1
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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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2
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Vallini L, Zampieri C, Shoaee MJ, Bortolini E, Marciani G, Aneli S, Pievani T, Benazzi S, Barausse A, Mezzavilla M, Petraglia MD, Pagani L. The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal. Nat Commun 2024; 15:1882. [PMID: 38528002 DOI: 10.1038/s41467-024-46161-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
A combination of evidence, based on genetic, fossil and archaeological findings, indicates that Homo sapiens spread out of Africa between ~70-60 thousand years ago (kya). However, it appears that once outside of Africa, human populations did not expand across all of Eurasia until ~45 kya. The geographic whereabouts of these early settlers in the timeframe between ~70-60 to 45 kya has been difficult to reconcile. Here we combine genetic evidence and palaeoecological models to infer the geographic location that acted as the Hub for our species during the early phases of colonisation of Eurasia. Leveraging on available genomic evidence we show that populations from the Persian Plateau carry an ancestry component that closely matches the population that settled the Hub outside Africa. With the paleoclimatic data available to date, we built ecological models showing that the Persian Plateau was suitable for human occupation and that it could sustain a larger population compared to other West Asian regions, strengthening this claim.
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Affiliation(s)
| | - Carlo Zampieri
- Department of Biology, University of Padova, Padova, Italy
| | - Mohamed Javad Shoaee
- Department of Archaeology, Max Planck Institute for Geoanthropology, Jena, Germany
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
- Research Unit Prehistory and Anthropology, Department of Physical Sciences, Earth and Environment, University of Siena, Siena, Italy
| | - Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Telmo Pievani
- Department of Biology, University of Padova, Padova, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
| | - Alberto Barausse
- Department of Biology, University of Padova, Padova, Italy
- Department of Industrial Engineering, University of Padova, Padova, Italy
| | | | - Michael D Petraglia
- Human Origins Program, Smithsonian Institution, Washington, DC, 20560, USA
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, QLD, Australia
| | - Luca Pagani
- Department of Biology, University of Padova, Padova, Italy.
- Institute of Genomics, University of Tartu, Tartu, Estonia.
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3
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Kessler C, Shafer ABA. Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid. Mol Biol Evol 2024; 41:msae038. [PMID: 38378172 PMCID: PMC10917209 DOI: 10.1093/molbev/msae038] [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: 08/15/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.
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Affiliation(s)
- Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
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4
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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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5
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Tao Y, Wei Y, Ge J, Pan Y, Wang W, Bi Q, Sheng P, Fu C, Pan W, Jin L, Zheng HX, Zhang M. Phylogenetic evidence reveals early Kra-Dai divergence and dispersal in the late Holocene. Nat Commun 2023; 14:6924. [PMID: 37903755 PMCID: PMC10616200 DOI: 10.1038/s41467-023-42761-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Studying language evolution brings a crucial perspective to bear on questions of human prehistory. As the most linguistically diverse region on earth, East and Southeast Asia have witnessed extensive sociocultural and ethnic contacts among different language communities. Especially, the Kra-Dai language family exhibits tremendous socio-cultural importance in these regions. Due to limited historical accounts, however, there are several controversies on their linguistic relatedness, ambiguities regarding the divergence time, and uncertainties on the dispersal patterns. To address these issues, here we apply Bayesian phylogenetic methods to analyze the largest lexical dataset containing 646 cognate sets compiled for 100 Kra-Dai languages. Our dated phylogenetic tree showed their initial divergence occurring approximately 4000 years BP. Phylogeographic results supported the early Kra-Dai language dispersal from the Guangxi-Guangdong area of South China towards Mainland Southeast Asia. Coupled with genetic, archaeological, paleoecologic, and paleoclimatic data, we demonstrated that the Kra-Dai language diversification could have coincided with their demic diffusion and agricultural spread shaped by the global climate change in the late Holocene. The interdisciplinary alignments shed light on reconstructing the prehistory of Kra-Dai languages and provide an indispensable piece of the puzzle for further studying prehistoric human activities in East and Southeast Asia.
