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Moreno-Mayar JV, Sousa da Mota B, Higham T, Klemm S, Gorman Edmunds M, Stenderup J, Iraeta-Orbegozo M, Laborde V, Heyer E, Torres Hochstetter F, Friess M, Allentoft ME, Schroeder H, Delaneau O, Malaspinas AS. Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas. Nature 2024; 633:389-397. [PMID: 39261618 DOI: 10.1038/s41586-024-07881-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 07/26/2024] [Indexed: 09/13/2024]
Abstract
Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai1. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse-the 'ecocide' theory2-4. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated5-7. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670-1950 CE) and whole-genome sequenced (0.4-25.6×). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250-1430 CE.
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Affiliation(s)
- J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tom Higham
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS) Network, University of Vienna, Vienna, Austria
| | - Signe Klemm
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper Stenderup
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Miren Iraeta-Orbegozo
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Véronique Laborde
- Direction Générale Déléguée aux Collections, Muséum national d'Histoire naturelle, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie (EA), Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | | | - Martin Friess
- Eco-anthropologie (EA), Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - 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, Western Australia, Australia
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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2
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Barquera R, Del Castillo-Chávez O, Nägele K, Pérez-Ramallo P, Hernández-Zaragoza DI, Szolek A, Rohrlach AB, Librado P, Childebayeva A, Bianco RA, Penman BS, Acuña-Alonzo V, Lucas M, Lara-Riegos JC, Moo-Mezeta ME, Torres-Romero JC, Roberts P, Kohlbacher O, Warinner C, Krause J. Ancient genomes reveal insights into ritual life at Chichén Itzá. Nature 2024; 630:912-919. [PMID: 38867041 PMCID: PMC11208145 DOI: 10.1038/s41586-024-07509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/02/2024] [Indexed: 06/14/2024]
Abstract
The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1-4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
| | - Oana Del Castillo-Chávez
- Centro INAH Yucatán, Instituto Nacional de Antropología e Historia (INAH), Mérida, Yucatán, Mexico.
| | - Kathrin Nägele
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- University of the Basque Country (EHU), San Sebastián-Donostia, Spain
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology and Cultural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Diana Iraíz Hernández-Zaragoza
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - András Szolek
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Pablo Librado
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - Raffaela Angelina Bianco
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Bridget S Penman
- The Zeeman Institute and the School of Life Sciences, University of Warwick, Coventry, UK
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mary Lucas
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | | | | | | | - Patrick Roberts
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
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3
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Saltré F, Chadœuf J, Higham T, Ochocki M, Block S, Bunney E, Llamas B, Bradshaw CJA. Environmental conditions associated with initial northern expansion of anatomically modern humans. Nat Commun 2024; 15:4364. [PMID: 38777837 PMCID: PMC11111671 DOI: 10.1038/s41467-024-48762-8] [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: 04/28/2022] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
The ability of our ancestors to switch food sources and to migrate to more favourable environments enabled the rapid global expansion of anatomically modern humans beyond Africa as early as 120,000 years ago. Whether this versatility was largely the result of environmentally determined processes or was instead dominated by cultural drivers, social structures, and interactions among different groups, is unclear. We develop a statistical approach that combines both archaeological and genetic data to infer the more-likely initial expansion routes in northern Eurasia and the Americas. We then quantify the main differences in past environmental conditions between the more-likely routes and other potential (less-likely) routes of expansion. We establish that, even though cultural drivers remain plausible at finer scales, the emergent migration corridors were predominantly constrained by a combination of regional environmental conditions, including the presence of a forest-grassland ecotone, changes in temperature and precipitation, and proximity to rivers.
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Affiliation(s)
- Frédérik Saltré
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia.
| | - Joël Chadœuf
- UR 1052, French National Institute for Agricultural Research (INRA), Montfavet, France
| | - Thomas Higham
- Department of Evolutionary Biology, University of Vienna, University Biology Building, Carl Djerassi Platz 1, A-1030, Wien, Austria
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3TG, UK
| | - Monty Ochocki
- Department of Evolutionary Biology, University of Vienna, University Biology Building, Carl Djerassi Platz 1, A-1030, Wien, Austria
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3TG, UK
| | - Sebastián Block
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544-1003, USA
| | - Ellyse Bunney
- Commonwealth Scientific and Industrial Research Organisation, Urrbrae, SA, 5064, Australia
| | - Bastien Llamas
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences, The Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, 5000, Australia
| | - Corey J A Bradshaw
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
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4
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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] [Grants] [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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Affiliation(s)
- Leonardo N. M. Iasi
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
| | - Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
| | - Laurits Skov
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
| | - Alba Bossoms Mesa
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
| | - Mateja Hajdinjak
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Benjamin M. Peter
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
- Department of Biology, University of Rochester; Rochester NY, 14620,USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
- Center for Computational Biology, University of California Berkeley; Berkeley, CA 94720, USA
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5
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de Smith AJ, Wahlster L, Jeon S, Kachuri L, Black S, Langie J, Cato LD, Nakatsuka N, Chan TF, Xia G, Mazumder S, Yang W, Gazal S, Eng C, Hu D, Burchard EG, Ziv E, Metayer C, Mancuso N, Yang JJ, Ma X, Wiemels JL, Yu F, Chiang CWK, Sankaran VG. A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children. CELL GENOMICS 2024; 4:100526. [PMID: 38537633 PMCID: PMC11019360 DOI: 10.1016/j.xgen.2024.100526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Hispanic/Latino children have the highest risk of acute lymphoblastic leukemia (ALL) in the US compared to other racial/ethnic groups, yet the basis of this remains incompletely understood. Through genetic fine-mapping analyses, we identified a new independent childhood ALL risk signal near IKZF1 in self-reported Hispanic/Latino individuals, but not in non-Hispanic White individuals, with an effect size of ∼1.44 (95% confidence interval = 1.33-1.55) and a risk allele frequency of ∼18% in Hispanic/Latino populations and <0.5% in European populations. This risk allele was positively associated with Indigenous American ancestry, showed evidence of selection in human history, and was associated with reduced IKZF1 expression. We identified a putative causal variant in a downstream enhancer that is most active in pro-B cells and interacts with the IKZF1 promoter. This variant disrupts IKZF1 autoregulation at this enhancer and results in reduced enhancer activity in B cell progenitors. Our study reveals a genetic basis for the increased ALL risk in Hispanic/Latino children.
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Affiliation(s)
- Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susan Black
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tsz-Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Guangze Xia
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Soumyaa Mazumder
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Celeste Eng
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Esteban González Burchard
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaomei Ma
- Yale School of Public Health, New Haven, CT 06520, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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6
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Rider DF, Wolf ACE, Murray J, de Flamingh A, dos Santos ALC, Lanoë F, Zedeño MN, DeGiorgio M, Lindo J, Malhi RS. Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times. SCIENCE ADVANCES 2024; 10:eadl6595. [PMID: 38569022 PMCID: PMC10990285 DOI: 10.1126/sciadv.adl6595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
Mutually beneficial partnerships between genomics researchers and North American Indigenous Nations are rare yet becoming more common. Here, we present one such partnership that provides insight into the peopling of the Americas and furnishes another line of evidence that can be used to further treaty and Indigenous rights. We show that the genomics of sampled individuals from the Blackfoot Confederacy belong to a previously undescribed ancient lineage that diverged from other genomic lineages in the Americas in Late Pleistocene times. Using multiple complementary forms of knowledge, we provide a scenario for Blackfoot population history that fits with oral tradition and provides a plausible model for the evolutionary process of the peopling of the Americas.
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Affiliation(s)
| | | | - John Murray
- Blackfeet Tribal Historic Preservation Office, Browning, MT 59417, USA
| | - Alida de Flamingh
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | | | - François Lanoë
- Bureau of Applied Research in Anthropology, School of Anthropology, The University of Arizona, Tucson, AZ 85721, USA
| | - Maria N. Zedeño
- Bureau of Applied Research in Anthropology, School of Anthropology, The University of Arizona, Tucson, AZ 85721, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Ripan S. Malhi
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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7
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Reynolds AZ, Niedbalski SD. Sex-biased gene regulation varies across human populations as a result of adaptive evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24888. [PMID: 38100225 PMCID: PMC11279473 DOI: 10.1002/ajpa.24888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 03/03/2024]
Abstract
OBJECTIVES Studies of human sexual dimorphism and gender disparities in health focus on ostensibly universal molecular sex differences, such as sex chromosomes and circulating hormone levels, while ignoring the extraordinary diversity in biology, behavior, and culture acquired by different human populations over their unique evolutionary histories. MATERIALS AND METHODS Using RNA-Seq data and whole genome sequences from 1000G and HGDP, we investigate variation in sex-biased gene expression across 11 human populations and test whether population-level variation in sex-biased expression may have resulted from adaptive evolution in regions containing sex-specific regulatory variants. RESULTS We find that sex-biased gene expression in humans is highly variable, mostly population-specific, and demonstrates between population reversals. Expression quantitative trait locus mapping reveals sex-specific regulatory regions with evidence of recent positive natural selection, suggesting that variation in sex-biased expression may have evolved as an adaptive response to ancestral environments experienced by human populations. DISCUSSION These results indicate that sex-biased gene expression is more flexible than previously thought and is not generally shared among human populations. Instead, molecular phenotypes associated with sex depend on complex interactions between population-specific molecular evolution and physiological responses to contemporary socioecologies.
