UMR 5805 EPOC, Pessac, France
| | - Naja Mikkelsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Antoon Kuijpers
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Jesper Olsen
- Aarhus AMS Centre (AARAMS), Department of Physics and Astronomy, Aarhus University, Roskilde, Denmark
| | | | - Martin Nissen
- Agency for Data Supply and Efficiency, Copenhagen, Denmark
| | - Thorbjørn J Andersen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Københav, Denmark
| | - Astrid Strunk
- Department of Geoscience, Aarhus University, Aarhus, Denmark
| | - Sebastian Wetterich
- Department of Permafrost Research, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Potsdam, Germany
| | - Jari Syväranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Jovensuu, Finland
| | - Andrew C G Henderson
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK
| | - Helen Mackay
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK.,Department of Geography, Durham University, Durham, UK
| | - Sami Taipale
- Department of Biological and Environmental Science, Nanoscience center, University of Jyväskylä, Jyväskylä, Finland
| | - Erik Jeppesen
- Lake Group & Arctic Research Centre, Department of Bioscience, Aarhus University, Roskilde, Silkeborg, Denmark.,Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara, Turkey.,Sino Danish Centre for education and Research, Beijing, China
| | - Nicolaj K Larsen
- Department of Geoscience, Aarhus University, Aarhus, Denmark.,Centre for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xavier Crosta
- Université de Bordeaux, CNRS, UMR 5805 EPOC, Pessac, France
| | | | - Simone Wengrat
- Department of Biology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Mark Nuttall
- Pinngortitaleriffik/Greenland Institute for Natural Resources, Nuuk, Greenland.,University of Alberta, Edmonton, AB, Canada
| | | | - Anders Mosbech
- Department of Bioscience, Arctic Research Center, Aarhus University, Roskilde, Denmark
| | - Thomas A Davidson
- Lake Group & Arctic Research Centre, Department of Bioscience, Aarhus University, Roskilde, Silkeborg, Denmark.
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18
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Bisso-Machado R, Fagundes NJR. Uniparental genetic markers in Native Americans: A summary of all available data from ancient and contemporary populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:445-458. [PMID: 34184252 DOI: 10.1002/ajpa.24357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/26/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVES The aim of this study was to create a comprehensive summary of available mtDNA and Y-chromosome data for Native Americans from North, Central, and South America, including both modern and ancient DNA. To illustrate the usefulness of this dataset we present a broad picture of the genetic variation for both markers across the Americas. METHODS We searched PubMed, ResearchGate, Google Scholar for studies about mtDNA or Y-chromosome variation in Native American populations, including geographic, linguistic, ecological (ecoregion), archeological and chronological information. We used AMOVA to estimate the genetic structure associated with language and ecoregion grouping and Mantel tests to evaluate the correlation between genetic and geographic distances. RESULTS Genetic data were obtained from 321 primary sources, including 22,569 individuals from 298 contemporary populations, and 3628 individuals from 202 archeological populations. MtDNA lineages of probable non-Amerindian origin were rare, in contrast with Y-chromosome lineages. Mantel tests showed a statistically significant correlation for the whole continent considering mtDNA but not the Y-chromosome. Genetic structure between groups was always stronger for mtDNA than for the Y-chromosome. CONCLUSIONS This study summarizes decades of research conducted in Native American populations for both mtDNA and the Y-chromosome. Continental or sub-continental patterns of variation reveal that most of the genetic variation occurs within populations rather than among linguistic or ecoregional groups, and that isolation by distance is barely detectable in most population sets. The genetic structure among groups was always larger for mtDNA than for the Y-chromosome, suggesting between-sex differences in gene flow.
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Affiliation(s)
- Rafael Bisso-Machado
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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19
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Chen J, He G, Ren Z, Wang Q, Liu Y, Zhang H, Yang M, Zhang H, Ji J, Zhao J, Guo J, Zhu K, Yang X, Wang R, Ma H, Wang CC, Huang J. Genomic Insights Into the Admixture History of Mongolic- and Tungusic-Speaking Populations From Southwestern East Asia. Front Genet 2021; 12:685285. [PMID: 34239544 PMCID: PMC8258170 DOI: 10.3389/fgene.2021.685285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic-speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.
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Affiliation(s)
- Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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20
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Abstract
The peopling of Siberia and the Americas is intriguing for archaeologists, linguists, and human geneticists, but despite significant recent developments, many details remain controversial. Here, we provide insights based on genetic diversity within Helicobacter pylori, a bacterium that infects 50% of all humans. H. pylori strains were collected from across eastern Eurasia and the Americas. Sequence analyses indicated that Siberia contains both anciently diverged and recently admixed bacteria, supporting both human persistence over the last glacial maximum and more recent human recolonization. We inferred a single migration across the Bering land bridge, accompanied by a dramatic reduction in effective population size, followed by bidirectional Holocene gene flow between Asia and the Americas. The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.
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21
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Senftleber NK, Overvad M, Dahl-Petersen IK, Bjerregaard P, Jørgensen ME. Diet and physical activity in Greenland: genetic interactions and associations with obesity and diabetes. Appl Physiol Nutr Metab 2021; 46:849-855. [PMID: 34107227 DOI: 10.1139/apnm-2021-0020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The Inuit in Greenland have gone through dramatic lifestyle changes during the last half century. More time is spent being sedentary and imported foods replaces traditional foods like seal and whale. The population has also experienced a rapid growth in obesity and metabolic disturbances and diabetes is today common despite being almost unknown few decades ago. In this paper, we describe and discuss the role of lifestyle changes and genetics for Inuit metabolic health. Novelty: Cardiometabolic disease risk has increased in Greenland. Lifestyle changes and possibly gene-lifestyle interactions play a role.