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Affiliation(s)
- Yuxin Tao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Yuancheng Wei
- School of Chinese Language and Literature, Guangxi Minzu University, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jiaqi Ge
- Department of Chinese Language and Literature, Fudan University, Shanghai, China
| | - Yan Pan
- Department of Cultural Heritage and Museology, Fudan University, Shanghai, China
| | - Wenmin Wang
- College of Nationalities, Guangdong Polytechnic Normal University, Guangzhou, China
| | - Qianqi Bi
- College of Communication, East China University of Political Science and Law, Shanghai, China
| | - Pengfei Sheng
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Changzhong Fu
- College of Nationalities, Guangdong Polytechnic Normal University, Guangzhou, China
| | - Wuyun Pan
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai, China
- Institute for Humanities and Social Science Data, School of Data Science, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Hong-Xiang Zheng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.
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6
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Ávila-Arcos MC, Raghavan M, Schlebusch C. Going local with ancient DNA: A review of human histories from regional perspectives. Science 2023; 382:53-58. [PMID: 37797024 DOI: 10.1126/science.adh8140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- SciLifeLab, Uppsala, Sweden
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7
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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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8
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Menéndez LP, Barbieri C, López Cruz IG, Schmelzle T, Breidenstein A, Barquera R, Borzi G, Schuenemann VJ, Sánchez-Villagra MR. On Roth's "human fossil" from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis. SWISS JOURNAL OF PALAEONTOLOGY 2023; 142:26. [PMID: 37810206 PMCID: PMC10550872 DOI: 10.1186/s13358-023-00293-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
The "human fossil" from Baradero, Buenos Aires Province, Argentina, is a collection of skeleton parts first recovered by the paleontologist Santiago Roth and further studied by the anthropologist Rudolf Martin. By the end of the nineteenth century and beginning of the twentieth century it was considered one of the oldest human skeletons from South America's southern cone. Here, we present the results of an interdisciplinary approach to study and contextualize the ancient individual remains. We discuss the context of the finding by first compiling the available evidence associated with the historical information and any previous scientific publications on this individual. Then, we conducted an osteobiographical assessment, by which we evaluated the sex, age, and overall preservation of the skeleton based on morphological features. To obtain a 3D virtual reconstruction of the skull, we performed high resolution CT-scans on selected skull fragments and the mandible. This was followed by the extraction of bone tissue and tooth samples for radiocarbon and genetic analyses, which brought only limited results due to poor preservation and possible contamination. We estimate that the individual from Baradero is a middle-aged adult male. We conclude that the revision of foundational collections with current methodological tools brings new insights and clarifies long held assumptions on the significance of samples that were recovered when archaeology was not yet professionalized.
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Affiliation(s)
- Lumila Paula Menéndez
- Department for the Anthropology of the Americas, University of Bonn, Bonn, Germany
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Thomas Schmelzle
- Department of Paleontology, University of Zurich, Zurich, Switzerland
| | - Abagail Breidenstein
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Department of Anthropology, Binghamton University, Binghamton, USA
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guido Borzi
- Centro de Investigaciones Geológicas, La Plata, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
- Centro de Investigaciones Geológicas, CONICET-UNLP, La Plata, Argentina
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9
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O'Keefe FR, Dunn RE, Weitzel EM, Waters MR, Martinez LN, Binder WJ, Southon JR, Cohen JE, Meachen JA, DeSantis LRG, Kirby ME, Ghezzo E, Coltrain JB, Fuller BT, Farrell AB, Takeuchi GT, MacDonald G, Davis EB, Lindsey EL. Pre-Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift. Science 2023; 381:eabo3594. [PMID: 37590347 DOI: 10.1126/science.abo3594] [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: 01/28/2022] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
Abstract
The cause, or causes, of the Pleistocene megafaunal extinctions have been difficult to establish, in part because poor spatiotemporal resolution in the fossil record hinders alignment of species disappearances with archeological and environmental data. We obtained 172 new radiocarbon dates on megafauna from Rancho La Brea in California spanning 15.6 to 10.0 thousand calendar years before present (ka). Seven species of extinct megafauna disappeared by 12.9 ka, before the onset of the Younger Dryas. Comparison with high-resolution regional datasets revealed that these disappearances coincided with an ecological state shift that followed aridification and vegetation changes during the Bølling-Allerød (14.69 to 12.89 ka). Time-series modeling implicates large-scale fires as the primary cause of the extirpations, and the catalyst of this state shift may have been mounting human impacts in a drying, warming, and increasingly fire-prone ecosystem.