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Affiliation(s)
- Adam Z. Reynolds
- Department of Anthropology, University of New Mexico, Albuquerque, NM
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8
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Butovskaya ML, Rostovstseva VV, Mezentseva AA, Kavina A, Rizwan M, Shi Y, Vilimek V, Davletshin A. Cross-cultural perception of strength, attractiveness, aggressiveness and helpfulness of Maasai male faces calibrated to handgrip strength. Sci Rep 2024; 14:5880. [PMID: 38467751 PMCID: PMC10928163 DOI: 10.1038/s41598-024-56607-z] [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: 10/19/2023] [Accepted: 03/08/2024] [Indexed: 03/13/2024] Open
Abstract
Previous research has demonstrated that Maasai and Europeans tend to align in their ratings of the physical strength and aggressiveness of Maasai male faces, calibrated to hand grip strength (HGS). However, perceptions of attractiveness of these faces differed among populations. In this study, three morphs of young Maasai men created by means of geometric morphometrics, and depicting the average sample and two extrema (± 4 SD of HGS), were assessed by men and women from Tanzania, Czech Republic, Russia, Pakistan, China, and Mexico (total sample = 1540). The aim of this study was to test cross-cultural differences in the perception of young Maasai men's composites calibrated to HGS, focusing on four traits: physical strength, attractiveness, aggressiveness, and helpfulness. Individuals from all six cultures were able to distinguish between low, medium, and high HGS portraits. Across all study populations, portrait of Maasai men with lower HGS was perceived as less attractive, more aggressive, and less helpful. This suggests that people from diverse populations share similar perceptions of physical strength based on facial shape, as well as attribute similar social qualities like aggressiveness and helpfulness to these facial images. Participants from all samples rated the composite image of weak Maasai men as the least attractive.
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Affiliation(s)
- Marina L Butovskaya
- Institute of Ethnology and Anthropology Russian Academy of Sciences, Leninsky Prospect 32a, 119334, Moscow, Russia.
- National Research University, Higher School of Economics, Moscow, Russia.
| | - Victoria V Rostovstseva
- Institute of Ethnology and Anthropology Russian Academy of Sciences, Leninsky Prospect 32a, 119334, Moscow, Russia
| | - Anna A Mezentseva
- Institute of Ethnology and Anthropology Russian Academy of Sciences, Leninsky Prospect 32a, 119334, Moscow, Russia
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9
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Steffen ML. New age constraints for human entry into the Americas on the north Pacific coast. Sci Rep 2024; 14:4291. [PMID: 38383701 PMCID: PMC10881565 DOI: 10.1038/s41598-024-54592-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
The timing of the initial peopling of the Americas is unresolved. Because the archaeological record necessitates discussion of human entry from Beringia into southern North America during the last glaciation, addressing this problem routinely involves evaluating environmental parameters then targeting areas suitable for human settlement. Vertebrate remains indicate landscape quality and are a key dataset for assessing coastal migration theories and the viability of coastal routes. Here, radiocarbon dates on vertebrate specimens and archaeological sites are calibrated to document species occurrences and the ages of human settlements across the western expansion and decay of the Cordilleran Ice Sheet (CIS) during the Late Wisconsin Fraser Glaciation in four subregions of the north Pacific coast of North America. The results show archaeological sites occur after glacial maxima and are generally consistent with the age of other securely dated earliest sites in southern North America. They also highlight gaps in the vertebrate chronologies around CIS maxima in each of the subregions that point to species redistributions and extirpations and signal times of low potential for human settlement and subsistence in a key portion of the proposed coastal migration route. This study, therefore, defines new age constraints for human coastal migration theories in the peopling of the Americas debate.
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10
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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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11
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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12
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Espitia Fajardo M, Rivera Franco N, Braga Y, Barreto G. New Y-SNPs in QM3 indigenous populations of Colombia. PLoS One 2023; 18:e0294516. [PMID: 38055663 PMCID: PMC10699635 DOI: 10.1371/journal.pone.0294516] [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: 08/01/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
In evolutionary studies of human populations based on the Y chromosome, the majority of Native Americans belong to the QM3 lineage. Therefore, to study the history of groups inhabiting northern South America, it is necessary to have a higher resolution of the tree. The objective of this work was to identify new SNPs of the QM3 lineage that would allow the evaluation of the phylogenetic relationships between Andean and Amazonian populations of Colombia. Sequences previously obtained from two Y chromosomes of Amazonian populations were used, from which 13 potential SNPs were selected and typed in 171 Amazonian samples from the Vaupés region and in 60 samples from the Pasto, Nasa, Embera, Arhuaco and Kogüi ethnic groups of the Andean region. In addition, the main SNPs/markers (L56, L54, M346, M848, Z780, CTS11780) defining autochthonous Q lineages were typed, along with others defined by different SNPs/markers as reported in the literature (CTS11357, SA05, Z19319, Z5915, and Z19384). It was found that all the new SNPs are present in the Amazonian samples and only 2 of them are shared with the Embera, Nasa and Pasto, but none with the Kogüi and Arhuaco from the northern Andes, in the Colombian Caribbean. Combining the 13 variants of the present study with 14 previously reported and using TMRCA, a new QM3 tree proposal is generated. This method makes it possible to increase the number of sublineages of QM3 with a higher resolution and to detect differences between the different populations of Vaupés in the Amazon, as in the case of the Kubeos and Pisamiras, the latter of which is in grave danger of extinction. These new sublineages are useful for microevolutionary studies of the Amerindian populations of South America.
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Affiliation(s)
- Marisol Espitia Fajardo
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
| | - Nelson Rivera Franco
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
| | - Yamid Braga
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
- Research Group in Biology, Languages and History, IMGB, Corpodihva, Mitú, Colombia
| | - Guillermo Barreto
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
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13
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Borodko DD, Zhenilo SV, Sharko FS. Search for differentially methylated regions in ancient and modern genomes. Vavilovskii Zhurnal Genet Selektsii 2023; 27:820-828. [PMID: 38213708 PMCID: PMC10777292 DOI: 10.18699/vjgb-23-95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 01/13/2024] Open
Abstract
Currently, active research is focused on investigating the mechanisms that regulate the development of various pathologies and their evolutionary dynamics. Epigenetic mechanisms, such as DNA methylation, play a significant role in evolutionary processes, as their changes have a faster impact on the phenotype compared to mutagenesis. In this study, we attempted to develop an algorithm for identifying differentially methylated regions associated with metabolic syndrome, which have undergone methylation changes in humans during the transition from a hunter-gatherer to a sedentary lifestyle. The application of existing whole-genome bisulfite sequencing methods is limited for ancient samples due to their low quality and fragmentation, and the approach to obtaining DNA methylation profiles differs significantly between ancient hunter-gatherer samples and modern tissues. In this study, we validated DamMet, an algorithm for reconstructing ancient methylomes. Application of DamMet to Neanderthal and Denisovan genomes showed a moderate level of correlation with previously published methylation profiles and demonstrated an underestimation of methylation levels in the reconstructed profiles by an average of 15-20 %. Additionally, we developed a new Python-based algorithm that allows for the comparison of methylomes in ancient and modern samples, despite the absence of methylation profiles in modern bone tissue within the context of obesity. This analysis involves a two-step data processing approach, where the first step involves the identification and filtration of tissue-specific methylation regions, and the second step focuses on the direct search for differentially methylated regions in specific areas associated with the researcher's target condition. By applying this algorithm to test data, we identified 38 differentially methylated regions associated with obesity, the majority of which were located in promoter regions. The pipeline demonstrated sufficient efficiency in detecting these regions. These results confirm the feasibility of reconstructing DNA methylation profiles in ancient samples and comparing them with modern methylomes. Furthermore, possibilities for further methodological development and the implementation of a new step for studying differentially methylated positions associated with evolutionary processes are discussed.