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Affiliation(s)
| | | | | | - Peter Bjerregaard
- National Institute of Public Health, Southern Denmark University, Copenhagen, Denmark
| | - Marit Eika Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark.,National Institute of Public Health, Southern Denmark University, Copenhagen, Denmark.,University of Greenland, Nuuk, Greenland
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22
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Willerslev E, Meltzer DJ. Peopling of the Americas as inferred from ancient genomics. Nature 2021; 594:356-364. [PMID: 34135521 DOI: 10.1038/s41586-021-03499-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.
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Affiliation(s)
- Eske Willerslev
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Wellcome Trust Sanger Institute, Cambridge, UK.
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Anthropology, Southern Methodist University, Dallas, TX, USA.
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23
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The genetic history of Greenlandic-European contact. Curr Biol 2021; 31:2214-2219.e4. [PMID: 33711251 PMCID: PMC8284823 DOI: 10.1016/j.cub.2021.02.041] [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: 03/02/2020] [Revised: 11/03/2020] [Accepted: 02/16/2021] [Indexed: 11/22/2022]
Abstract
The Inuit ancestors of the Greenlandic people arrived in Greenland close to 1,000 years ago.1 Since then, Europeans from many different countries have been present in Greenland. Consequently, the present-day Greenlandic population has ~25% of its genetic ancestry from Europe.2 In this study, we investigated to what extent different European countries have contributed to this genetic ancestry. We combined dense SNP chip data from 3,972 Greenlanders and 8,275 Europeans from 14 countries and inferred the ancestry contribution from each of these 14 countries using haplotype-based methods. Due to the rapid increase in population size in Greenland over the past ~100 years, we hypothesized that earlier European interactions, such as pre-colonial Dutch whalers and early German and Danish-Norwegian missionaries, as well as the later Danish colonists and post-colonial immigrants, all contributed European genetic ancestry. However, we found that the European ancestry is almost entirely Danish and that a substantial fraction is from admixture that took place within the last few generations. The Greenlandic Inuit have had extensive historical contact with Europeans, and the present-day Greenlandic population has substantial amounts of European ancestry. Waples et al. use genetic data to investigate the origin of this ancestry. They show that much of it is Danish and find little evidence of it being from pre-colonial European contact.
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24
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Clemente F, Unterländer M, Dolgova O, Amorim CEG, Coroado-Santos F, Neuenschwander S, Ganiatsou E, Cruz Dávalos DI, Anchieri L, Michaud F, Winkelbach L, Blöcher J, Arizmendi Cárdenas YO, Sousa da Mota B, Kalliga E, Souleles A, Kontopoulos I, Karamitrou-Mentessidi G, Philaniotou O, Sampson A, Theodorou D, Tsipopoulou M, Akamatis I, Halstead P, Kotsakis K, Urem-Kotsou D, Panagiotopoulos D, Ziota C, Triantaphyllou S, Delaneau O, Jensen JD, Moreno-Mayar JV, Burger J, Sousa VC, Lao O, Malaspinas AS, Papageorgopoulou C. The genomic history of the Aegean palatial civilizations. Cell 2021; 184:2565-2586.e21. [PMID: 33930288 PMCID: PMC8127963 DOI: 10.1016/j.cell.2021.03.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022]
Abstract
The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.
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Affiliation(s)
- Florian Clemente
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Martina Unterländer
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece; Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Olga Dolgova
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carlos Eduardo G Amorim
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Francisco Coroado-Santos
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Elissavet Ganiatsou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diana I Cruz Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lucas Anchieri
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Frédéric Michaud
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Yami Ommar Arizmendi Cárdenas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Eleni Kalliga
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Ioannis Kontopoulos
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Olga Philaniotou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece
| | - Dimitra Theodorou
- Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture and Sports, 50004 Kozani, Greece
| | - Metaxia Tsipopoulou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Ioannis Akamatis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paul Halstead
- Department of Archaeology, University of Sheffield, Minalloy House, 10-16 Regent St., Sheffield S1 3NJ, UK
| | - Kostas Kotsakis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diamantis Panagiotopoulos
- Institute of Classical Archaeology, University of Heidelberg, Marstallhof 4, 69117 Heidelberg, Germany
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100 Florina, Greece
| | - Sevasti Triantaphyllou
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - J Víctor Moreno-Mayar
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark; National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Vitor C Sousa
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece.
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25
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Keighley X, Bro‐Jørgensen MH, Ahlgren H, Szpak P, Ciucani MM, Sánchez Barreiro F, Howse L, Gotfredsen AB, Glykou A, Jordan P, Lidén K, Olsen MT. Predicting sample success for large-scale ancient DNA studies on marine mammals. Mol Ecol Resour 2021; 21:1149-1166. [PMID: 33463014 PMCID: PMC8248401 DOI: 10.1111/1755-0998.13331] [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: 10/14/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.