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Affiliation(s)
- F Robin O'Keefe
- Department of Biological Sciences, Marshall University, Huntington, WV, USA
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
| | - Regan E Dunn
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Elic M Weitzel
- Department of Anthropology, University of Connecticut, Storrs, CT, USA
| | - Michael R Waters
- Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - Lisa N Martinez
- Department of Geography, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wendy J Binder
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
- Department of Biology, Loyola Marymount University, Los Angeles, CA, USA
| | - John R Southon
- Department of Earth System Science, University California, Irvine, Irvine, CA, USA
| | - Joshua E Cohen
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
- Department of Biology, Loyola Marymount University, Los Angeles, CA, USA
- Department of Biology, Pace University, New York, NY, USA
| | - Julie A Meachen
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
- Department of Anatomy, Des Moines University, Des Moines, IA, USA
| | - Larisa R G DeSantis
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Earth and Environmental Science, Vanderbilt University, Nashville, TN, USA
| | - Matthew E Kirby
- Department of Geological Sciences, California State University, Fullerton, Fullerton, CA, USA
| | - Elena Ghezzo
- Department of Environmental Sciences, Informatics, and Statistics, Università Ca' Foscari Venezia, Venice, Italy
- Department of Earth Sciences, University Oregon, Eugene, OR, USA
| | - Joan B Coltrain
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | - Benjamin T Fuller
- Géosciences Environnement Toulouse, UMR 5563, CNRS, Observatoire Midi-Pyrénées, Toulouse, France
| | - Aisling B Farrell
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
| | - Gary T Takeuchi
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
| | - Glen MacDonald
- Department of Geography, University of California, Los Angeles, Los Angeles, CA, USA
| | - Edward B Davis
- Department of Environmental Sciences, Informatics, and Statistics, Università Ca' Foscari Venezia, Venice, Italy
- Department of Earth Sciences, University Oregon, Eugene, OR, USA
| | - Emily L Lindsey
- La Brea Tar Pits and Museum, Natural History Museums of Los Angeles County, Los Angeles, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
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10
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Horimoto AR, Boyken LA, Blue EE, Grinde KE, Nafikov RA, Sohi HK, Nato AQ, Bis JC, Brusco LI, Morelli L, Ramirez A, Dalmasso MC, Temple S, Satizabal C, Browning SR, Seshadri S, Wijsman EM, Thornton TA. Admixture mapping implicates 13q33.3 as ancestry-of-origin locus for Alzheimer disease in Hispanic and Latino populations. HGG ADVANCES 2023; 4:100207. [PMID: 37333771 PMCID: PMC10276158 DOI: 10.1016/j.xhgg.2023.100207] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
Alzheimer disease (AD) is the most common form of senile dementia, with high incidence late in life in many populations including Caribbean Hispanic (CH) populations. Such admixed populations, descended from more than one ancestral population, can present challenges for genetic studies, including limited sample sizes and unique analytical constraints. Therefore, CH populations and other admixed populations have not been well represented in studies of AD, and much of the genetic variation contributing to AD risk in these populations remains unknown. Here, we conduct genome-wide analysis of AD in multiplex CH families from the Alzheimer Disease Sequencing Project (ADSP). We developed, validated, and applied an implementation of a logistic mixed model for admixture mapping with binary traits that leverages genetic ancestry to identify ancestry-of-origin loci contributing to AD. We identified three loci on chromosome 13q33.3 associated with reduced risk of AD, where associations were driven by Native American (NAM) ancestry. This AD admixture mapping signal spans the FAM155A, ABHD13, TNFSF13B, LIG4, and MYO16 genes and was supported by evidence for association in an independent sample from the Alzheimer's Genetics in Argentina-Alzheimer Argentina consortium (AGA-ALZAR) study with considerable NAM ancestry. We also provide evidence of NAM haplotypes and key variants within 13q33.3 that segregate with AD in the ADSP whole-genome sequencing data. Interestingly, the widely used genome-wide association study approach failed to identify associations in this region. Our findings underscore the potential of leveraging genetic ancestry diversity in recently admixed populations to improve genetic mapping, in this case for AD-relevant loci.