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Affiliation(s)
- D D Borodko
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - S V Zhenilo
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - F S Sharko
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
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14
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Izarraras-Gomez A, Ortega-Del Vecchyo D. Ancient DNA uncovers past migrations in California. Nature 2023; 624:43-44. [PMID: 37993617 DOI: 10.1038/d41586-023-03503-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
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15
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Nakatsuka N, Holguin B, Sedig J, Langenwalter PE, Carpenter J, Culleton BJ, García-Moreno C, Harper TK, Martin D, Martínez-Ramírez J, Porcayo-Michelini A, Tiesler V, Villapando-Canchola ME, Valdes Herrera A, Callan K, Curtis E, Kearns A, Iliev L, Lawson AM, Mah M, Mallick S, Micco A, Michel M, Workman JN, Oppenheimer J, Qiu L, Zalzala F, Rohland N, Punzo Diaz JL, Johnson JR, Reich D. Genetic continuity and change among the Indigenous peoples of California. Nature 2023; 624:122-129. [PMID: 37993721 PMCID: PMC10872549 DOI: 10.1038/s41586-023-06771-5] [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: 05/22/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity1. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico2-4. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions1,5. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA.
| | - Brian Holguin
- Department of Anthropology, University of California at Santa Barbara, Santa Barbara, CA, USA
| | - Jakob Sedig
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - John Carpenter
- Instituto Nacional de Antropología e Historia, Sonora, Hermosillo, México
| | - Brendan J Culleton
- Institute of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | | | - Thomas K Harper
- Institute of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Debra Martin
- Department of Anthropology, University of Nevada, Las Vegas, NV, USA
| | | | | | - Vera Tiesler
- Universidad Autónoma de Yucatán, Facultad de Ciencias Antropológicas, Mérida, México
| | | | | | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Aisling Kearns
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, 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
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, 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
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - John R Johnson
- Santa Barbara Museum of Natural History, Santa Barbara, CA, USA.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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16
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Scott GR, Navega D, Vlemincq-Mendieta T, Dern LL, O'Rourke DH, Hlusko LJ, Hoffecker JF. Peopling of the Americas: A new approach to assessing dental morphological variation in Asian and Native American populations. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 38018312 DOI: 10.1002/ajpa.24878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023]
Abstract
OBJECTIVES Through biodistance analyses, anthropologists have used dental morphology to elucidate how people moved into and throughout the Americas. Here, we apply a method that focuses on individuals rather than sample frequencies through the application rASUDAS2, based on a naïve Bayes' algorithm. MATERIALS AND METHODS Using the database of C.G. Turner II, we calculated the probability that an individual could be assigned to one of seven biogeographic groups (American Arctic, North & South America, East Asia, Southeast Asia & Polynesia, Australo-Melanesia, Western Eurasia, & Sub-Saharan Africa) through rASUDAS2. The frequency of classifications for each biogeographic group was determined for 1418 individuals from six regions across Asia and the Americas. RESULTS Southeast Asians show mixed assignments but rarely to American Arctic or "American Indian." East Asians are assigned to East Asia half the time while 30% are assigned as Native American. People from the American Arctic and North & South America are assigned to Arctic America or non-Arctic America 75%-80% of the time, with 10%-15% classified as East Asian. DISCUSSION All Native American groups have a similar degree of morphological affinity to East Asia, as 10%-15% are classified as East Asian. East Asians are classified as Native American in 30% of cases. Individuals in the Western Hemisphere are decreasingly classified as Arctic the farther south they are located. Equivalent levels of classification as East Asian across all Native American groups suggests one divergence between East Asians and the population ancestral to all Native Americans. Non-arctic Native American groups are derived from the Arctic population, which represents the Native American founder group.
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Affiliation(s)
- G Richard Scott
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, USA
| | - David Navega
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Laresa L Dern
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, USA
| | - Dennis H O'Rourke
- Department of Anthropology, University of Kansas, Lawrence, Kansas, USA
| | | | - John F Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
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17
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Davidson R, Williams MP, Roca-Rada X, Kassadjikova K, Tobler R, Fehren-Schmitz L, Llamas B. Allelic bias when performing in-solution enrichment of ancient human DNA. Mol Ecol Resour 2023; 23:1823-1840. [PMID: 37712846 DOI: 10.1111/1755-0998.13869] [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: 05/09/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.
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Affiliation(s)
- Roberta Davidson
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew P Williams
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Biology Department, The Pennsylvania State University, Pennsylvania, USA
| | - Xavier Roca-Rada
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kalina Kassadjikova
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
| | - Raymond Tobler
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
- UCSC Genomics Institute, University of California, California, USA
| | - Bastien Llamas
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
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18
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Yüncü E, Işıldak U, Williams MP, Huber CD, Flegontova O, Vyazov LA, Changmai P, Flegontov P. False discovery rates of qpAdm-based screens for genetic admixture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538339. [PMID: 37904998 PMCID: PMC10614728 DOI: 10.1101/2023.04.25.538339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Although a broad range of methods exists for reconstructing population history from genome-wide single nucleotide polymorphism data, just a few methods gained popularity in archaeogenetics: principal component analysis (PCA); ADMIXTURE, an algorithm that models individuals as mixtures of multiple ancestral sources represented by actual or inferred populations; formal tests for admixture such as f3-statistics and D/f4-statistics; and qpAdm, a tool for fitting two-component and more complex admixture models to groups or individuals. Despite their popularity in archaeogenetics, which is explained by modest computational requirements and ability to analyze data of various types and qualities, protocols relying on qpAdm that screen numerous alternative models of varying complexity and find "fitting" models (often considering both estimated admixture proportions and p-values as a composite criterion of model fit) remain untested on complex simulated population histories in the form of admixture graphs of random topology. We analyzed genotype data extracted from such simulations and tested various types of high-throughput qpAdm protocols ("rotating" and "non-rotating", with or without temporal stratification of target groups and proxy ancestry sources, and with or without a "model competition" step). We caution that high-throughput qpAdm protocols may be inappropriate for exploratory analyses in poorly studied regions/periods since their false discovery rates varied between 12% and 68% depending on the details of the protocol and on the amount and quality of simulated data (i.e., >12% of fitting two-way admixture models imply gene flows that were not simulated). We demonstrate that for reducing false discovery rates of qpAdm protocols to nearly 0% it is advisable to use large SNP sets with low missing data rates, the rotating qpAdm protocol with a strictly enforced rule that target groups do not pre-date their proxy sources, and an unsupervised ADMIXTURE analysis as a way to verify feasible qpAdm models. Our study has a number of limitations: for instance, these recommendations depend on the assumption that the underlying genetic history is a complex admixture graph and not a stepping-stone model.
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Affiliation(s)
- Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Matthew P. Williams
- Department of Biology, Eberly College of Science, Pennsylvania State University, PA, USA
| | - Christian D. Huber
- Department of Biology, Eberly College of Science, Pennsylvania State University, PA, USA
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Leonid A. Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
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19
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Medina-Muñoz SG, Ortega-Del Vecchyo D, Cruz-Hervert LP, Ferreyra-Reyes L, García-García L, Moreno-Estrada A, Ragsdale AP. Demographic modeling of admixed Latin American populations from whole genomes. Am J Hum Genet 2023; 110:1804-1816. [PMID: 37725976 PMCID: PMC10577084 DOI: 10.1016/j.ajhg.2023.08.015] [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: 03/07/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Demographic models of Latin American populations often fail to fully capture their complex evolutionary history, which has been shaped by both recent admixture and deeper-in-time demographic events. To address this gap, we used high-coverage whole-genome data from Indigenous American ancestries in present-day Mexico and existing genomes from across Latin America to infer multiple demographic models that capture the impact of different timescales on genetic diversity. Our approach, which combines analyses of allele frequencies and ancestry tract length distributions, represents a significant improvement over current models in predicting patterns of genetic variation in admixed Latin American populations. We jointly modeled the contribution of European, African, East Asian, and Indigenous American ancestries into present-day Latin American populations. We infer that the ancestors of Indigenous Americans and East Asians diverged ∼30 thousand years ago, and we characterize genetic contributions of recent migrations from East and Southeast Asia to Peru and Mexico. Our inferred demographic histories are consistent across different genomic regions and annotations, suggesting that our inferences are robust to the potential effects of linked selection. In conjunction with published distributions of fitness effects for new nonsynonymous mutations in humans, we show in large-scale simulations that our models recover important features of both neutral and deleterious variation. By providing a more realistic framework for understanding the evolutionary history of Latin American populations, our models can help address the historical under-representation of admixed groups in genomics research and can be a valuable resource for future studies of populations with complex admixture and demographic histories.