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Affiliation(s)
- Xénia Keighley
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Arctic Centre/Groningen Institute of ArchaeologyFaculty of ArtsUniversity of GroningenAS GroningenThe Netherlands
| | - Maiken Hemme Bro‐Jørgensen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Hans Ahlgren
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Paul Szpak
- Department of AnthropologyTrent UniversityPeterboroughOntarioCanada
| | - Marta Maria Ciucani
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
| | | | - Lesley Howse
- Archaeology CentreUniversity of TorontoTorontoOntarioCanada
| | | | - Aikaterini Glykou
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Peter Jordan
- Department of Archaeology and Ancient HistoryLund UniversityLundSweden
| | - Kerstin Lidén
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Morten Tange Olsen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
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26
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Ávila-Arcos MC, McManus KF, Sandoval K, Rodríguez-Rodríguez JE, Villa-Islas V, Martin AR, Luisi P, Peñaloza-Espinosa RI, Eng C, Huntsman S, Burchard EG, Gignoux CR, Bustamante CD, Moreno-Estrada A. Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes. Mol Biol Evol 2021; 37:994-1006. [PMID: 31848607 PMCID: PMC7086176 DOI: 10.1093/molbev/msz282] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico’s Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Kimberly F McManus
- Department of Biology, Stanford University, Stanford, CA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), UGA, CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | | | - Viridiana Villa-Islas
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alicia R Martin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Pierre Luisi
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas, Consejo Nacional de Investigaciones Científicas y Técnicas, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rosenda I Peñaloza-Espinosa
- Division of Biological and Health Sciences, Department of Biological Systems, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Celeste Eng
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Scott Huntsman
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Esteban G Burchard
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), UGA, CINVESTAV, Irapuato, Guanajuato 36821, Mexico
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27
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Jain A, Sharma D, Bajaj A, Gupta V, Scaria V. Founder variants and population genomes-Toward precision medicine. ADVANCES IN GENETICS 2021; 107:121-152. [PMID: 33641745 DOI: 10.1016/bs.adgen.2020.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Human migration and community specific cultural practices have contributed to founder events and enrichment of the variants associated with genetic diseases. While many founder events in isolated populations have remained uncharacterized, the application of genomics in clinical settings as well as for population scale studies in the recent years have provided an unprecedented push towards identification of founder variants associated with human health and disease. The discovery and characterization of founder variants could have far reaching implications not only in understanding the history or genealogy of the disease, but also in implementing evidence based policies and genetic testing frameworks. This further enables precise diagnosis and prevention in an attempt towards precision medicine. This review provides an overview of founder variants along with methods and resources cataloging them. We have also discussed the public health implications and examples of prevalent disease associated founder variants in specific populations.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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28
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Riede F, Walsh MJ, Nowell A, Langley MC, Johannsen NN. Children and innovation: play, play objects and object play in cultural evolution. EVOLUTIONARY HUMAN SCIENCES 2021; 3:e11. [PMID: 37588535 PMCID: PMC10427281 DOI: 10.1017/ehs.2021.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cultural evolutionary theory conceptualises culture as an information-transmission system whose dynamics take on evolutionary properties. Within this framework, however, innovation has been likened to random mutations, reducing its occurrence to chance or fortuitous transmission error. In introducing the special collection on children and innovation, we here place object play and play objects - especially functional miniatures - from carefully chosen archaeological contexts in a niche construction perspective. Given that play, including object play, is ubiquitous in human societies, we suggest that plaything construction, provisioning and use have, over evolutionary timescales, paid substantial selective dividends via ontogenetic niche modification. Combining findings from cognitive science, ethology and ethnography with insights into hominin early developmental life-history, we show how play objects and object play probably had decisive roles in the emergence of innovative capabilities. Importantly, we argue that closer attention to play objects can go some way towards addressing changes in innovation rates that occurred throughout human biocultural evolution and why innovations are observable within certain technological domains but not others.
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Affiliation(s)
- Felix Riede
- Department of Archaeology and Heritage Studies, Aarhus University, Moesgård Allé 20, 8270 Højbjerg, Denmark
- Interacting Minds Centre, Aarhus University, 8000 Aarhus C, Denmark
| | - Matthew J. Walsh
- Department of Ethnography, Numismatics, Classical Archaeology and University History, Museum of Cultural History, University of Oslo, 0164Oslo, Norway
| | - April Nowell
- Department of Anthropology, University of Victoria, Victoria, British Columbia, Canada
| | - Michelle C. Langley
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, Australia
- Forensics and Archaeology, School of Environment and Science, Griffith University, Brisbane, Australia
| | - Niels N. Johannsen
- Department of Archaeology and Heritage Studies, Aarhus University, Moesgård Allé 20, 8270 Højbjerg, Denmark
- Interacting Minds Centre, Aarhus University, 8000 Aarhus C, Denmark
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29
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KOGANEBUCHI KAE, OOTA HIROKI. Paleogenomics of human remains in East Asia and Yaponesia focusing on current advances and future directions. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.2011302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- KAE KOGANEBUCHI
- Laboratory of Genome Anthropology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
| | - HIROKI OOTA
- Laboratory of Genome Anthropology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
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30
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Peyrégne S, Peter BM. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol 2020; 21:246. [PMID: 32933569 PMCID: PMC7490890 DOI: 10.1186/s13059-020-02123-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/27/2020] [Indexed: 12/31/2022] Open
Abstract
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
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31
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Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, Oota H. Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Commun Biol 2020; 3:437. [PMID: 32843717 PMCID: PMC7447786 DOI: 10.1038/s42003-020-01162-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/16/2020] [Indexed: 12/28/2022] Open
Abstract
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia. Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.
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Affiliation(s)
- Takashi Gakuhari
- Center for Cultural Resource Studies, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Kitasato University School of Medicine, Sagamihara, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, the University of Dublin, Dublin, Ireland
| | - Simon Rasmussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Ryan Schmidt
- Kitasato University School of Medicine, Sagamihara, Japan
| | - Souichiro Mizushima
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Toshiyuki Tsurumoto
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Tetsuaki Wakebe
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Hiromi Shitara
- Department of Archaeology, The University of Tokyo, Tokyo, Japan
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,GeoGenetics Groups, Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Japan. .,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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32
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Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images. Sci Rep 2020; 10:11850. [PMID: 32678112 PMCID: PMC7367291 DOI: 10.1038/s41598-020-68259-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/19/2020] [Indexed: 11/17/2022] Open
Abstract
Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case–control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.
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33
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Mendes M, Alvim I, Borda V, Tarazona-Santos E. The history behind the mosaic of the Americas. Curr Opin Genet Dev 2020; 62:72-77. [PMID: 32659643 DOI: 10.1016/j.gde.2020.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
Focusing on literature published in 2018-2020, we review inferences about: (i) how ancient DNA is contributing to clarify the peopling of the Americas and the dispersal of its first inhabitants, (ii) how the interplay between environmental diversity and culture has influenced the genetic structure and adaptation of Andean and Amazon populations, (iii) how genetics has contributed to our understanding of the Pre-Columbian Tupi expansion in Eastern South America, (iv) the subcontinental origins and dynamics of Post-Columbian admixture in the Americas, and finally, (v) episodes of adaptive natural selection in the American continent, particularly in the high altitudes of the Andes.
