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Akbari A, Barton AR, Gazal S, Li Z, Kariminejad M, Perry A, Zeng Y, Mittnik A, Patterson N, Mah M, Zhou X, Price AL, Lander ES, Pinhasi R, Rohland N, Mallick S, Reich D. Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.14.613021. [PMID: 39314480 PMCID: PMC11419161 DOI: 10.1101/2024.09.14.613021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ~0% to ~20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from ~0% to ~8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ~2% to ~9% from ~5500 to ~3000 years ago before dropping to ~3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.
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Affiliation(s)
- Ali Akbari
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alison R Barton
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Zheng Li
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Annabel Perry
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yating Zeng
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Alkes L Price
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ron Pinhasi
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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2
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Alaçamlı E, Naidoo T, Güler MN, Sağlıcan E, Aktürk Ş, Mapelli I, Vural KB, Somel M, Malmström H, Günther T. READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics. Genome Biol 2024; 25:216. [PMID: 39135108 PMCID: PMC11318251 DOI: 10.1186/s13059-024-03350-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/24/2024] [Indexed: 08/16/2024] Open
Abstract
The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.
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Affiliation(s)
- Erkin Alaçamlı
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Present Address: Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Thijessen Naidoo
- Ancient DNA Unit, Science for Life Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Merve N Güler
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Şevval Aktürk
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
- Ancient DNA Unit, Science for Life Laboratory, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
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3
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Anastasiadou K, Silva M, Booth T, Speidel L, Audsley T, Barrington C, Buckberry J, Fernandes D, Ford B, Gibson M, Gilardet A, Glocke I, Keefe K, Kelly M, Masters M, McCabe J, McIntyre L, Ponce P, Rowland S, Ruiz Ventura J, Swali P, Tait F, Walker D, Webb H, Williams M, Witkin A, Holst M, Loe L, Armit I, Schulting R, Skoglund P. Detection of chromosomal aneuploidy in ancient genomes. Commun Biol 2024; 7:14. [PMID: 38212558 PMCID: PMC10784527 DOI: 10.1038/s42003-023-05642-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024] Open
Abstract
Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.
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Affiliation(s)
- Kyriaki Anastasiadou
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom.
| | - Marina Silva
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Booth
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Leo Speidel
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
- Genetics Institute, University College London, London, United Kingdom
| | | | - Christopher Barrington
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Jo Buckberry
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | | | - Ben Ford
- Oxford Archaeology, Oxford, United Kingdom
| | | | - Alexandre Gilardet
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Isabelle Glocke
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Katie Keefe
- York Osteoarchaeology, York, United Kingdom
- On-Site Archaeology, York, United Kingdom
| | - Monica Kelly
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mackenzie Masters
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Jesse McCabe
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Paola Ponce
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | | | - Jordi Ruiz Ventura
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Pooja Swali
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Frankie Tait
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Helen Webb
- Oxford Archaeology, Oxford, United Kingdom
| | - Mia Williams
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Malin Holst
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Louise Loe
- Oxford Archaeology, Oxford, United Kingdom
| | - Ian Armit
- Department of Archaeology, University of York, York, United Kingdom
| | - Rick Schulting
- School of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Pontus Skoglund
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom.