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Affiliation(s)
| | - Lisa A. Boyken
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth E. Blue
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Kelsey E. Grinde
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Department of Mathematics, Statistics and Computer Science, Macalester College, Saint Paul, MN 55105, USA
| | - Rafael A. Nafikov
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Harkirat K. Sohi
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Biomedical and Health Informatics Program, University of Washington, Seattle, WA 98195, USA
| | - Alejandro Q. Nato
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Luis I. Brusco
- CENECON - Center of Behavioural Neurology and Neuropsychiatry, School of Medicine, University of Buenos Aires, C1121A6B Buenos Aires, Argentina
| | - Laura Morelli
- Laboratory of Brain Aging and Neurodegeneration-Fundación Instituto Leloir-IIBBA- National Scientific and Technical Research Council (CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Argentina
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) University of Cologne, 50674 Cologne, Germany
- Department of Psychiatry, UT Health San Antonio, San Antonio, TX 78229, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Maria Carolina Dalmasso
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
- Neurosciences and Complex Systems Unit (EnyS), CONICET, Hospital El Cruce, National University A. Jauretche (UNAJ), B1888AAE Florencio Varela, Argentina
| | - Seth Temple
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Claudia Satizabal
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas, San Antonio, TX 78229, USA
- Department of Neurology, University of Texas, San Antonio, TX 78229, USA
| | - Sharon R. Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sudha Seshadri
- Department of Neurology, University of Texas, San Antonio, TX 78229, USA
| | - Ellen M. Wijsman
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
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11
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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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12
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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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13
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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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14
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Li YC, Gao ZL, Liu KJ, Tian JY, Yang BY, Rahman ZU, Yang LQ, Zhang SH, Li CT, Achilli A, Semino O, Torroni A, Kong QP. Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan. Cell Rep 2023:112413. [PMID: 37164007 DOI: 10.1016/j.celrep.2023.112413] [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: 07/28/2022] [Revised: 01/05/2023] [Accepted: 04/04/2023] [Indexed: 05/12/2023] Open
Abstract
Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zong-Liang Gao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Kai-Jun Liu
- Chengdu 23Mofang Biotechnology Co., Ltd., Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Bin-Yu Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Su-Hua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Cheng-Tao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China.
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15
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Capodiferro MR, Chero Osorio AM, Rambaldi Migliore N, Tineo Tineo DH, Raveane A, Xavier C, Bodner M, Simão F, Ongaro L, Montinaro F, Lindo J, Huerta-Sanchez E, Politis G, Barbieri C, Parson W, Gusmão L, Achilli A. The multifaceted genomic history of Ashaninka from Amazonian Peru. Curr Biol 2023; 33:1573-1581.e5. [PMID: 36931272 DOI: 10.1016/j.cub.2023.02.046] [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: 09/20/2022] [Revised: 12/14/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,1,2,3,4,5,6,7,8 including central America and the Caribbean.9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,13 and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.14,15.
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Affiliation(s)
- Marco Rosario Capodiferro
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy; Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland.
| | - Ana María Chero Osorio
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Dean Herman Tineo Tineo
- Laboratorio de Biología Forense, Instituto de Medicina Legal y Ciencias Forenses, Ministerio Público, Lima 15033, Perú
| | | | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Filipa Simão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Linda Ongaro
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, 70125 Bari, Italy; Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Emilia Huerta-Sanchez
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland; Ecology and Evolutionary Biology and Center for Computational and Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; Forensic Science Program, Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
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16
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Corach D, Caputo M. Social injustice unveiled by genetic analysis: Argentina as a case study. Am J Hum Biol 2023; 35:e23820. [PMID: 36256489 DOI: 10.1002/ajhb.23820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/09/2022] [Accepted: 10/01/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The population of the American countries is genetically heterogeneous, whose genesis result from of recent admixture events. In this process, the transoceanic European component displaced the original inhabitants of the continent. AIM To investigate whether socially differentiated cohorts exhibit underlying ancestry components within an urban admixed population, two cohorts of individuals inhabiting Argentina were studied. One cohort included genetically unrelated individuals involved in voluntary paternity testing while the other included sexual or blood-crime suspects. MATERIALS & METHODS We analyzed over 2500 unrelated individuals: four Native American maternal lineage mtDNA markers in 1024 samples, five Y chromosome haplogroups in 658 male samples, 24 autosomal ancestry informative markers (AIMs) in 205 samples, and 15 autosomal short tandem repeats (STRs) in 1557 samples; countrywide and divided by regions. RESULTS While our results confirm a tricontinental ethnic contribution to both cohorts, their proportions showed statistically significant differences, with a higher proportion of Native American ancestry in the cohort linked to violent crimes compared to those in paternity testing. This hallmark was observed with all the marker sets used and at various levels of analysis. DISCUSSION Since paternity tests are costly, socio-economic differences might help to interpret our observations. The effect of discrimination against descendants of Native American minorities, and exposure to violent social environments, might link marginal groups to criminality. CONCLUSION Our findings underscore the relevance of proper social management since only by improving living conditions, reducing discrimination, promoting education, and providing job opportunities will it be possible to attain equality in a heterogeneous society. Genetic markers proved to be highly informative in unveiling unexpected social differences.