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Affiliation(s)
- Marla Mendes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Isabela Alvim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Victor Borda
- Laboratório de Bioinformática, LABINFO, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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34
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Sinding MHS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Carøe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jørgensen MP, Dietz R, Sonne C, Meldgaard M, Dalén L, Larson G, Petersen B, Sicheritz-Pontén T, Bachmann L, Wiig Ø, Marques-Bonet T, Hansen AJ, Gilbert MTP. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition. Science 2020; 368:1495-1499. [PMID: 32587022 DOI: 10.1126/science.aaz8599] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
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Affiliation(s)
- Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Natural History Museum, University of Oslo, Oslo, Norway.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | | | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Filipe G Vieira
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,BioArch, Department of Archaeology, University of York, York, UK
| | | | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emilie U Andersen-Ranberg
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Clinical Veterinary Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter D Jordan
- Arctic Centre and Groningen Institute of Archaeology, University of Groningen, Netherlands
| | - Elena Y Pavlova
- Arctic and Antarctic Research Institute, St. Petersburg, Russia
| | | | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Varvara V Ivanova
- VNIIOkeangeologia Research Institute (The All-Russian Research Institute of Geology and Mineral Resources of the World Ocean), St. Petersburg, Russia
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Danish Institute for Advanced Study (D-IAS), University of Southern Denmark, Odense, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Francis Crick Institute, London, UK
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sanne Eline Wennerberg
- Ministry of Fisheries, Hunting and Agriculture, Government of Greenland, Nuuk, Greenland
| | | | - Rune Dietz
- Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
| | - Christian Sonne
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark.,Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Morten Meldgaard
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Bent Petersen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Pontén
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain. .,Catalan Institution of Research and Advanced Studies, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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35
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Genetic study of the Arctic CPT1A variant suggests that its effect on fatty acid levels is modulated by traditional Inuit diet. Eur J Hum Genet 2020; 28:1592-1601. [PMID: 32561900 DOI: 10.1038/s41431-020-0674-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/29/2020] [Accepted: 06/09/2020] [Indexed: 12/23/2022] Open
Abstract
Several recent studies have found signs of recent selection on the carnitine palmitoyl-transferase 1A (CPT1A) gene in the ancestors of Arctic populations likely as a result of their traditional diet. CPT1A is involved in fatty acid transportation and is known to affect circulating fatty acid profiles in Inuit as does the unique traditional diet rich in marine animals. We aimed to assess which fatty acids may have driven the selection of rs80356779, a c.1436C>T (p.(Pro479Leu)) variant in CPT1A, by analyzing a potential interaction between the variant and traditional Inuit diet. We included 3005 genome-wide genotyped individuals living in Greenland, who had blood cell membrane fatty acid levels measured. Consumption of 25 traditional food items was expressed as percentage of total energy intake. We tested for CPT1A × traditional diet interaction while taking relatedness and admixture into account. Increasing intakes of traditional diet was estimated to attenuate the effect of 479L on 20:3 omega-6 levels (p = 0.000399), but increase the effect of the variant on 22:5 omega-3 levels (p = 0.000963). The 479L effect on 22:5 omega-3 more than doubled in individuals with a high intake of traditional diet (90% percentile) compared with individuals with a low intake (10% percentile). Similar results were found when assessing interactions with marine foods. Our results suggest that the association between traditional diet and blood cell fatty acid composition is affected by the CPT1A genotype, or other variants in linkage disequilibrium, and support the hypothesis that omega-3 fatty acids may have been important for adaptation to the Arctic diet.
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36
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Yu H, Spyrou MA, Karapetian M, Shnaider S, Radzevičiūtė R, Nägele K, Neumann GU, Penske S, Zech J, Lucas M, LeRoux P, Roberts P, Pavlenok G, Buzhilova A, Posth C, Jeong C, Krause J. Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia. Cell 2020; 181:1232-1245.e20. [DOI: 10.1016/j.cell.2020.04.037] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/16/2020] [Accepted: 04/21/2020] [Indexed: 12/30/2022]
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37
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Cuyler C, Rowell J, Adamczewski J, Anderson M, Blake J, Bretten T, Brodeur V, Campbell M, Checkley SL, Cluff HD, Côté SD, Davison T, Dumond M, Ford B, Gruzdev A, Gunn A, Jones P, Kutz S, Leclerc LM, Mallory C, Mavrot F, Mosbacher JB, Okhlopkov IM, Reynolds P, Schmidt NM, Sipko T, Suitor M, Tomaselli M, Ytrehus B. Muskox status, recent variation, and uncertain future. AMBIO 2020; 49:805-819. [PMID: 31187429 PMCID: PMC6989413 DOI: 10.1007/s13280-019-01205-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/08/2019] [Accepted: 05/15/2019] [Indexed: 05/26/2023]
Abstract
Muskoxen (Ovibos moschatus) are an integral component of Arctic biodiversity. Given low genetic diversity, their ability to respond to future and rapid Arctic change is unknown, although paleontological history demonstrates adaptability within limits. We discuss status and limitations of current monitoring, and summarize circumpolar status and recent variations, delineating all 55 endemic or translocated populations. Acknowledging uncertainties, global abundance is ca 170 000 muskoxen. Not all populations are thriving. Six populations are in decline, and as recently as the turn of the century, one of these was the largest population in the world, equaling ca 41% of today's total abundance. Climate, diseases, and anthropogenic changes are likely the principal drivers of muskox population change and result in multiple stressors that vary temporally and spatially. Impacts to muskoxen are precipitated by habitat loss/degradation, altered vegetation and species associations, pollution, and harvest. Which elements are relevant for a specific population will vary, as will their cumulative interactions. Our summaries highlight the importance of harmonizing existing data, intensifying long-term monitoring efforts including demographics and health assessments, standardizing and implementing monitoring protocols, and increasing stakeholder engagement/contributions.