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4
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Ávila-Arcos MC, Raghavan M, Schlebusch C. Going local with ancient DNA: A review of human histories from regional perspectives. Science 2023; 382:53-58. [PMID: 37797024 DOI: 10.1126/science.adh8140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- SciLifeLab, Uppsala, Sweden
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5
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Smith EA, Smith JE, Codding BF. Toward an evolutionary ecology of (in)equality. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220287. [PMID: 37381851 PMCID: PMC10291428 DOI: 10.1098/rstb.2022.0287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/30/2023] Open
Abstract
Inequality is increasingly recognized as a major problem in contemporary society. The causes and consequences of inequality in wealth and power have long been central concerns in the social sciences, whereas comparable research in biology has focused on dominance and reproductive skew. This theme issue builds on these existing research traditions, exploring ways they might enrich each other, with evolutionary ecology as a possibly unifying framework. Contributors investigate ways in which inequality is resisted or avoided and developed or imposed in societies of past and contemporary humans, as well as a variety of social mammals. Particular attention is paid to systematic, socially driven inequality in wealth (defined broadly) and the effects this has on differential power, health, survival and reproduction. Analyses include field studies, simulations, archaeological and ethnographic case studies, and analytical models. The results reveal similarities and divergences between human and non-human patterns in wealth, power and social dynamics. We draw on these insights to present a unifying conceptual framework for analysing the evolutionary ecology of (in)equality, with the hope of both understanding the past and improving our collective future. This article is part of the theme issue 'Evolutionary ecology of inequality'.
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Affiliation(s)
- Eric Alden Smith
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
| | - Jennifer E Smith
- Department of Biology, University of Wisconsin Eau Claire, 105 Garfield Avenue, Eau Claire, WI 54702, USA
| | - Brian F Codding
- Department of Anthropology and Archaeological Center, University of Utah, Salt Lake City, UT 84112, USA
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6
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Penske S, Rohrlach AB, Childebayeva A, Gnecchi-Ruscone G, Schmid C, Spyrou MA, Neumann GU, Atanassova N, Beutler K, Boyadzhiev K, Boyadzhiev Y, Bruyako I, Chohadzhiev A, Govedarica B, Karaucak M, Krauss R, Leppek M, Manzura I, Privat K, Ross S, Slavchev V, Sobotkova A, Toderaş M, Valchev T, Ringbauer H, Stockhammer PW, Hansen S, Krause J, Haak W. Early contact between late farming and pastoralist societies in southeastern Europe. Nature 2023; 620:358-365. [PMID: 37468624 PMCID: PMC10412445 DOI: 10.1038/s41586-023-06334-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 06/16/2023] [Indexed: 07/21/2023]
Abstract
Archaeogenetic studies have described two main genetic turnover events in prehistoric western Eurasia: one associated with the spread of farming and a sedentary lifestyle starting around 7000-6000 BC (refs. 1-3) and a second with the expansion of pastoralist groups from the Eurasian steppes starting around 3300 BC (refs. 4,5). The period between these events saw new economies emerging on the basis of key innovations, including metallurgy, wheel and wagon and horse domestication6-9. However, what happened between the demise of the Copper Age settlements around 4250 BC and the expansion of pastoralists remains poorly understood. To address this question, we analysed genome-wide data from 135 ancient individuals from the contact zone between southeastern Europe and the northwestern Black Sea region spanning this critical time period. While we observe genetic continuity between Neolithic and Copper Age groups from major sites in the same region, from around 4500 BC on, groups from the northwestern Black Sea region carried varying amounts of mixed ancestries derived from Copper Age groups and those from the forest/steppe zones, indicating genetic and cultural contact over a period of around 1,000 years earlier than anticipated. We propose that the transfer of critical innovations between farmers and transitional foragers/herders from different ecogeographic zones during this early contact was integral to the formation, rise and expansion of pastoralist groups around 3300 BC.