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Affiliation(s)
- Daniel Corach
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Mariela Caputo
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
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17
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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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18
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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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19
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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] [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
- *Correspondence: Evelyn Jane Collen, ; Bastien Llamas,
| | - 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
- *Correspondence: Evelyn Jane Collen, ; Bastien Llamas,
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20
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Buikstra JE, DeWitte SN, Agarwal SC, Baker BJ, Bartelink EJ, Berger E, Blevins KE, Bolhofner K, Boutin AT, Brickley MB, Buzon MR, de la Cova C, Goldstein L, Gowland R, Grauer AL, Gregoricka LA, Halcrow SE, Hall SA, Hillson S, Kakaliouras AM, Klaus HD, Knudson KJ, Knüsel CJ, Larsen CS, Martin DL, Milner GR, Novak M, Nystrom KC, Pacheco-Forés SI, Prowse TL, Robbins Schug G, Roberts CA, Rothwell JE, Santos AL, Stojanowski C, Stone AC, Stull KE, Temple DH, Torres CM, Toyne JM, Tung TA, Ullinger J, Wiltschke-Schrotta K, Zakrzewski SR. Twenty-first century bioarchaeology: Taking stock and moving forward. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 178 Suppl 74:54-114. [PMID: 36790761 DOI: 10.1002/ajpa.24494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 12/18/2022]
Abstract
This article presents outcomes from a Workshop entitled "Bioarchaeology: Taking Stock and Moving Forward," which was held at Arizona State University (ASU) on March 6-8, 2020. Funded by the National Science Foundation (NSF), the School of Human Evolution and Social Change (ASU), and the Center for Bioarchaeological Research (CBR, ASU), the Workshop's overall goal was to explore reasons why research proposals submitted by bioarchaeologists, both graduate students and established scholars, fared disproportionately poorly within recent NSF Anthropology Program competitions and to offer advice for increasing success. Therefore, this Workshop comprised 43 international scholars and four advanced graduate students with a history of successful grant acquisition, primarily from the United States. Ultimately, we focused on two related aims: (1) best practices for improving research designs and training and (2) evaluating topics of contemporary significance that reverberate through history and beyond as promising trajectories for bioarchaeological research. Among the former were contextual grounding, research question/hypothesis generation, statistical procedures appropriate for small samples and mixed qualitative/quantitative data, the salience of Bayesian methods, and training program content. Topical foci included ethics, social inequality, identity (including intersectionality), climate change, migration, violence, epidemic disease, adaptability/plasticity, the osteological paradox, and the developmental origins of health and disease. Given the profound changes required globally to address decolonization in the 21st century, this concern also entered many formal and informal discussions.