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Affiliation(s)
- Christine Cuyler
- Greenland Institute of Natural Resources, PO Box 570, 3900 Nuuk, Greenland
| | - Janice Rowell
- School of Natural Resources and Extension, University of Alaska Fairbanks, Fairbanks, AK 99775 USA
| | - Jan Adamczewski
- Wildlife Division, Environment and Natural Resources, Government of Northwest Territories, PO Box 1320, Yellowknife, NT X1A 2L9 Canada
| | - Morgan Anderson
- BC Ministry of Forests, Lands, Natural Resources Operations and Rural Development, 2000 South Ospika Blvd, Prince George, BC V2N 4W5 Canada
| | - John Blake
- Animal Resources Center, University of Alaska Fairbanks, PO Box 756980, Fairbanks, AK 99775 USA
| | - Tord Bretten
- Norwegian Environment Agency, PO Box 5672 Torgarden, 7485 Trondheim, Norway
| | - Vincent Brodeur
- Department of Wildlife Management of Northern Québec, Ministry of Forests, Wildlife and Parks of Québec, 951 Hamel Boulevard, Chibougamau, QC G8P 2Z3 Canada
| | - Mitch Campbell
- Department of Environment, Government of Nunavut, PO Box 120, Arviat, NT X0C 0E0 Canada
| | - Sylvia L. Checkley
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6 Canada
| | - H. Dean Cluff
- Environment and Natural Resources, Government of the Northwest Territories, PO Box 2668, 3803 Bretzlaff Drive, Yellowknife, NT X1A 2P9 Canada
| | - Steeve D. Côté
- Département de biologie & Centre for Northern Studies, Université Laval, 1045 avenue de la Médecine, Québec, G1V 0A6 Canada
| | - Tracy Davison
- Department of Environment and Natural Resources, Wildlife Management, Inuvik Region, PO Box 2749, Inuvik, NT X0E 0T0 Canada
| | | | - Barrie Ford
- Nunavik Research Centre, Makivik Corporation, PO Box 179, Kuujjuaq, QC J0M 1C0 Canada
| | | | - Anne Gunn
- 368 Roland Road, Salt Spring Island, V8K 1V1 BC Canada
| | - Patrick Jones
- Division of Wildlife Conservation, Alaska Department of Fish and Game, PO Box 1467, Bethel, AK 99559 USA
| | - Susan Kutz
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6 Canada
| | - Lisa-Marie Leclerc
- Department of Environment, Government of Nunavut, PO Box 377, Kugluktuk, NU X0B 0A2 Canada
| | - Conor Mallory
- Department of Environment, Government of Nunavut, PO Box 209, Iglulik, NU X0A 0L0 Canada
| | - Fabien Mavrot
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6 Canada
| | - Jesper Bruun Mosbacher
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6 Canada
| | - Innokentiy Mikhailovich Okhlopkov
- Institute of Biological Problems of Cryolithozone of the Siberian Branch of Russian Academy of Science (IBPC SB RAS), 41 Lenina Ave., Yakutsk, Russia 677980
| | | | - Niels Martin Schmidt
- Arctic Research Centre, Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Taras Sipko
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, PO Box 11, Moscow, Russia 119071
| | - Mike Suitor
- Inuvialuit and Migratory Caribou, Fish and Wildlife, Environment Yukon, PO Box 600, Dawson City, YT Y0B 1G0 Canada
| | - Matilde Tomaselli
- Polar Knowledge Canada, Canadian High Arctic Research Station, 1 Uvajuq Road, PO Box 2150, Cambridge Bay, NU X0B 0C0 Canada
| | - Bjørnar Ytrehus
- Norwegian Institute for Nature Research (NINA), PO Box 5685 Torgarden, 7485 Trondheim, Norway
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Khrunin AV, Khvorykh GV, Fedorov AN, Limborska SA. Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia. PLoS One 2020; 15:e0228778. [PMID: 32023328 PMCID: PMC7001972 DOI: 10.1371/journal.pone.0228778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
Natural selection of beneficial genetic variants played a critical role in human adaptation to a wide range of environmental conditions. Northern Eurasia, despite its severe climate, is home to lots of ethnically diverse populations. The genetic variants associated with the survival of these populations have hardly been analyzed. We searched for the genomic signatures of positive selection in (1) the genome-wide microarray data of 432 people from eight different northern Russian populations and (2) the whole-genome sequences of 250 people from Northern Eurasia from a public repository through testing the extended haplotype homozigosity (EHH) and direct comparison of allele frequency, respectively. The 20 loci with the strongest selection signals were characterized in detail. Among the top EHH hits were the NRG3 and NBEA genes, which are involved in the development and functioning of the neural system, the PTPRM gene, which mediates cell-cell interactions and adhesion, and a region on chromosome 4 (chr4:28.7-28.9 Mb) that contained several loci affiliated with different classes of non-coding RNAs (RN7SL101P, MIR4275, MESTP3, and LINC02364). NBEA and the region on chromosome 4 were novel selection targets that were identified for the first time in Western Siberian populations. Cross-population comparisons of EHH profiles suggested a particular role for the chr4:28.7-28.9 Mb region in the local adaptation of Western Siberians. The strongest selection signal identified in Siberian sequenced genomes was formed by six SNPs on chromosome 11 (chr11:124.9-125.2 Mb). This region included well-known genes SLC37A2 and PKNOX2. SLC37A2 is most-highly expressed in the gut. Its expression is regulated by vitamin D, which is often deficient in northern regions. The PKNOX2 gene is a transcription factor of the homeobox family that is expressed in the brain and many other tissues. This gene is associated with alcohol addiction, which is widespread in many Northern Eurasian populations.