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Affiliation(s)
- Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guido Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Clemens Schmid
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nadezhda Atanassova
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Katrin Beutler
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | | | - Mehmet Karaucak
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Raiko Krauss
- Institute for Prehistory, Early History and Medieval Archaeology, Tübingen, Germany
| | - Maleen Leppek
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, Munich, Germany
| | - Igor Manzura
- National Museum of History of Moldova, Chişinău, Republic of Moldova
| | - Karen Privat
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
- Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Shawn Ross
- Department of History and Archaeology, Macquarie University, Sydney, New South Wales, Australia
| | | | | | - Meda Toderaş
- Institutul de Arheologie "Vasile Pârvan" Academia Română, Bucharest, Romania
| | | | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, Munich, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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7
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Pryor Y, Lindo J. Deconstructing Eurocentrism in skin pigmentation research via the incorporation of diverse populations and theoretical perspectives. Evol Anthropol 2023; 32:195-205. [PMID: 37450551 DOI: 10.1002/evan.21993] [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: 12/11/2022] [Revised: 03/29/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
The evolution of skin pigmentation has been shaped by numerous biological and cultural shifts throughout human history. Vitamin D is considered a driver of depigmentation evolution in humans, given the deleterious health effects associated with vitamin D deficiency, which is often shaped by cultural factors. New advancements in genomics and epigenomics have opened the door to a deeper exploration of skin pigmentation evolution in both contemporary and ancient populations. Data from ancient Europeans has offered great context to the spread of depigmentation alleles via the evaluation of migration events and cultural shifts that occurred during the Neolithic. However, novel insights can further be gained via the inclusion of diverse ancient and contemporary populations. Here we present on how potential biases and limitations in skin pigmentation research can be overcome with the integration of interdisciplinary data that includes both cultural and biological elements, which have shaped the evolutionary history of skin pigmentation in humans.
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Affiliation(s)
- Yemko Pryor
- Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, Georgia, USA
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8
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9
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Badillo-Sanchez DA, Jones DJL, Inskip SA, Scheib CL. Human Archaeological Dentin as Source of Polar and Less Polar Metabolites for Untargeted Metabolomic Research: The Case of Yersinia pestis. Metabolites 2023; 13:588. [PMID: 37233629 PMCID: PMC10223108 DOI: 10.3390/metabo13050588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted from archaeological human dentin. Dentin obtained from micro sampling the dental pulp of teeth of victims and non-victims of Yersinia pestis (plague) from a 6th century Cambridgeshire site are used to evaluate the potential use of such unique material for untargeted metabolomic studies on disease state through liquid chromatography hyphenated to high-resolution mass spectrometry (LC-HRMS). Results show that small molecules of both likely endogenous and exogenous sources are preserved for a range of polar and less polar/apolar metabolites in archaeological dentin; however, untargeted metabolomic profiles show no clear differentiation between healthy and infected individuals in the small sample analysed (n = 20). This study discusses the potential of dentin as a source of small molecules for metabolomic assays and highlights: (1) the need for follow up research to optimise sampling protocols, (2) the requirements of studies with larger sample numbers and (3) the necessity of more databases to amplify the positive results achievable with this Omic technique in the archaeological sciences.
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Affiliation(s)
| | - Donald J L Jones
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester LE1 7RH, UK
- The Leicester van Geest MultiOmics Facility, University of Leicester, Leicester LE1 7RH, UK
| | - Sarah A Inskip
- School of Archaeology and Ancient History, University of Leicester, Leicester LE1 7RH, UK
| | - Christiana L Scheib
- Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
- St. John's College, University of Cambridge, Cambridge CB2 1TP, UK
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10
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Guarino-Vignon P, Lefeuvre M, Chimènes A, Monnereau A, Guliyev F, Pecqueur L, Jovenet E, Lyonnet B, Bon C. Genome-wide analysis of a collective grave from Mentesh Tepe provides insight into the population structure of early neolithic population in the South Caucasus. Commun Biol 2023; 6:319. [PMID: 36966245 PMCID: PMC10039893 DOI: 10.1038/s42003-023-04681-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/08/2023] [Indexed: 03/27/2023] Open
Abstract
Despite the localisation of the southern Caucasus at the outskirt of the Fertile Crescent, the Neolithisation process started there only at the beginning of the sixth millennium with the Shomutepe-Shulaveri culture of yet unclear origins. We present here genomic data for three new individuals from Mentesh Tepe in Azerbaijan, dating back to the beginnings of the Shomutepe-Shulaveri culture. We evidence that two juveniles, buried embracing each other, were brothers. We show that the Mentesh Tepe Neolithic population is the product of a recent gene flow between the Anatolian farmer-related population and the Caucasus/Iranian population, demonstrating that population admixture was at the core of the development of agriculture in the South Caucasus. By comparing Bronze Age individuals from the South Caucasus with Neolithic individuals from the same region, including Mentesh Tepe, we evidence that gene flows between Pontic Steppe populations and Mentesh Tepe-related groups contributed to the makeup of the Late Bronze Age and modern Caucasian populations. Our results show that the high cultural diversity during the Neolithic period of the South Caucasus deserves close genetic analysis.