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Affiliation(s)
- Jane E Buikstra
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, South Carolina, USA
| | - Sabrina C Agarwal
- Department of Anthropology, University of California Berkeley, Berkeley, California, USA
| | - Brenda J Baker
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Eric J Bartelink
- Department of Anthropology, California State University, Chico, California, USA
| | - Elizabeth Berger
- Department of Anthropology, University of California, Riverside, California, USA
| | | | - Katelyn Bolhofner
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University, Phoenix, Arizona, USA
| | - Alexis T Boutin
- Department of Anthropology, Sonoma State University, Rohnert Park, California, USA
| | - Megan B Brickley
- Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Michele R Buzon
- Department of Anthropology, Purdue University, West Lafayette, Indiana, USA
| | - Carlina de la Cova
- Department of Anthropology, University of South Carolina, Columbia, South Carolina, USA
| | - Lynne Goldstein
- Department of Anthropology, Michigan State University, East Lansing, Michigan, USA
| | | | - Anne L Grauer
- Department of Anthropology, Loyola University Chicago, Chicago, Illinois, USA
| | - Lesley A Gregoricka
- Department of Sociology, Anthropology, & Social Work, University of South Alabama, Mobile, Alabama, USA
| | - Siân E Halcrow
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Sarah A Hall
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Simon Hillson
- Institute of Archaeology, University College London, London, UK
| | - Ann M Kakaliouras
- Department of Anthropology, Whittier College, Whittier, California, USA
| | - Haagen D Klaus
- Department of Sociology and Anthropology, George Mason University, Fairfax, Virginia, USA
| | - Kelly J Knudson
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Christopher J Knüsel
- Préhistoire à l'Actuel: Culture, Environnement et Anthropologie, University of Bordeaux, CNRS, MC, PACEA, UMR5199, F-33615, Pessac, France
| | | | - Debra L Martin
- Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - George R Milner
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Mario Novak
- Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Kenneth C Nystrom
- Department of Anthropology, State University of New York at New Paltz, New Paltz, New York, USA
| | | | - Tracy L Prowse
- Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Gwen Robbins Schug
- Environmental Health Program, University of North Carolina, Greensboro, North Carolina, USA
| | | | - Jessica E Rothwell
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Ana Luisa Santos
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Christopher Stojanowski
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Anne C Stone
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Kyra E Stull
- Department of Anthropology, University of Nevada, Reno, Reno, Nevada, USA
| | - Daniel H Temple
- Department of Sociology and Anthropology, George Mason University, Fairfax, Virginia, USA
| | - Christina M Torres
- Department of Anthropology and Heritage Studies, University of California, Merced, USA, and Instituto de Arqueología y Antropología, Universidad Católica del Norte, Antofagasta, Chile
| | - J Marla Toyne
- Department of Anthropology, University of Central Florida, Orlando, Florida, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jaime Ullinger
- Bioanthropology Research Institute, Quinnipiac University, Hamden, Connecticut, USA
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21
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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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22
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Morphometric affinities and direct radiocarbon dating of the Toca dos Coqueiros' skull (Serra da Capivara, Brazil). Sci Rep 2022; 12:7807. [PMID: 35550576 PMCID: PMC9098637 DOI: 10.1038/s41598-022-11893-3] [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: 10/10/2021] [Accepted: 04/29/2022] [Indexed: 11/14/2022] Open
Abstract
The biological variation of the earliest skeletons of South America has been intensely debated for the last two centuries. One of the major research constraints has been the limited number of available samples dating to the early Holocene. We here present the first direct radiocarbon-date for the early Holocene human skeleton from Toca dos Coqueiros (Serra da Capivara, Brazil), also known as “Zuzu” (8640 ± 30 BP; 9526–9681 cal years BP). We performed craniometric analyses using exclusively samples from Brazil, to revisit the sex of the skeleton, and to discuss the evolutionary processes involved in the occupation of the continent. The sex of the individual was estimated as a female when compared to late and early Holocene individuals, but as a male when compared only to the early Holocene series. We also found that Zuzu presents the strongest differences with the late Holocene Guajajara individuals, located nearby, and the strongest similarities with the early Holocene series from Lagoa Santa, attesting for solid biological affinities among early Holocene individuals from Brazil, as well as a moderate level of morphological variation among them. This suggests that the early individuals were part of the same heterogeneous lineage, possibly a different one from which late Holocene populations diverged.