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Affiliation(s)
- Santiago G Medina-Muñoz
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de Mexico, Juriquilla, Querétaro 76230, Mexico
| | | | | | | | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico.
| | - Aaron P Ragsdale
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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20
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Ferraz T, Suarez Villagran X, Nägele K, Radzevičiūtė R, Barbosa Lemes R, Salazar-García DC, Wesolowski V, Lopes Alves M, Bastos M, Rapp Py-Daniel A, Pinto Lima H, Mendes Cardoso J, Estevam R, Liryo A, Guimarães GM, Figuti L, Eggers S, Plens CR, Azevedo Erler DM, Valadares Costa HA, da Silva Erler I, Koole E, Henriques G, Solari A, Martin G, Serafim Monteiro da Silva SF, Kipnis R, Müller LM, Ferreira M, Carvalho Resende J, Chim E, da Silva CA, Borella AC, Tomé T, Müller Plumm Gomes L, Barros Fonseca D, Santos da Rosa C, de Moura Saldanha JD, Costa Leite L, Cunha CMS, Viana SA, Ozorio Almeida F, Klokler D, Fernandes HLA, Talamo S, DeBlasis P, Mendonça de Souza S, de Paula Moraes C, Elias Oliveira R, Hünemeier T, Strauss A, Posth C. Genomic history of coastal societies from eastern South America. Nat Ecol Evol 2023; 7:1315-1330. [PMID: 37524799 PMCID: PMC10406606 DOI: 10.1038/s41559-023-02114-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 06/08/2023] [Indexed: 08/02/2023]
Abstract
Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-colonial South America, extending from approximately 8,000 to 1,000 years before present (yr BP) across 3,000 km on the Atlantic coast. However, little is known about their connection to early Holocene hunter-gatherers, how this may have contributed to different historical pathways and the processes through which late Holocene ceramists came to rule the coast shortly before European contact. To contribute to our understanding of the population history of indigenous societies on the eastern coast of South America, we produced genome-wide data from 34 ancient individuals as early as 10,000 yr BP from four different regions in Brazil. Early Holocene hunter-gatherers were found to lack shared genetic drift among themselves and with later populations from eastern South America, suggesting that they derived from a common radiation and did not contribute substantially to later coastal groups. Our analyses show genetic heterogeneity among contemporaneous Sambaqui groups from the southeastern and southern Brazilian coast, contrary to the similarity expressed in the archaeological record. The complex history of intercultural contact between inland horticulturists and coastal populations becomes genetically evident during the final horizon of Sambaqui societies, from around 2,200 yr BP, corroborating evidence of cultural change.
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Affiliation(s)
- Tiago Ferraz
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Renan Barbosa Lemes
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Verônica Wesolowski
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Marcony Lopes Alves
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Murilo Bastos
- Departamento de Antropologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Jéssica Mendes Cardoso
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Géosciences Environnement Toulouse, Observatoire Midi Pyrénées, UMR 5563, CNRS, Toulouse, France
| | - Renata Estevam
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Andersen Liryo
- National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Geovan M Guimarães
- Grupo de Pesquisa em Educação Patrimonial e Arqueologia (Grupep), Universidade do Sul de Santa Catarina, Santa Catarina, Brazil
| | - Levy Figuti
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | - Cláudia R Plens
- Laboratory of Archaeological Studies, Department of History, Federal University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Ana Solari
- Fundação Museu do Homem Americano, Piauí, Brazil
| | | | | | | | - Letícia Morgana Müller
- Scientia Consultoria Científica, São Paulo, Brazil
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Mariane Ferreira
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Scientia Consultoria Científica, São Paulo, Brazil
| | - Janine Carvalho Resende
- Instituto Goiano de Pré-história e Arqueologia, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Eliane Chim
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | - Ana Claudia Borella
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Tiago Tomé
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lisiane Müller Plumm Gomes
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | | | - João Darcy de Moura Saldanha
- Universidade de Évora, Évora, Portugal
- Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Brazil
| | - Lúcio Costa Leite
- Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Brazil
| | - Claudia M S Cunha
- Federal University of Piauí, Piauí, Brazil
- Centro de Investigação em Antropologia e Saúde, Universidade de Coimbra, Coimbra, Portugal
| | - Sibeli Aparecida Viana
- Instituto Goiano de Pré-história e Arqueologia, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Fernando Ozorio Almeida
- Programa de Pós-Graduação em Arqueologia, Universidade Federal de Sergipe, Sergipe, Brazil
- Departamento de Arqueologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniela Klokler
- Programa de Pós-Graduação em Arqueologia, Universidade Federal de Sergipe, Sergipe, Brazil
- Departamento de Antropologia e Arqueologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henry Luydy Abraham Fernandes
- Programa de Pós-Graduação em Arqueologia e Patrimônio Cultural, Universidade Federal do Recôncavo da Bahia, Bahia, Brazil
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paulo DeBlasis
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | | | - Rodrigo Elias Oliveira
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
| | - Tábita Hünemeier
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil.
- Institut de Biologia Evolutiva, CSIC/Universitat Pompeu Fabra, Barcelona, Spain.
| | - André Strauss
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.
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21
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Carlo Colonese A, McGrath K. Genetic insights into Brazil's ancient shell mound builders. Nat Ecol Evol 2023; 7:1179-1180. [PMID: 37524798 DOI: 10.1038/s41559-023-02134-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Affiliation(s)
- André Carlo Colonese
- Institute of Environmental Science and Technology (ICTA-UAB), ICTA-ICP, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Prehistory, Facultat de Filosofia i Lletres, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Krista McGrath
- Institute of Environmental Science and Technology (ICTA-UAB), ICTA-ICP, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Prehistory, Facultat de Filosofia i Lletres, Universitat Autònoma de Barcelona, Barcelona, Spain.
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22
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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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23
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Salazar L, Burger R, Forst J, Barquera R, Nesbitt J, Calero J, Washburn E, Verano J, Zhu K, Sop K, Kassadjikova K, Ibarra Asencios B, Davidson R, Bradley B, Krause J, Fehren-Schmitz L. Insights into the genetic histories and lifeways of Machu Picchu's occupants. SCIENCE ADVANCES 2023; 9:eadg3377. [PMID: 37494435 PMCID: PMC11318671 DOI: 10.1126/sciadv.adg3377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.
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Affiliation(s)
- Lucy Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511-3707, USA
- Department of Archaeology, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru
| | - Richard Burger
- Department of Anthropology, Yale University, New Haven, CT 06511-3707, USA
| | - Janine Forst
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Jason Nesbitt
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
| | - Jorge Calero
- Department of Archaeology, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru
| | - Eden Washburn
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John Verano
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
| | - Kimberly Zhu
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Korey Sop
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kalina Kassadjikova
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bebel Ibarra Asencios
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
- Department of Archaeology, Universidad Nacional Santiago Antúnez de Mayolo, Huaraz 02002, Peru
| | - Roberta Davidson
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Brenda Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
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24
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Chian JS, Li J, Wang SM. Evolutionary Origin of Human PALB2 Germline Pathogenic Variants. Int J Mol Sci 2023; 24:11343. [PMID: 37511102 PMCID: PMC10379391 DOI: 10.3390/ijms241411343] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
PALB2 (Partner and localizer of BRCA2) is crucial for repairing DNA double-stranded breaks (DSBs) through homologous recombination (HR). Germline pathogenic variation in PALB2 disrupts DNA damage repair and increases the risk of Fanconi Anemia, breast cancer, and ovarian cancer. Determination of the evolutionary origin of human PALB2 variants will promote a deeper understanding of the biological basis of PALB2 germline variation and its roles in human diseases. We tested the evolution origin for 1444 human PALB2 germline variants, including 484 pathogenic and 960 benign variants. We performed a phylogenic analysis by tracing the variants in 100 vertebrates. However, we found no evidence to show that cross-species conservation was the origin of PALB2 germline pathogenic variants, but it is indeed a rich source for PALB2 germline benign variants. We performed a paleoanthropological analysis by tracing the variants in over 5000 ancient humans. We identified 50 pathogenic in 71 ancient humans dated from 32,895 to 689 before the present, of which 90.1% were dated within the recent 10,000 years. PALB2 benign variants were also highly shared with ancient humans. Data from our study reveal that human PALB2 pathogenic variants mostly arose in recent human history.
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Affiliation(s)
- Jia Sheng Chian
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
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25
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Moreno-Mayar JV. Human genetics: Rich genomic history of two isolated Indigenous peoples of South America. Curr Biol 2023; 33:R715-R717. [PMID: 37433271 DOI: 10.1016/j.cub.2023.05.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Genome-wide data from two Indigenous South American groups reveal their dynamic population history. The Mapuche from Southern Chile and the Ashaninka from Amazonian Peru remained largely isolated over time. Yet, both groups interacted with other South American peoples sporadically.