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Affiliation(s)
- Perle Guarino-Vignon
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France.
- UMR5288 CAGT, CNRS, Université Paul Sabatier, Toulouse, France.
| | - Maël Lefeuvre
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Amélie Chimènes
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Aurore Monnereau
- Department of Archaeology, University of York, BioArCh, Environment Building Wentworth Way Heslington, York, YO10 5NG, UK
| | - Farhad Guliyev
- Head of the Science Fund and the Museum Department of the Institute of Archeology, Ethnography and Anthropology, Azerbaijan National Academy of Science, Baku, Azerbaijan
| | - Laure Pecqueur
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
- Institut National de Recherches Archéologiques Préventives, Centre-île de France, Paris, France
| | - Elsa Jovenet
- Institut National de Recherches Archéologiques Préventives, Centre-île de France, Paris, France
| | - Bertille Lyonnet
- UMR7192 PROCLAC « Proche-Orient - Caucase: langues, archéologie, cultures », CNRS, Paris, France
| | - Céline Bon
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France.
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11
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Carlberg C. Nutrigenomics in the context of evolution. Redox Biol 2023; 62:102656. [PMID: 36933390 PMCID: PMC10036735 DOI: 10.1016/j.redox.2023.102656] [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: 01/18/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Nutrigenomics describes the interaction between nutrients and our genome. Since the origin of our species most of these nutrient-gene communication pathways have not changed. However, our genome experienced over the past 50,000 years a number of evolutionary pressures, which are based on the migration to new environments concerning geography and climate, the transition from hunter-gatherers to farmers including the zoonotic transfer of many pathogenic microbes and the rather recent change of societies to a preferentially sedentary lifestyle and the dominance of Western diet. Human populations responded to these challenges not only by specific anthropometric adaptations, such as skin color and body stature, but also through diversity in dietary intake and different resistance to complex diseases like the metabolic syndrome, cancer and immune disorders. The genetic basis of this adaptation process has been investigated by whole genome genotyping and sequencing including that of DNA extracted from ancient bones. In addition to genomic changes, also the programming of epigenomes in pre- and postnatal phases of life has an important contribution to the response to environmental changes. Thus, insight into the variation of our (epi)genome in the context of our individual's risk for developing complex diseases, helps to understand the evolutionary basis how and why we become ill. This review will discuss the relation of diet, modern environment and our (epi)genome including aspects of redox biology. This has numerous implications for the interpretation of the risks for disease and their prevention.
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Affiliation(s)
- Carsten Carlberg
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Juliana Tuwima 10, PL-10748, Olsztyn, Poland; School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211, Kuopio, Finland.
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12
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Ringbauer H, Huang Y, Akbari A, Mallick S, Patterson N, Reich D. ancIBD - Screening for identity by descent segments in human ancient DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531671. [PMID: 36945531 PMCID: PMC10028887 DOI: 10.1101/2023.03.08.531671] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set ('1240k'). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.