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Affiliation(s)
- Andrey V. Khrunin
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Gennady V. Khvorykh
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Alexei N. Fedorov
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
- Department of Medicine, University of Toledo, Toledo, Ohio, United States of America
| | - Svetlana A. Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
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Tackney J, Jensen AM, Kisielinski C, O'Rourke DH. Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168:303-317. [PMID: 30628076 DOI: 10.1002/ajpa.23746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 10/05/2018] [Accepted: 10/16/2018] [Indexed: 11/09/2022]
Abstract
OBJECTIVES The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo-Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo-Inuit. Origins of the Neo-Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo-Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post-contact Iñupiat. MATERIALS AND METHODS We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub-Arctic population movements. RESULTS We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub-Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations. DISCUSSION The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo-Inuit and Paleo-Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two-wave scenario of Neo-Inuit and Paleo-Inuit.
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Affiliation(s)
- Justin Tackney
- Department of Anthropology, University of Kansas, Lawrence, Kansas
| | - Anne M Jensen
- UIC Science LLC, Barrow, Alaska.,Department of Anthropology, University of Alaska Fairbanks, Fairbanks, Alaska
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Ameen C, Feuerborn TR, Brown SK, Linderholm A, Hulme-Beaman A, Lebrasseur O, Sinding MHS, Lounsberry ZT, Lin AT, Appelt M, Bachmann L, Betts M, Britton K, Darwent J, Dietz R, Fredholm M, Gopalakrishnan S, Goriunova OI, Grønnow B, Haile J, Hallsson JH, Harrison R, Heide-Jørgensen MP, Knecht R, Losey RJ, Masson-MacLean E, McGovern TH, McManus-Fry E, Meldgaard M, Midtdal Å, Moss ML, Nikitin IG, Nomokonova T, Pálsdóttir AH, Perri A, Popov AN, Rankin L, Reuther JD, Sablin M, Schmidt AL, Shirar S, Smiarowski K, Sonne C, Stiner MC, Vasyukov M, West CF, Ween GB, Wennerberg SE, Wiig Ø, Woollett J, Dalén L, Hansen AJ, P Gilbert MT, Sacks BN, Frantz L, Larson G, Dobney K, Darwent CM, Evin A. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic. Proc Biol Sci 2019; 286:20191929. [PMID: 31771471 PMCID: PMC6939252 DOI: 10.1098/rspb.2019.1929] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
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Affiliation(s)
- Carly Ameen
- Department of Archaeology, University of Exeter, Exeter, Devon, UK.,Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, Merseyside, UK
| | - Tatiana R Feuerborn
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Sarah K Brown
- Department of Anthropology, University of California Davis, Davis, CA, USA.,Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California Davis, Davis, CA, USA.,Washington Department of Fish and Wildlife, Olympia, WA, USA
| | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, TX, USA.,The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, Merseyside, UK.,The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Ophélie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, Merseyside, UK.,The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,GCRF One Health Regional Network for the Horn of Africa (HORN) Project, Institute of Infection and Global Health, Liverpool, UK
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Natural History Museum, University of Oslo, Oslo, Norway.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Zachary T Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California Davis, Davis, CA, USA
| | - Audrey T Lin
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | | | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Matthew Betts
- Canadian Museum of History, Gatineau, Quebec, Canada.,Department of Anthropology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Kate Britton
- Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Sachsen, Germany
| | - John Darwent
- Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Rune Dietz
- Arctic Research Centre, Aarhus Universitet, Aarhus, Denmark.,Department of Bioscience Roskilde, Aarhus Universitet, Roskilde, Denmark
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, University of Oslo, Oslo, Norway
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Olga I Goriunova
- Laboratory of Archaeology and Paleoecology of the Institute of Archaeology and Ethnography (Siberian Branch of Russian Academy of Science), Irkutsk, Russian Federation
| | | | - James Haile
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Jón Hallsteinn Hallsson
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Reykjavik, Iceland
| | - Ramona Harrison
- Department of Archaeology, History, Cultural Studies, and Religion, University of Bergen, Bergen, Hordaland, Norway
| | | | - Rick Knecht
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
| | - Robert J Losey
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Thomas H McGovern
- Department of Anthropology, Hunter College CUNY, New York, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | | | - Morten Meldgaard
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | | | - Madonna L Moss
- Department of Anthropology, University of Oregon, Eugene, OR, USA
| | - Iurii G Nikitin
- Museum of Archaeology and Ethnography at the Institute of History, Archaeology and Ethnography of the Peoples of the Far East (Far Eastern Branch of Russian Academy of Science), Vladivostok, Russian Federation
| | - Tatiana Nomokonova
- Department of Archaeology and Anthropology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Albína Hulda Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences, University of Oslo, Oslo, Norway.,Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Reykjavik, Iceland
| | - Angela Perri
- Department of Archaeology, Durham University, Durham, UK
| | - Aleksandr N Popov
- Museum of Archaeology and Ethnography at the Institute of History, Archaeology and Ethnography of the Peoples of the Far East (Far Eastern Branch of Russian Academy of Science), Vladivostok, Russian Federation
| | - Lisa Rankin
- Department of Archaeology, Memorial University of Newfoundland, St John's, Canada
| | - Joshua D Reuther
- Department of Anthropology, University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Mikhail Sablin
- Zoological Institute of Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | - Scott Shirar
- Department of Anthropology, University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Konrad Smiarowski
- The Graduate Center, City University of New York, New York, NY, USA.,Section for Cultural Heritage Management, Department of Cultural History, University Museum of Bergen, Bergen, Norway
| | - Christian Sonne
- Arctic Research Centre, Aarhus Universitet, Aarhus, Denmark.,Department of Bioscience, Aarhus Universitet, Aarhus, Denmark.,School of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Mary C Stiner
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Mitya Vasyukov
- Department of Biological Diversity and Sustainable Use of Biological Resources, Russian Academy of Sciences, Moskow, Russian Federation