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Affiliation(s)
- J Víctor Moreno-Mayar
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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26
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Malyarchuk BA. The role of Beringia in human adaptation to Arctic conditions based on results of genomic studies of modern and ancient populations. Vavilovskii Zhurnal Genet Selektsii 2023; 27:373-382. [PMID: 37465192 PMCID: PMC10350865 DOI: 10.18699/vjgb-23-45] [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: 08/03/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 07/20/2023] Open
Abstract
The results of studies in Quaternary geology, archeology, paleoanthropology and human genetics demonstrate that the ancestors of Native Americans arrived in mid-latitude North America mainly along the Pacific Northwest Coast, but had previously inhabited the Arctic and during the last glacial maximum were in a refugium in Beringia, a land bridge connecting Eurasia and North America. The gene pool of Native Americans is represented by unique haplogroups of mitochondrial DNA and the Y chromosome, the evolutionary age of which ranges from 13 to 22 thousand years. The results of a paleogenomic analysis also show that during the last glacial maximum Beringia was populated by human groups that had arisen as a result of interaction between the most ancient Upper Paleolithic populations of Northern Eurasia and newcomer groups from East Asia. Approximately 20 thousand years ago the Beringian populations began to form, and the duration of their existence in relative isolation is estimated at about 5 thousand years. Thus, the adaptation of the Beringians to the Arctic conditions could have taken several millennia. The adaptation of Amerindian ancestors to high latitudes and cold climates is supported by genomic data showing that adaptive genetic variants in Native Americans are associated with various metabolic pathways: melanin production processes in the skin, hair and eyes, the functioning of the cardiovascular system, energy metabolism and immune response characteristics. Meanwhile, the analysis of the existing hypotheses about the selection of some genetic variants in the Beringian ancestors of the Amerindians in connection with adaptation to the Arctic conditions (for example, in the FADS, ACTN3, EDAR genes) shows the ambiguity of the testing results, which may be due to the loss of some traces of the "Beringian" adaptation in the gene pools of modern Native Americans. The most optimal strategy for further research seems to be the search for adaptive variant.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
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27
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Sousa da Mota B, Rubinacci S, Cruz Dávalos DI, G Amorim CE, Sikora M, Johannsen NN, Szmyt MH, Włodarczak P, Szczepanek A, Przybyła MM, Schroeder H, Allentoft ME, Willerslev E, Malaspinas AS, Delaneau O. Imputation of ancient human genomes. Nat Commun 2023; 14:3660. [PMID: 37339987 PMCID: PMC10282092 DOI: 10.1038/s41467-023-39202-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 06/02/2023] [Indexed: 06/22/2023] Open
Abstract
Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.
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Affiliation(s)
- Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Simone Rubinacci
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Diana Ivette Cruz Dávalos
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Niels N Johannsen
- Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark
| | - Marzena H Szmyt
- Institute for Eastern Research, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
- Department of Anatomy, Jagiellonian University, Medical College, Kraków, Poland
| | | | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, 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 Science, Curtin University, Bentley, WA, Australia
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- MARUM, University of Bremen, Bremen, Germany
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
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28
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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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29
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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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30
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Villa-Islas V, Izarraras-Gomez A, Larena M, Campos EMP, Sandoval-Velasco M, Rodríguez-Rodríguez JE, Bravo-Lopez M, Moguel B, Fregel R, Garfias-Morales E, Medina Tretmanis J, Velázquez-Ramírez DA, Herrera-Muñóz A, Sandoval K, Nieves-Colón MA, Zepeda García Moreno G, Villanea FA, Medina EFV, Aguayo-Haro R, Valdiosera C, Ioannidis AG, Moreno-Estrada A, Jay F, Huerta-Sanchez E, Moreno-Mayar JV, Sánchez-Quinto F, Ávila-Arcos MC. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 2023; 380:eadd6142. [PMID: 37167382 DOI: 10.1126/science.add6142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.
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Affiliation(s)
- Viridiana Villa-Islas
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Alan Izarraras-Gomez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Maximilian Larena
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cuidad de México, Mexico
| | | | - Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Barbara Moguel
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
- Centro de Geociencias, UNAM Juriquilla, Juriquilla, Querétaro, México
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Ernesto Garfias-Morales
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | | | | | | | - Karla Sandoval
- Equity and Gender Office of the Centre for Research and Advanced Studies (CODIGO-C), CINVESTAV, Mexico City, Mexico
| | - Maria A Nieves-Colón
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | | | - Fernando A Villanea
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Cristina Valdiosera
- Departamento de Historia, Geografía y Comunicaciones, Universidad de Burgos, Burgos, Spain
- Department of History and Archaeology, La Trobe University, Melbourne, Australia
| | - Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Flora Jay
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, CNRS, INRIA, 91400 Orsay, France
| | | | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
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31
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Llamas B, Roca-Rada X. Paleogenomic study of the Mexican past. Science 2023; 380:578-579. [PMID: 37167404 DOI: 10.1126/science.adh7902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Ancient DNA analysis of ancestral Mexicans reveals a complex demographic history.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Xavier Roca-Rada
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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32
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da Silva Coelho FA, Gill S, Tomlin CM, Papavassiliou M, Farley SD, Cook JA, Sonsthagen SA, Sage GK, Heaton TH, Talbot SL, Lindqvist C. Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska. Mol Ecol 2023. [PMID: 37096383 DOI: 10.1111/mec.16960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.
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Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | | | - Sean D Farley
- Alaska Department of Fish and Game, Anchorage, Alaska, USA
| | - Joseph A Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Sarah A Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, University of Nebraska-Lincoln, School of Natural Resources, Lincoln, Nebraska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, South Dakota, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
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dos Santos ALC, Sullasi HSL, Gokcumen O, Lindo J, DeGiorgio M. Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:703-714. [PMID: 39081397 PMCID: PMC11288623 DOI: 10.1002/ajpa.24673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/15/2022] [Indexed: 08/02/2024]
Abstract
Objectives Since 2010, genome-wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present-day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019. Materials and Methods The genomic data from ancient Americas was merged with a worldwide reference panel of 278 present-day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE, D-statistics, PCA, t-SNE, and UMAP. Results We find largely similar population structures in ancient and present-day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present-day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample. Discussion Overall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level.
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Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
- Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, Georgia, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
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Souther S, Colombo S, Lyndon NN. Integrating traditional ecological knowledge into US public land management: Knowledge gaps and research priorities. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.988126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Traditional Ecological Knowledge (TEK) is an understanding of natural systems acquired through long-term human interactions with particular landscapes. Traditional knowledge systems complement western scientific disciplines by providing a holistic assessment of ecosystem dynamics and extending the time horizon of ecological observations. Integration of TEK into land management is a key priority of numerous groups, including the United Nations and US public land management agencies; however, TEK principles have rarely been enshrined in national-level US policy or planning. We review over 20 years of TEK literature to describe key applications of TEK to ecological understanding, conservation, restoration and land management generally. By identifying knowledge gaps, we highlight research avenues to support the integration of TEK into US public land management, in order to enhance conservation approaches and participation of historically underrepresented groups, particularly American Indian Tribes, in the stewardship of ancestral lands critical to the practice of living cultural traditions.
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35
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Hoffecker JF, Elias SA, Scott GR, O'Rourke DH, Hlusko LJ, Potapova O, Pitulko V, Pavlova E, Bourgeon L, Vachula RS. Beringia and the peopling of the Western Hemisphere. Proc Biol Sci 2023; 290:20222246. [PMID: 36629115 PMCID: PMC9832545 DOI: 10.1098/rspb.2022.2246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Did Beringian environments represent an ecological barrier to humans until less than 15 000 years ago or was access to the Americas controlled by the spatial-temporal distribution of North American ice sheets? Beringian environments varied with respect to climate and biota, especially in the two major areas of exposed continental shelf. The East Siberian Arctic Shelf ('Great Arctic Plain' (GAP)) supported a dry steppe-tundra biome inhabited by a diverse large-mammal community, while the southern Bering-Chukchi Platform ('Bering Land Bridge' (BLB)) supported mesic tundra and probably a lower large-mammal biomass. A human population with west Eurasian roots occupied the GAP before the Last Glacial Maximum (LGM) and may have accessed mid-latitude North America via an interior ice-free corridor. Re-opening of the corridor less than 14 000 years ago indicates that the primary ancestors of living First Peoples, who already had spread widely in the Americas at this time, probably dispersed from the NW Pacific coast. A genetic 'arctic signal' in non-arctic First Peoples suggests that their parent population inhabited the GAP during the LGM, before their split from the former. We infer a shift from GAP terrestrial to a subarctic maritime economy on the southern BLB coast before dispersal in the Americas from the NW Pacific coast.