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Affiliation(s)
- Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germanÿ
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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13
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The transmission of pottery technology among prehistoric European hunter-gatherers. Nat Hum Behav 2023; 7:171-183. [PMID: 36550220 PMCID: PMC9957732 DOI: 10.1038/s41562-022-01491-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2022]
Abstract
Human history has been shaped by global dispersals of technologies, although understanding of what enabled these processes is limited. Here, we explore the behavioural mechanisms that led to the emergence of pottery among hunter-gatherer communities in Europe during the mid-Holocene. Through radiocarbon dating, we propose this dispersal occurred at a far faster rate than previously thought. Chemical characterization of organic residues shows that European hunter-gatherer pottery had a function structured around regional culinary practices rather than environmental factors. Analysis of the forms, decoration and technological choices suggests that knowledge of pottery spread through a process of cultural transmission. We demonstrate a correlation between the physical properties of pots and how they were used, reflecting social traditions inherited by successive generations of hunter-gatherers. Taken together the evidence supports kinship-driven, super-regional communication networks that existed long before other major innovations such as agriculture, writing, urbanism or metallurgy.
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14
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Muktupavela RA, Petr M, Ségurel L, Korneliussen T, Novembre J, Racimo F. Modeling the spatiotemporal spread of beneficial alleles using ancient genomes. eLife 2022; 11:e73767. [PMID: 36537881 PMCID: PMC9767474 DOI: 10.7554/elife.73767] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.
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Affiliation(s)
- Rasa A Muktupavela
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
| | - Martin Petr
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
| | - Laure Ségurel
- UMR5558 Biométrie et Biologie Evolutive, CNRS - Université Lyon 1VilleurbanneFrance
| | | | - John Novembre
- Department of Human Genetics, University of ChicagoChicagoUnited States
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
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15
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Lalueza-Fox C. Human genetics: A tale of two historical Jewish communities. Curr Biol 2022; 32:R1023-R1025. [PMID: 36283348 DOI: 10.1016/j.cub.2022.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The first studies to retrieve genome-wide data from two Medieval European Jewish communities from England and Germany illustrate the complex interplay of ancestry, disease, religion, culture and ethics.
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Affiliation(s)
- Carles Lalueza-Fox
- Museu de Ciències Naturals de Barcelona, 08019 Barcelona, Spain; Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain.
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16
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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17
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Argüelles JM, Fuentes A, Yáñez B. Analyzing asymmetries and praxis in aDNA research: A bioanthropological critique. AMERICAN ANTHROPOLOGIST 2022. [DOI: 10.1111/aman.13692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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Cox SL, Moots HM, Stock JT, Shbat A, Bitarello BD, Nicklisch N, Alt KW, Haak W, Rosenstock E, Ruff CB, Mathieson I. Predicting skeletal stature using ancient
DNA. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2021. [PMCID: PMC9298243 DOI: 10.1002/ajpa.24426] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samantha L. Cox
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
- Physical Anthropology Section, Penn Museum University of Pennsylvania Philadelphia Pennsylvania USA
| | - Hannah M. Moots
- Department of Anthropology Stanford University Stanford California USA
| | - Jay T. Stock
- Department of Anthropology Western University London Ontario Canada
- Department of Archaeology Max Planck Institute for the Science of Human History Jena Germany
| | - Andrej Shbat
- Institute of Anatomy, First Faculty of Medicine Charles University Prague Czech Republic
| | - Bárbara D. Bitarello
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History Danube Private University Krems Austria
| | - Kurt W. Alt
- Center of Natural and Cultural Human History Danube Private University Krems Austria
| | - Wolfgang Haak
- Department of Archaeogenetics Max Planck Institute for the Science of Human History Jena Germany
| | - Eva Rosenstock
- Bonn Center for ArchaeoSciences Institut für Archäologie und Kulturanthropologie, Universität Bonn Bonn Germany
| | - Christopher B. Ruff
- Center for Functional Anatomy and Evolution Johns Hopkins University School of Medicine Baltimore Maryland USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
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19
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Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat Commun 2021; 12:5425. [PMID: 34521843 PMCID: PMC8440622 DOI: 10.1038/s41467-021-25289-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 07/21/2021] [Indexed: 02/08/2023] Open
Abstract
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.