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23
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The age of the opening of the Ice-Free Corridor and implications for the peopling of the Americas. Proc Natl Acad Sci U S A 2022; 119:e2118558119. [PMID: 35312340 PMCID: PMC9168949 DOI: 10.1073/pnas.2118558119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Ice-Free Corridor (IFC) has long played a key role in hypotheses about the peopling of the Americas. Earlier assessments of its age suggested that the IFC was available for a Clovis-first migration, but subsequent developments now suggest a pre-Clovis occupation of the Americas that occurred before the opening of the IFC, thus supporting a Pacific coastal migration route instead. However, large uncertainties in existing ages from the IFC cannot preclude its availability as a route for the first migrations. Resolving this debate over migration route is important for addressing the questions of when and how the first Americans arrived. We report cosmogenic nuclide exposure ages that show that the final opening of the IFC occurred well after pre-Clovis occupation. The Clovis-first model for the peopling of the Americas by ∼13.4 ka has long invoked the Ice-Free Corridor (IFC) between the retreating margins of the Cordilleran and Laurentide ice sheets as the migration route from Alaska and the Yukon down to the Great Plains. Evidence from archaeology and ancient genomics, however, now suggests that pre-Clovis migrations occurred by at least ∼15.5 to 16.0 ka or earlier than most recent assessments of the age of IFC opening at ∼14 to 15 ka, lending support to the use of a Pacific coast migration route instead. Uncertainties in ages from the IFC used in these assessments, however, allow for an earlier IFC opening which would be consistent with the availability of the IFC as a migration route by ∼15.5 to 16.0 ka. Here, we use 64 cosmogenic (10Be) exposure ages to closely date the age of the full opening of the IFC at 13.8 ± 0.5 ka. Our results thus clearly establish that the IFC was not available for the first peopling of the Americas after the Last Glacial Maximum, whereas extensive geochronological data from the Pacific coast support its earlier availability as a coastal migration route.
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24
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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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25
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Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent. Genes (Basel) 2022; 13:genes13020220. [PMID: 35205264 PMCID: PMC8871784 DOI: 10.3390/genes13020220] [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] [Received: 12/21/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/24/2022] Open
Abstract
Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).
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26
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Madsen DB, Davis LG, Rhode D, Oviatt CG. Comment on "Evidence of humans in North America during the Last Glacial Maximum". Science 2022; 375:eabm4678. [PMID: 35025634 DOI: 10.1126/science.abm4678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bennett et al. (Reports, 24 September 2021, p. 1528) report human footprints from Lake Otero, New Mexico, USA ~22,000 years ago. Critical assessment suggests that their radiocarbon chronology may be inaccurate. Reservoir effects may have caused radiocarbon ages to appear thousands of years too old. Independent verification of the ages of the footprint horizons is imperative and is possible through other means.
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Affiliation(s)
- David B Madsen
- Department of Anthropology, University of Nevada, Reno, NV 89557, USA
| | - Loren G Davis
- Department of Anthropology, Oregon State University, Corvallis, OR 97331, USA
| | - David Rhode
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV 89512, USA
| | - Charles G Oviatt
- Department of Geology, Kansas State University, Manhattan, KS 66506, USA
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27
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Rambaldi Migliore N, Colombo G, Capodiferro MR, Mazzocchi L, Chero Osorio AM, Raveane A, Tribaldos M, Perego UA, Mendizábal T, Montón AG, Lombardo G, Grugni V, Garofalo M, Ferretti L, Cereda C, Gagliardi S, Cooke R, Smith-Guzmán N, Olivieri A, Aram B, Torroni A, Motta J, Semino O, Achilli A. Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas. Genes (Basel) 2021; 12:genes12121921. [PMID: 34946870 PMCID: PMC8702192 DOI: 10.3390/genes12121921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Giulia Colombo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Marco Rosario Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Lucia Mazzocchi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Ana Maria Chero Osorio
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Department of Math and Science, Southeastern Community College, West Burlington, IA 52655, USA
| | - Tomás Mendizábal
- Center for Historical, Anthropological and Cultural Research—AIP, Panama City 0816-07812, Panama;
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
| | - Alejandro García Montón
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Gianluca Lombardo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Viola Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Maria Garofalo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Luca Ferretti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Nicole Smith-Guzmán
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Bethany Aram
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ornella Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
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Liu Y, Mao X, Krause J, Fu Q. Insights into human history from the first decade of ancient human genomics. Science 2021; 373:1479-1484. [PMID: 34554811 DOI: 10.1126/science.abi8202] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
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