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Affiliation(s)
- John F. Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA,Department of Anthropology, University of Kansas, 622 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Scott A. Elias
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA
| | - G. Richard Scott
- Department of Anthropology, University of Nevada-Reno, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Dennis H. O'Rourke
- Department of Anthropology, University of Kansas, 622 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Leslea J. Hlusko
- Human Evolution Research Center, University of California-Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720-3140, USA,Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Olga Potapova
- Pleistocene Park Foundation, Philadelphia, PA 19006, USA,Department of Mammoth Fauna Studies, Academy of Sciences of Sakha, Yakutsk, Russia,The Mammoth Site of Hot Springs, Hot Springs, SD 57747, USA
| | - Vladimir Pitulko
- Institute of the History of Material Culture, Russian Academy of Sciences, Dvortsovaya nab., 18, 191186 St Petersburg, Russia,Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, 3, Universitetskaya nab., St Petersburg 199034, Russian Federation
| | - Elena Pavlova
- Arctic and Antarctic Research Institute, Russian Federal Service for Hydrometeorology and Environmental Monitoring, 38 Bering Street, 199397 St Petersburg, Russia
| | - Lauriane Bourgeon
- Kansas Geological Survey, University of Kansas, 1930 Constant Ave., Lawrence, KS 66047, USA
| | - Richard S. Vachula
- Department of Geosciences, Auburn University, 2050 Beard Eaves Coliseum, Auburn, AL 36849-5305, USA
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Balentine CM, Alfonso-Durruty M, Reynolds AW, Vilar M, Morello F, Román MS, Springs LC, Smith RWA, Archer SM, Mata-Míguez J, Wing N, Bolnick DA. Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:144-161. [PMID: 36790637 DOI: 10.1002/ajpa.24638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVES This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region. METHODS Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed. RESULTS Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FST comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout. DISCUSSION These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia.
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Affiliation(s)
- Christina M Balentine
- Department of Integrative Biology, University of Texas, Austin, Texas, USA.,Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA
| | - Marta Alfonso-Durruty
- Department of Sociology, Anthropology, and Social Work, Kansas State University, Manhattan, Kansas, USA
| | | | - Miguel Vilar
- Department of Anthropology, University of Maryland, College Park, Maryland, USA.,National Geographic Society, Washington, DC, USA
| | - Flavia Morello
- Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas, Chile.,Cape Horn International Center, Puerto Williams, Chile
| | - Manuel San Román
- Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas, Chile.,Cape Horn International Center, Puerto Williams, Chile
| | - Lauren C Springs
- Department of Anthropology, University of Texas at Austin, Austin, Texas, USA
| | - Rick W A Smith
- Department of Sociology and Anthropology, George Mason University, Fairfax, Virginia, USA.,Women and Gender Studies, George Mason University, Fairfax, Virginia, USA
| | - Samantha M Archer
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA
| | - Jaime Mata-Míguez
- Department of Anthropology, University of Texas at Austin, Austin, Texas, USA
| | | | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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Davis LG, Madsen DB, Sisson DA, Becerra-Valdivia L, Higham T, Stueber D, Bean DW, Nyers AJ, Carroll A, Ryder C, Sponheimer M, Izuho M, Iizuka F, Li G, Epps CW, Halford FK. Dating of a large tool assemblage at the Cooper's Ferry site (Idaho, USA) to ~15,785 cal yr B.P. extends the age of stemmed points in the Americas. SCIENCE ADVANCES 2022; 8:eade1248. [PMID: 36563150 PMCID: PMC9788777 DOI: 10.1126/sciadv.ade1248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The timing and character of the Pleistocene peopling of the Americas are measured by the discovery of unequivocal artifacts from well-dated contexts. We report the discovery of a well-dated artifact assemblage containing 14 stemmed projectile points from the Cooper's Ferry site in western North America, dating to ~16,000 years ago. These stemmed points are several thousand years older than Clovis fluted points (~13,000 cal yr B.P.) and are ~2300 years older than stemmed points found previously at the site. These points date to the end of Marine Isotope Stage 2 when glaciers had closed off an interior land route into the Americas. This assemblage includes an array of stemmed projectile points that resemble pre-Jomon Late Upper Paleolithic tools from the northwestern Pacific Rim dating to ~20,000 to 19,000 years ago, leading us to hypothesize that some of the first technological traditions in the Americas may have originated in the region.
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Affiliation(s)
- Loren G. Davis
- Department of Anthropology, Oregon State University, 203 Waldo Hall, Corvallis, OR 97331, USA
| | - David B. Madsen
- Department of Anthropology, University of Nevada-Reno, 512 Ansari, Reno, NV 89557, USA
| | - David A. Sisson
- Bureau of Land Management, Cottonwood Field Office, 2 Butte Drive, Cottonwood, ID 83522, USA
| | - Lorena Becerra-Valdivia
- Oxford Radiocarbon Accelerator Unit, School of Archaeology, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Thomas Higham
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, A-1030 Vienna, Austria
| | - Daniel Stueber
- Department of Anthropology, University of Victoria, P.O. Box 1700 STN CSC, Victoria, BC V8W 2Y2, Canada
| | - Daniel W. Bean
- Department of Anthropology, Oregon State University, 203 Waldo Hall, Corvallis, OR 97331, USA
| | - Alexander J. Nyers
- Department of Anthropology, Oregon State University, 203 Waldo Hall, Corvallis, OR 97331, USA
- Northwest Archaeometrics, 5060 SW Philomath Blvd, #331, Corvallis, OR 97333, USA
| | - Amanda Carroll
- SWCA Environmental Consultants, 1800 NW Upshur St, Ste. 100, Portland, OR 97209, USA
| | - Christina Ryder
- Department of Anthropology, University of Colorado Boulder, Hale Science Building, 1350 Pleasant St., Boulder, CO 80309, USA
| | - Matt Sponheimer
- Department of Anthropology, University of Colorado Boulder, Hale Science Building, 1350 Pleasant St., Boulder, CO 80309, USA
| | - Masami Izuho
- Tokyo Metropolitan University, Faculty of Humanities and Social Sciences, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0397, Japan
| | - Fumie Iizuka
- Department of Anthropology and Research Reactor Center, University of Missouri, Swallow Hall, 112 S 9th Street, Columbia, MO 65211, USA
| | - Guoqiang Li
- Research School of Arid Environment and Climate Change, MOE Key Laboratory of West China’s Environmental System, Lanzhou University, 222 Tianshuinanlu, Lanzhou, Gansu 730000, China
| | - Clinton W. Epps
- Oregon State University Department of Fisheries, Wildlife, and Conservation Sciences, 104 Nash Hall, Corvallis, OR 97331, USA
| | - F. Kirk Halford
- Department of Anthropology, Boise State University, Boise, ID 83725, USA
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García-Ortiz H, Barajas-Olmos F, Contreras-Cubas C, Reynolds AW, Flores-Huacuja M, Snow M, Ramos-Madrigal J, Mendoza-Caamal E, Baca P, López-Escobar TA, Bolnick DA, Flores-Martínez SE, Ortiz-Lopez R, Kostic AD, Villafan-Bernal JR, Galaviz-Hernández C, Centeno-Cruz F, García-Zapién AG, Monge-Cázares T, Lazalde-Ramos BP, Loeza-Becerra F, Abrahantes-Pérez MDC, Rangel-Villalobos H, Sosa-Macías M, Rojas-Martínez A, Martínez-Hernández A, Orozco L. Unraveling Signatures of Local Adaptation among Indigenous Groups from Mexico. Genes (Basel) 2022; 13:genes13122251. [PMID: 36553518 PMCID: PMC9778281 DOI: 10.3390/genes13122251] [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: 09/24/2022] [Revised: 11/05/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Few studies have addressed how selective pressures have shaped the genetic structure of the current Native American populations, and they have mostly limited their inferences to admixed Latin American populations. Here, we searched for local adaptation signals, based on integrated haplotype scores and population branch statistics, in 325 Mexican Indigenous individuals with at least 99% Native American ancestry from five previously defined geographical regions. Although each region exhibited its own local adaptation profile, only PPARG and AJAP1, both negative regulators of the Wnt/β catenin signaling pathway, showed significant adaptation signals in all the tested regions. Several signals were found, mainly in the genes related to the metabolic processes and immune response. A pathway enrichment analysis revealed the overrepresentation of selected genes related to several biological phenotypes/conditions, such as the immune response and metabolic pathways, in agreement with previous studies, suggesting that immunological and metabolic pressures are major drivers of human adaptation. Genes related to the gut microbiome measurements were overrepresented in all the regions, highlighting the importance of studying how humans have coevolved with the microbial communities that colonize them. Our results provide a further explanation of the human evolutionary history in response to environmental pressures in this region.