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20
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Maisano Delser P, Jones ER, Hovhannisyan A, Cassidy L, Pinhasi R, Manica A. A curated dataset of modern and ancient high-coverage shotgun human genomes. Sci Data 2021; 8:202. [PMID: 34349118 PMCID: PMC8338957 DOI: 10.1038/s41597-021-00980-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/10/2021] [Indexed: 11/09/2022] Open
Abstract
Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10-18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.
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Affiliation(s)
- Pierpaolo Maisano Delser
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland.
| | - Eppie R Jones
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- Genomics Medicine Ireland, Dublin, Ireland
| | - Anahit Hovhannisyan
- Institute of Molecular Biology, National Academy of Sciences, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | - Lara Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.
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21
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Gelabert P, Sawyer S, Bergström A, Margaryan A, Collin TC, Meshveliani T, Belfer-Cohen A, Lordkipanidze D, Jakeli N, Matskevich Z, Bar-Oz G, Fernandes DM, Cheronet O, Özdoğan KT, Oberreiter V, Feeney RNM, Stahlschmidt MC, Skoglund P, Pinhasi R. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment. Curr Biol 2021; 31:3564-3574.e9. [PMID: 34256019 PMCID: PMC8409484 DOI: 10.1016/j.cub.2021.06.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023]
Abstract
Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ashot Margaryan
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas C Collin
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Tengiz Meshveliani
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Anna Belfer-Cohen
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Lordkipanidze
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Nino Jakeli
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Mareike C Stahlschmidt
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
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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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Žegarac A, Winkelbach L, Blöcher J, Diekmann Y, Krečković Gavrilović M, Porčić M, Stojković B, Milašinović L, Schreiber M, Wegmann D, Veeramah KR, Stefanović S, Burger J. Ancient genomes provide insights into family structure and the heredity of social status in the early Bronze Age of southeastern Europe. Sci Rep 2021; 11:10072. [PMID: 33980902 PMCID: PMC8115322 DOI: 10.1038/s41598-021-89090-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/20/2021] [Indexed: 12/31/2022] Open
Abstract
Twenty-four palaeogenomes from Mokrin, a major Early Bronze Age necropolis in southeastern Europe, were sequenced to analyse kinship between individuals and to better understand prehistoric social organization. 15 investigated individuals were involved in genetic relationships of varying degrees. The Mokrin sample resembles a genetically unstructured population, suggesting that the community’s social hierarchies were not accompanied by strict marriage barriers. We find evidence for female exogamy but no indications for strict patrilocality. Individual status differences at Mokrin, as indicated by grave goods, support the inference that females could inherit status, but could not transmit status to all their sons. We further show that sons had the possibility to acquire status during their lifetimes, but not necessarily to inherit it. Taken together, these findings suggest that Southeastern Europe in the Early Bronze Age had a significantly different family and social structure than Late Neolithic and Early Bronze Age societies of Central Europe.
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Affiliation(s)
- A Žegarac
- Laboratory of Bioarchaeology, Faculty of Philosophy, University of Belgrade, 11000, Belgrade, Serbia.,Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, 55099, Mainz, Germany
| | - L Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, 55099, Mainz, Germany
| | - J Blöcher
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, 55099, Mainz, Germany
| | - Y Diekmann
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, 55099, Mainz, Germany
| | - M Krečković Gavrilović
- Laboratory of Bioarchaeology, Faculty of Philosophy, University of Belgrade, 11000, Belgrade, Serbia
| | - M Porčić
- Laboratory of Bioarchaeology, Faculty of Philosophy, University of Belgrade, 11000, Belgrade, Serbia
| | - B Stojković
- Department of Genetics and Evolution, Faculty of Biology, University of Belgrade, 11000, Belgrade, Serbia
| | - L Milašinović
- National Museum of Kikinda, Trg Srpskih Dobrovoljaca 21, 23300, Kikinda, Serbia
| | - M Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - D Wegmann
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland
| | - K R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11790, USA
| | - S Stefanović
- Laboratory of Bioarchaeology, Faculty of Philosophy, University of Belgrade, 11000, Belgrade, Serbia.,Biosense Institute, University of Novi Sad, 21000, Novi Sad, Serbia
| | - J Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, 55099, Mainz, Germany.