| | - Catherine F West
- Department of Anthropology and Archaeology Program, Boston University, Boston, MA, USA
| | | | | | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - James Woollett
- Département des Sciences Historiques, Université Laval, Quebec, Canada
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Anders J Hansen
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Benjamin N Sacks
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, USA.,Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California Davis, Davis, CA, USA
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Greger Larson
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,School of Archaeology, University of Oxford, Oxford, UK
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, Merseyside, UK.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Allowen Evin
- Institut des Sciences de l'Evolution-Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, Occitanie, France
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Abstract
An enduring debate in the field of Arctic archaeology has been the extent to which climate change impacted cultural developments in the past. Long-term culture change across the circumpolar Arctic was often highly dynamic, with episodes of rapid migration, regional abandonment, and—in some cases—the disappearance or wholesale replacement of entire cultural traditions. By the 1960s, researchers were exploring the possibility that warming episodes had positive effects on cold-adapted premodern peoples in the Arctic by ( a) reducing the extent of sea ice, ( b) expanding the size and range of marine mammal populations, and ( c) opening new waterways and hunting areas for marine-adapted human groups. Although monocausal climatic arguments for change are now regarded as overly simplistic, the growing threat of contemporary Arctic warming to Indigenous livelihoods has given wider relevance to research into long-term culture–climate interactions. With their capacity to examine deeper cultural responses to climate change, archaeologists are in a unique position to generate human-scale climate adaptation insights that may inform future planning and mitigation efforts. The exceptionally well-preserved cultural and paleo-ecological sequences of the Arctic make it one of the best-suited regions on Earth to address such problems. Ironically, while archaeologists employ an exciting and highly promising new generation of methods and approaches to examine long-term fragility and resilience in Arctic social-ecological systems, many of these frozen paleo-societal archives are fast disappearing due to anthropogenic warming.
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Affiliation(s)
- Sean P.A. Desjardins
- Arctic Centre and the Groningen Institute of Archaeology, University of Groningen, 9718 CW Groningen, The Netherlands;,
| | - Peter D. Jordan
- Arctic Centre and the Groningen Institute of Archaeology, University of Groningen, 9718 CW Groningen, The Netherlands;,
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42
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Abstract
Analyzing genomic data from ancient humans illuminates South Asian ancestry
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Affiliation(s)
- Nathan K. Schaefer
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Beth Shapiro
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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43
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Mitochondrial DNA analysis of a Viking age mass grave in Sweden. Forensic Sci Int Genet 2019; 42:268-274. [DOI: 10.1016/j.fsigen.2019.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 01/12/2023]
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44
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Abstract
The Canadian Inuit have a distinct population background that may entail particular implications for the health of its individuals. However, the number of genetic studies examining this Inuit population is limited, and much remains to be discovered in regard to its genetic characteristics. In this study, we generated whole-exome sequences and genomewide genotypes for 170 Nunavik Inuit, a small and isolated founder population of Canadian Arctic indigenous people. Our study revealed the genetic background of Nunavik Inuit to be distinct from any known present-day population. The majority of Nunavik Inuit show little evidence of gene flow from European or present-day Native American peoples, and Inuit living around Hudson Bay are genetically distinct from those around Ungava Bay. We also inferred that Nunavik Inuit have a small effective population size of 3,000 and likely split from Greenlandic Inuit ∼10.5 kya. Nunavik Inuit went through a bottleneck at approximately the same time and might have admixed with a population related to the Paleo-Eskimos. Our study highlights population-specific genomic signatures in coding regions that show adaptations unique to Nunavik Inuit, particularly in pathways involving fatty acid metabolism and cellular adhesion (CPNE7, ICAM5, STAT2, and RAF1). Subsequent analyses in selection footprints and the risk of intracranial aneurysms (IAs) in Nunavik Inuit revealed an exonic variant under weak negative selection to be significantly associated with IA (rs77470587; P = 4.6 × 10-8).
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45
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Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan. Curr Biol 2019; 29:2526-2532.e4. [DOI: 10.1016/j.cub.2019.06.044] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/08/2019] [Accepted: 06/13/2019] [Indexed: 11/21/2022]
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Hollesen J, Matthiesen H, Fenger-Nielsen R, Abermann J, Westergaard-Nielsen A, Elberling B. Predicting the loss of organic archaeological deposits at a regional scale in Greenland. Sci Rep 2019; 9:9097. [PMID: 31296877 PMCID: PMC6624202 DOI: 10.1038/s41598-019-45200-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/03/2019] [Indexed: 12/05/2022] Open
Abstract
Across the Arctic, microbial degradation is actively destroying irreplaceable cultural and environmental records that have been preserved within archaeological deposits for millennia. Because it is not possible to survey the many sites in this remote part of the world, new methods are urgently needed to detect and assess the potential degradation. Here, we investigate organic deposits at seven archaeological sites located along the dominating west-east climatic gradient in West Greenland. We show that, regardless of age, depositional history and environmental conditions, all organic deposits are highly vulnerable to degradation. A state-of-the-art model that simulates the effect of future climate change on degradation indicates that 30–70% of the archaeological fraction of organic carbon (OC) could disappear within the next 80 years. This range reflects the variation within the climatic gradient and the future climate scenario applied (RCP 4.5 and RCP 8.5). All archaeological deposits are expected to experience a substantial loss, but the most rapid degradation seems to occur in the continental inland areas of the region, dominated by dry and warm summers. This suggests that organic remains from the Norse Viking Age settlers are especially under threat in the coming years.