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Affiliation(s)
- Humberto García-Ortiz
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
- Correspondence:
| | | | | | | | | | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, The GLOBE Institute, The University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | | | - Paulina Baca
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
| | | | - Deborah A. Bolnick
- Department of Anthropology and Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269-3003, USA
| | - Silvia Esperanza Flores-Martínez
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Mexico
| | - Rocio Ortiz-Lopez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Insitute for Obesity Research, Monterrey 64700, Mexico
- Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey 64460, Mexico
| | | | | | | | | | - Alejandra Guadalupe García-Zapién
- Departamento de Farmacobiología, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara 44430, Mexico
| | | | | | | | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara Ocotlán, Ocotlán 44100, Mexico
| | | | - Augusto Rojas-Martínez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Insitute for Obesity Research, Monterrey 64700, Mexico
- Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey 64460, Mexico
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
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Campelo dos Santos AL, Owings A, Sullasi HSL, Gokcumen O, DeGiorgio M, Lindo J. Genomic evidence for ancient human migration routes along South America's Atlantic coast. Proc Biol Sci 2022; 289:20221078. [PMID: 36322514 PMCID: PMC9629774 DOI: 10.1098/rspb.2022.1078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.
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Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA,Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - Amanda Owings
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | | | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
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Feng X, Merilä J, Löytynoja A. Complex population history affects admixture analyses in nine-spined sticklebacks. Mol Ecol 2022; 31:5386-5401. [PMID: 35962788 PMCID: PMC9828525 DOI: 10.1111/mec.16651] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 01/12/2023]
Abstract
Introgressive hybridization is an important process in evolution but challenging to identify, undermining the efforts to understand its role and significance. On the contrary, many analytical methods assume direct descent from a single common ancestor, and admixture among populations can violate their assumptions and lead to seriously biased results. A detailed analysis of 888 whole-genome sequences of nine-spined sticklebacks (Pungitius pungitius) revealed a complex pattern of population ancestry involving multiple waves of gene flow and introgression across northern Europe. The two recognized lineages were found to have drastically different histories, and their secondary contact zone was wider than anticipated, displaying a smooth gradient of foreign ancestry with some curious deviations from the expected pattern. Interestingly, the freshwater isolates provided peeks into the past and helped to understand the intermediate states of evolutionary processes. Our analyses and findings paint a detailed picture of the complex colonization history of northern Europe and provide backdrop against which introgression and its role in evolution can be investigated. However, they also expose the challenges in analyses of admixed populations and demonstrate how hidden admixture and colonization history misleads the estimation of admixture proportions and population split times.
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Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Area of Ecology and Biodiversity, Kadoorie Science Building, The University of Hong Kong, Hong Kong, SAR, China
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Silva MACE, Ferraz T, Hünemeier T. A genomic perspective on South American human history. Genet Mol Biol 2022; 45:e20220078. [PMID: 35925590 PMCID: PMC9351327 DOI: 10.1590/1678-4685-gmb-2022-0078] [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: 03/08/2022] [Accepted: 03/31/2022] [Indexed: 11/22/2022] Open
Abstract
It has generally been accepted that the current indigenous peoples of the Americas are derived from ancestors from northeastern Asia. The latter were believed to have spread into the American continent by the end of the Last Glacial Maximum. In this sense, a joint and in-depth study of the earliest settlement of East Asia and the Americas is required to elucidate these events accurately. The first Americans underwent an adaptation process to the Americas' vast environmental diversity, mediated by biological and cultural evolution and niche construction, resulting in enormous cultural diversity, a wealth of domesticated species, and extensive landscape modifications. Afterward, in the Late Holocene, the advent of intensive agricultural food production systems, sedentism, and climate change significantly reshaped genetic and cultural diversity across the continent, particularly in the Andes and Amazonia. Furthermore, starting around the end of the 15th century, European colonization resulted in massive extermination of indigenous peoples and extensive admixture. Thus, the present review aims to create a comprehensive picture of the main events involved in the formation of contemporary South American indigenous populations and the dynamics responsible for shaping their genetic diversity by integrating current genetic data with evidence from archeology, linguistics and other disciplines.
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Affiliation(s)
- Marcos Araújo Castro E Silva
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Tiago Ferraz
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Tábita Hünemeier
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
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Collen EJ, Johar AS, Teixeira JC, Llamas B. The immunogenetic impact of European colonization in the Americas. Front Genet 2022; 13:918227. [PMID: 35991555 PMCID: PMC9388791 DOI: 10.3389/fgene.2022.918227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.
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Affiliation(s)
- Evelyn Jane Collen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Angad Singh Johar
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Culture History and Language, The Australian National University, Canberra, ACT, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Telethon Kids Institute, Indigenous Genomics Research Group, Adelaide, SA, Australia
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43
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Caro-Consuegra R, Nieves-Colón MA, Rawls E, Rubin-de-Celis V, Lizárraga B, Vidaurre T, Sandoval K, Fejerman L, Stone AC, Moreno-Estrada A, Bosch E. Uncovering signals of positive selection in Peruvian populations from three ecological regions. Mol Biol Evol 2022; 39:6647595. [PMID: 35860855 PMCID: PMC9356722 DOI: 10.1093/molbev/msac158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Perú hosts extremely diverse ecosystems which can be broadly classified into three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might have differentially adapted to their contrasting environmental pressures. Previous studies have described several candidate genes underlying adaptation to hypobaric hypoxia among Andean highlanders. However, the adaptive genetic diversity of coastal and rainforest populations has been less studied. Here, we gathered genome-wide SNP-array data from 286 Peruvians living across the three ecoregions and analysed signals of recent positive selection through population differentiation and haplotype-based selection scans. Among highland populations, we identify candidate genes related to cardiovascular function (TLL1, DUSP27, TBX5, PLXNA4, SGCD), to the Hypoxia-Inducible Factor pathway (TGFA, APIP), to skin pigmentation (MITF), as well as to glucose (GLIS3) and glycogen metabolism (PPP1R3C, GANC). In contrast, most signatures of adaptation in coastal and rainforest populations comprise candidate genes related to the immune system (including SIGLEC8, TRIM21, CD44 and ICAM1 in the coast; CBLB and PRDM1 in rainforest and the BRD2- HLA-DOA- HLA-DPA1 region in both), possibly as a result of strong pathogen-driven selection. This study identifies candidate genes related to human adaptation to the diverse environments of South America.
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Affiliation(s)
- Rocio Caro-Consuegra
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Maria A Nieves-Colón
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Erin Rawls
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Verónica Rubin-de-Celis
- Laboratorio de Genómica Molecular Evolutiva, Instituto de Ciencia y Tecnología, Universidad Ricardo Palma, Lima, Perú
| | - Beatriz Lizárraga
- Emeritus Professor, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | | | - Karla Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Laura Fejerman
- Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Elena Bosch
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
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44
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Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C. The untapped potential of macrofossils in ancient plant DNA research. THE NEW PHYTOLOGIST 2022; 235:391-401. [PMID: 35306671 PMCID: PMC9322452 DOI: 10.1111/nph.18108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.
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Affiliation(s)
- Christoph Schwörer
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
| | - Maria Leunda
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
| | - Nadir Alvarez
- Natural History Museum of Geneva1208GenevaSwitzerland
- Department of Genetics and EvolutionUniversity of Geneva1205GenevaSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
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Huang X, Xia ZY, Bin X, He G, Guo J, Adnan A, Yin L, Huang Y, Zhao J, Yang Y, Ma F, Li Y, Hu R, Yang T, Wei LH, Wang CC. Genomic Insights Into the Demographic History of the Southern Chinese. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.853391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.