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24
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Saupe T, Montinaro F, Scaggion C, Carrara N, Kivisild T, D'Atanasio E, Hui R, Solnik A, Lebrasseur O, Larson G, Alessandri L, Arienzo I, De Angelis F, Rolfo MF, Skeates R, Silvestri L, Beckett J, Talamo S, Dolfini A, Miari M, Metspalu M, Benazzi S, Capelli C, Pagani L, Scheib CL. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula. Curr Biol 2021; 31:2576-2591.e12. [PMID: 33974848 DOI: 10.1016/j.cub.2021.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/28/2020] [Accepted: 04/09/2021] [Indexed: 12/30/2022]
Abstract
Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.
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Affiliation(s)
- Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia.
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Cinzia Scaggion
- Department of Geosciences, University of Padova, Via Gradenigo 6, Padova 35131, Italy
| | - Nicola Carrara
- Museum of Anthropology, University of Padova, Palazzo Cavalli, via Giotto 1, Padova 35121, Italy
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 49 3000, Belgium
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ophélie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK; Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Greger Larson
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Luca Alessandri
- Groningen Institute of Archaeology, University of Groningen, Poststraat 6, Groningen 9712, the Netherlands
| | - Ilenia Arienzo
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata," Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Letizia Silvestri
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | | | - Sahra Talamo
- Department of Chemistry "Giacomo Ciamician," University of Bologna, Via Selmi 2, Bologna 40126, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Andrea Dolfini
- School of History, Classics and Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Monica Miari
- Superintendency of Archeology, Fine Arts and Landscape for the metropolitan city of Bologna and the provinces of Modena, Reggio Emilia and Ferrara, Comune di Bologna, Sede Via Belle Arti n. 52, Bologna 40126, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1, Ravenna 40126, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi, 58/B, Padova 35122, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; St. John's College, University of Cambridge, St. John's Street, Cambridge CB2 1TP, UK.
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25
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Abstract
In the last ten years, the next generation sequencing revolution has multiplied the amount of genetic data for many organisms by orders of magnitude. This has not only led to evolutionary biologists having more data available but also to new and different types of data: from a handful of allozyme markers in the 70s, we got dozens of restriction fragment length polymorphisms (RFLPs) in the 80s, hundreds of microsatellites in the 90s, thousands to hundreds of thousands of single nucleotide polymorphisms (SNPs) in the 2000s, a few full genomes in the 2010s, and thousands of full genomes in the 2020s. These data have provided information not only on the genetic diversity and evolution of the organisms studied but also on genome-wide patterns of selection, linkage disequilibrium, as well as recombination and mutation processes. Below, we will describe how these new genomic data can be used to infer the past demographic history of populations.
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Affiliation(s)
- Nina Marchi
- CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland; Swiss Institute of Ecology and Evolution, 1015 Lausanne, Switzerland
| | - Flávia Schlichta
- CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland; Swiss Institute of Ecology and Evolution, 1015 Lausanne, Switzerland
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland; Swiss Institute of Ecology and Evolution, 1015 Lausanne, Switzerland.