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Affiliation(s)
- Jørgen Hollesen
- Environmental Archaeology and Materials Science, The National Museum of Denmark, IC Modewegsvej, Brede, DK-2800, Lyngby, Denmark. .,Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark.
| | - Henning Matthiesen
- Environmental Archaeology and Materials Science, The National Museum of Denmark, IC Modewegsvej, Brede, DK-2800, Lyngby, Denmark
| | - Rasmus Fenger-Nielsen
- Environmental Archaeology and Materials Science, The National Museum of Denmark, IC Modewegsvej, Brede, DK-2800, Lyngby, Denmark.,Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Jakob Abermann
- Asiaq, Greenland Survey, Postbox 1003, GL-3900, Nuuk, Greenland.,Department of Geography and Regional Science, Graz University, Heinrichstraße 36, 8010, Graz, Austria
| | - Andreas Westergaard-Nielsen
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Bo Elberling
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
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47
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Kovesi T. Respiratory medicine in Nunavut and Northern Canada. CANADIAN JOURNAL OF RESPIRATORY, CRITICAL CARE, AND SLEEP MEDICINE 2019. [DOI: 10.1080/24745332.2018.1483784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Thomas Kovesi
- Department of Pediatrics, Children’s Hospital of Eastern Ontrio, Ottawa, Ontario, Canada
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48
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49
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Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G, Yang MA, Fu Q, Dupanloup I, Giampoudakis K, Nogués-Bravo D, Rahbek C, Kroonen G, Peyrot M, McColl H, Vasilyev SV, Veselovskaya E, Gerasimova M, Pavlova EY, Chasnyk VG, Nikolskiy PA, Gromov AV, Khartanovich VI, Moiseyev V, Grebenyuk PS, Fedorchenko AY, Lebedintsev AI, Slobodin SB, Malyarchuk BA, Martiniano R, Meldgaard M, Arppe L, Palo JU, Sundell T, Mannermaa K, Putkonen M, Alexandersen V, Primeau C, Baimukhanov N, Malhi RS, Sjögren KG, Kristiansen K, Wessman A, Sajantila A, Lahr MM, Durbin R, Nielsen R, Meltzer DJ, Excoffier L, Willerslev E. The population history of northeastern Siberia since the Pleistocene. Nature 2019; 570:182-188. [PMID: 31168093 DOI: 10.1038/s41586-019-1279-z] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/07/2019] [Indexed: 12/30/2022]
Abstract
Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
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Affiliation(s)
- Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark.
| | - Vladimir V Pitulko
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia.
| | - Vitor C Sousa
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Constanza de la Fuente
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Human Genetics Department, University of Chicago, Chicago, IL, USA
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Center for Excellence in Life and Paleoenvironment, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Center for Excellence in Life and Paleoenvironment, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | | | - Konstantinos Giampoudakis
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David Nogués-Bravo
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Guus Kroonen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen, Denmark
- Leiden University Centre for Linguistics, Leiden University, Leiden, The Netherlands
| | - Michaël Peyrot
- Leiden University Centre for Linguistics, Leiden University, Leiden, The Netherlands
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sergey V Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
| | - Elizaveta Veselovskaya
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
- Russian State University for Humanities (RSUH), Moscow, Russia
| | - Margarita Gerasimova
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
| | - Elena Y Pavlova
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia
- Polar Geography Department, Arctic & Antarctic Research Institute, St Petersburg, Russia
| | | | - Pavel A Nikolskiy
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Andrei V Gromov
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Valeriy I Khartanovich
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Pavel S Grebenyuk
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
- Northeast State University, Magadan, Russia
| | - Alexander Yu Fedorchenko
- Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander I Lebedintsev
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Sergey B Slobodin
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Boris A Malyarchuk
- Institute of Biological Problems of the North, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Morten Meldgaard
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- University of Greenland, Nuuk, Greenland
| | - Laura Arppe
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Genetics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Tarja Sundell
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Mannermaa
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
| | - Mikko Putkonen
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Verner Alexandersen
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Primeau
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | | | - Anna Wessman
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
- Department of Archaeology, University of Turku, Turku, Finland
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Marta Mirazon Lahr
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark.
- Wellcome Sanger Institute, Cambridge, UK.
- GeoGenetics Groups, Department of Zoology, University of Cambridge, Cambridge, UK.
- The Danish Institute for Advanced Study, The University of Southern Denmark, Odense, Denmark.
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Flegontov P, Altınışık NE, Changmai P, Rohland N, Mallick S, Adamski N, Bolnick DA, Broomandkhoshbacht N, Candilio F, Culleton BJ, Flegontova O, Friesen TM, Jeong C, Harper TK, Keating D, Kennett DJ, Kim AM, Lamnidis TC, Lawson AM, Olalde I, Oppenheimer J, Potter BA, Raff J, Sattler RA, Skoglund P, Stewardson K, Vajda EJ, Vasilyev S, Veselovskaya E, Hayes MG, O'Rourke DH, Krause J, Pinhasi R, Reich D, Schiffels S. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America. Nature 2019; 570:236-240. [PMID: 31168094 PMCID: PMC6942545 DOI: 10.1038/s41586-019-1251-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/25/2019] [Indexed: 11/09/2022]
Abstract
Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik1-3. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain4-6. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques4,7-9, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup'ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.
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Affiliation(s)
- Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic.
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - N Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- School of Archaeology, University College Dublin, Dublin, Ireland
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la città metropolitana di Cagliari e le province di Oristano e Sud Sardegna, Cagliari, Italy
| | - Brendan J Culleton
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - T Max Friesen
- Department of Anthropology, University of Toronto, Toronto, ON, Canada
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Denise Keating
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Douglas J Kennett
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Alexander M Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ben A Potter
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Jennifer Raff
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | | | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Francis Crick Institute, London, UK
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Edward J Vajda
- Department of Modern and Classical Languages, Western Washington University, Bellingham, WA, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - M Geoffrey Hayes
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
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