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Rodrigues JCG, Fernandes MR, Ribeiro-dos-Santos AM, de Araújo GS, de Souza SJ, Guerreiro JF, Ribeiro-dos-Santos Â, de Assumpção PP, dos Santos NPC, Santos S. Pharmacogenomic Profile of Amazonian Amerindians. J Pers Med 2022; 12:jpm12060952. [PMID: 35743738 PMCID: PMC9224798 DOI: 10.3390/jpm12060952] [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: 05/15/2022] [Revised: 06/05/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
Given the role of pharmacogenomics in the large variability observed in drug efficacy/safety, an assessment about the pharmacogenomic profile of patients prior to drug prescription or dose adjustment is paramount to improve adherence to treatment and prevent adverse drug reaction events. A population commonly underrepresented in pharmacogenomic studies is the Native American populations, which have a unique genetic profile due to a long process of geographic isolation and other genetic and evolutionary processes. Here, we describe the pharmacogenetic variability of Native American populations regarding 160 pharmacogenes involved in absorption, distribution, metabolism, and excretion processes and biological pathways of different therapies. Data were obtained through complete exome sequencing of individuals from 12 different Amerindian groups of the Brazilian Amazon. The study reports a total of 3311 variants; of this, 167 are exclusive to Amerindian populations, and 1183 are located in coding regions. Among these new variants, we found non-synonymous coding variants in the DPYD and the IFNL4 genes and variants with high allelic frequencies in intronic regions of the MTHFR, TYMS, GSTT1, and CYP2D6 genes. Additionally, 332 variants with either high or moderate (disruptive or non-disruptive impact in protein effectiveness, respectively) significance were found with a minimum of 1% frequency in the Amazonian Amerindian population. The data reported here serve as scientific basis for future design of specific treatment protocols for Amazonian Amerindian populations as well as for populations admixed with them, such as the Northern Brazilian population.
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Affiliation(s)
- Juliana Carla Gomes Rodrigues
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belem 66073-000, Brazil; (M.R.F.); (Â.R.-d.-S.); (P.P.d.A.); (N.P.C.d.S.); (S.S.)
- Correspondence: ; Tel.: +55-(91)-983973173
| | - Marianne Rodrigues Fernandes
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belem 66073-000, Brazil; (M.R.F.); (Â.R.-d.-S.); (P.P.d.A.); (N.P.C.d.S.); (S.S.)
| | - André Maurício Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belem 66075-110, Brazil; (A.M.R.-d.-S.); (G.S.d.A.); (J.F.G.)
| | - Gilderlanio Santana de Araújo
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belem 66075-110, Brazil; (A.M.R.-d.-S.); (G.S.d.A.); (J.F.G.)
| | | | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belem 66075-110, Brazil; (A.M.R.-d.-S.); (G.S.d.A.); (J.F.G.)
| | - Ândrea Ribeiro-dos-Santos
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belem 66073-000, Brazil; (M.R.F.); (Â.R.-d.-S.); (P.P.d.A.); (N.P.C.d.S.); (S.S.)
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belem 66075-110, Brazil; (A.M.R.-d.-S.); (G.S.d.A.); (J.F.G.)
| | - Paulo Pimentel de Assumpção
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belem 66073-000, Brazil; (M.R.F.); (Â.R.-d.-S.); (P.P.d.A.); (N.P.C.d.S.); (S.S.)
| | - Ney Pereira Carneiro dos Santos
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belem 66073-000, Brazil; (M.R.F.); (Â.R.-d.-S.); (P.P.d.A.); (N.P.C.d.S.); (S.S.)
| | - Sidney Santos
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belem 66073-000, Brazil; (M.R.F.); (Â.R.-d.-S.); (P.P.d.A.); (N.P.C.d.S.); (S.S.)
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belem 66075-110, Brazil; (A.M.R.-d.-S.); (G.S.d.A.); (J.F.G.)
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Lindo J, De La Rosa R, Santos ALCD, Sans M, DeGiorgio M, Figueiro G. The genomic prehistory of the Indigenous peoples of Uruguay. PNAS NEXUS 2022; 1:pgac047. [PMID: 36713318 PMCID: PMC9802099 DOI: 10.1093/pnasnexus/pgac047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/14/2022] [Indexed: 02/01/2023]
Abstract
The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former Indigenous ethnic diversity into the narrative of a singular people that all but died out. Here, we present the first whole genome sequences of the Indigenous people of the region before the arrival of Europeans, from an archaeological site in eastern Uruguay that dates from 2,000 years before present. We find a surprising connection to ancient individuals from Panama and eastern Brazil, but not to modern Amazonians. This result may be indicative of a migration route into South America that may have occurred along the Atlantic coast. We also find a distinct ancestry previously undetected in South America. Though this work begins to piece together some of the demographic nuance of the region, the sequencing of ancient individuals from across Uruguay is needed to better understand the ancient prehistory and genetic diversity that existed before European contact, thereby helping to rebuild the history of the Indigenous population of what is now Uruguay.
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Affiliation(s)
- John Lindo
- To whom correspondence should be addressed:
| | | | - Andre L C d Santos
- Department of Archeology, Federal University of Pernambuco, Recife, Brazil,Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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Rodríguez-Rodríguez JE, Ioannidis AG, Medina-Muñoz SG, Barberena-Jonas C, Blanco-Portillo J, Quinto-Cortés CD, Moreno-Estrada A. The genetic legacy of the Manila galleon trade in Mexico. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200419. [PMID: 35430879 PMCID: PMC9014187 DOI: 10.1098/rstb.2020.0419] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The population of Mexico has a considerable genetic substructure due to both its pre-Columbian diversity and due to genetic admixture from post-Columbian trans-oceanic migrations. The latter primarily originated in Europe and Africa, but also, to a lesser extent, in Asia. We analyze previously understudied genetic connections between Asia and Mexico to infer the timing and source of this genetic ancestry in Mexico. We identify the predominant origin within Southeast Asia—specifically western Indonesian and non-Negrito Filipino sources—and we date its arrival in Mexico to approximately 13 generations ago (1620 CE). This points to a genetic legacy from the seventeenth century Manila galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco. Indeed, within Mexico we observe the highest level of this trans-Pacific ancestry in Acapulco, located in the state of Guerrero. This colonial Spanish trade route from East Asia to Europe was centred on Mexico and appears in historical records, but its legacy has been largely ignored. Identities and stories were suppressed due to slavery, assimilation of the immigrants as ‘Indios’ and incomplete historical records. Here we characterize this understudied Mexican ancestry. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Santiago G. Medina-Muñoz
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
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49
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Menéndez LP, Paul KS, de la Fuente C, Almeida T, Delgado M, Figueiro G, Jorgensen K, Kuzminsky S, López-Sosa MC, Nichols J, Roksandic M, Scott GR, O'Rourke D, Hubbe M. Towards an interdisciplinary perspective for the study of human expansions and biocultural diversity in the Americas. Evol Anthropol 2022; 31:62-68. [PMID: 35043498 DOI: 10.1002/evan.21937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Lumila P Menéndez
- Department of Anthropology of the Americas, University of Bonn, Bonn, Germany.,Theoretical Biology Unit, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Kathleen S Paul
- Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, USA
| | | | - Tatiana Almeida
- Clinical Laboratory & BigData and Analytics, Hospital Israelita Albert Einstein, São Paulo, Brazil.,Laboratório de Estudos em Antropologia Biológica, Bioarqueologia e Evolução Humana, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Miguel Delgado
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), República Argentina (CONICET), División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, República Argentina.,Ministry of Education Key Laboratory of Contemporary Anthropology Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute Fudan University, Shanghai, China
| | - Gonzalo Figueiro
- Departamento de Antropología Biológica, Universidad de la República, Montevideo, Uruguay
| | - Kelsey Jorgensen
- Department of Anthropology, Wayne State University, Detroit, Michigan, USA
| | - Susan Kuzminsky
- Department of Anthropology and Applied Archaeology, Eastern New Mexico University, Portales, New Mexico, USA.,Anthropology Department, University of California, Santa Cruz, California, USA
| | | | - Johanna Nichols
- Department of Slavic Languages and Literatures, University of California, Berkeley, California, USA
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, Manitoba, Canada
| | | | - Dennis O'Rourke
- Department of Anthropology, University of Kansas, Lawrence, Kansas, USA
| | - Mark Hubbe
- Department of Anthropology, Ohio State University, Columbus, Ohio, USA.,Instituto de Arqueología y Antropología, Universidad Católica del Norte, Antofagasta, Chile
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50
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Abstract
SignificanceCalifornia supports a high cultural and linguistic diversity of Indigenous peoples. In a partnership of researchers with the Muwekma Ohlone tribe, we studied genomes of eight present-day tribal members and 12 ancient individuals from two archaeological sites in the San Francisco Bay Area, spanning ∼2,000 y. We find that compared to genomes of Indigenous individuals from throughout the Americas, the 12 ancient individuals are most genetically similar to ancient individuals from Southern California, and that despite spanning a large time period, they share distinctive ancestry. This ancestry is also shared with present-day tribal members, providing evidence of genetic continuity between past and present Indigenous individuals in the region, in contrast to some popular reconstructions based on archaeological and linguistic information.
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