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26
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Abstract
The study of ancient genomes has burgeoned at an incredible rate in the last decade. The result is a shift in archaeological narratives, bringing with it a fierce debate on the place of genetics in anthropological research. Archaeogenomics has challenged and scrutinized fundamental themes of anthropological research, including human origins, movement of ancient and modern populations, the role of social organization in shaping material culture, and the relationship between culture, language, and ancestry. Moreover, the discussion has inevitably invoked new debates on indigenous rights, ownership of ancient materials, inclusion in the scientific process, and even the meaning of what it is to be a human. We argue that the broad and seemingly daunting ethical, methodological, and theoretical challenges posed by archaeogenomics, in fact, represent the very cutting edge of social science research. Here, we provide a general review of the field by introducing the contemporary discussion points and summarizing methodological and ethical concerns, while highlighting the exciting possibilities of ancient genome studies in archaeology from an anthropological perspective.
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Affiliation(s)
- Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14221, USA
| | - Michael Frachetti
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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27
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Gibbon VE. African ancient DNA research requires robust ethics and permission protocols. Nat Rev Genet 2020; 21:645-647. [PMID: 32939074 DOI: 10.1038/s41576-020-00285-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Victoria E Gibbon
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Observatory, Cape Town, South Africa.
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28
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Hanel A, Carlberg C. Skin colour and vitamin D: An update. Exp Dermatol 2020; 29:864-875. [PMID: 32621306 DOI: 10.1111/exd.14142] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/14/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
Homo sapiens evolved in East Africa and had dark skin, hair, and eyes, in order to protect against deleterious consequences of intensive UV radiation at equatorial latitudes. Intensive skin pigmentation was thought to bear the risk of inefficient vitamin D3 synthesis in the skin. This initiated the hypothesis that within the past 75 000 years, in which humans migrated to higher latitudes in Asia and Europe, the need for vitamin D3 synthesis served as an evolutionary driver for skin lightening. In this review, we summarize the recent archeogenomic reconstruction of population admixture in Europe and demonstrate that skin lightening happened as late as 5000 years ago through immigration of lighter pigmented populations from western Anatolia and the Russian steppe but not primarily via evolutionary pressure for vitamin D3 synthesis. We show that variations in genes encoding for proteins being responsible for the transport, metabolism and signalling of vitamin D provide alternative mechanisms of adaptation to a life in northern latitudes without suffering from consequences of vitamin D deficiency. This includes hypotheses explaining differences in the vitamin D status and response index of European populations.
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Affiliation(s)
- Andrea Hanel
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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29
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Tsosie KS, Begay RL, Fox K, Garrison NA. Generations of genomes: advances in paleogenomics technology and engagement for Indigenous people of the Americas. Curr Opin Genet Dev 2020; 62:91-96. [PMID: 32721847 PMCID: PMC7484015 DOI: 10.1016/j.gde.2020.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
For decades, scientists have collected genomic information from Indigenous peoples and their ancestors with the goal of elucidating human migration events, understanding ancestral origins, and identifying ancestral variants contributing to disease. However, such studies may not have offered much benefit to the Indigenous groups who contributed DNA, and many have instead perpetuated stereotypes and other harms. With recent advances in genomic technology facilitating the study of both ancient and present-day DNA, researchers and Indigenous communities have new opportunities to begin collaboratively addressing important questions about human health and history. Yet, while there are increased efforts to ethically engage Indigenous communities, more work is still needed as the discipline struggles to absolve itself of the racialized science and extractive biocolonialism that defined its past.
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Affiliation(s)
- Krystal S Tsosie
- Vanderbilt University, Nashville, TN 37325, USA; Native BioData Consortium, Eagle Butte, SD 57625, USA
| | - Rene L Begay
- Centers for American Indian and Alaska Native Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Keolu Fox
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Global Health, University of California, San Diego, La Jolla, CA 92093, USA; Indigenous Futures Lab, University of California, San Diego, La Jolla, CA 92093, USA; Native BioData Consortium, Eagle Butte, SD 57625, USA
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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30
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Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans. Sci Rep 2020; 10:6843. [PMID: 32321996 PMCID: PMC7176696 DOI: 10.1038/s41598-020-64007-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/06/2020] [Indexed: 11/08/2022] Open
Abstract
Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual- that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present.
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31
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