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Labarca R, Frugone-Álvarez M, Vilches L, Blanco JF, Peñaloza Á, Godoy-Aguirre C, Lizama-Catalán Á, Oyarzo C, Tornero C, González-Guarda E, Delgado A, Sepúlveda M, Soto-Huenchuman P. Taguatagua 3: A new late Pleistocene settlement in a highly suitable lacustrine habitat in central Chile (34°S). PLoS One 2024; 19:e0302465. [PMID: 38776357 PMCID: PMC11111044 DOI: 10.1371/journal.pone.0302465] [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: 10/28/2023] [Accepted: 04/03/2024] [Indexed: 05/24/2024] Open
Abstract
We present the results of the excavations and analyses of the diverse and exceptional archaeological assemblage of Taguatagua 3, a new late Pleistocene site located in the ancient Tagua Tagua lake in Central Chile (34°S). The anthropogenic context is constrained in a coherently dated stratigraphic deposit which adds new information about the mobility, subsistence strategies, and settlement of the early hunter-gatherers of southern South America. The age model constructed, as well as radiocarbon dates obtained directly from a combustion structure, indicate that the human occupation occurred over a brief time span around 12,440-12,550 cal yr BP. Considering taphonomic, geoarchaeological, lithic, archaeobotanical, and zooarchaeological evidence, as well as the spatial distribution combined with ethnographic data, we interpret Taguatagua 3 as a logistic and temporary camp associated mainly with gomphothere hunting and butchering. Nevertheless, several other activities were carried out here as well, such as hide and/or bone preparation, small vertebrate and plant processing and consumption, and red ochre grinding. Botanical and eggshell remains suggest that the anthropic occupation occurred during the dry season. Considering the contemporaneous sites recorded in the basin, we conclude that the ancient Tagua Tagua lake was a key location along the region's early hunter-gatherer mobility circuits. In this context, it acted as a recurrent hunting/scavenging place during the Late Pleistocene due to its abundant, diverse, and predictable resources.
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Affiliation(s)
- Rafael Labarca
- Facultad de Ciencias Sociales, Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Matías Frugone-Álvarez
- Facultad de Ciencias, Departamento de Química Ambiental, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | | | | | - Ángela Peñaloza
- Facultad de Filosofía y Letras, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Carolina Godoy-Aguirre
- Facultad de Ciencias Sociales, Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Carlos Tornero
- Department of Prehistory, Autonomous University of Barcelona (UAB), Bellaterra, Spain
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES-CERCA), Tarragona, Spain
| | | | - Ayelen Delgado
- Institute of Archaeology, University College London, London, United Kingdom
| | - Marcela Sepúlveda
- Facultad de Ciencias Sociales, Departamento de Ciencias Sociales, Universidad de Tarapacá, Iquique, Chile
| | - Paula Soto-Huenchuman
- Facultad de Ciencias, Laboratorio de Ontogenia y Filogenia, Red Paleontológica U-Chile, Universidad de Chile, Santiago, Chile
- Unidad de Patrimonio Paleontológico, Consejo de Monumentos Nacionales, Santiago, Chile
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Steffen ML. New age constraints for human entry into the Americas on the north Pacific coast. Sci Rep 2024; 14:4291. [PMID: 38383701 PMCID: PMC10881565 DOI: 10.1038/s41598-024-54592-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
The timing of the initial peopling of the Americas is unresolved. Because the archaeological record necessitates discussion of human entry from Beringia into southern North America during the last glaciation, addressing this problem routinely involves evaluating environmental parameters then targeting areas suitable for human settlement. Vertebrate remains indicate landscape quality and are a key dataset for assessing coastal migration theories and the viability of coastal routes. Here, radiocarbon dates on vertebrate specimens and archaeological sites are calibrated to document species occurrences and the ages of human settlements across the western expansion and decay of the Cordilleran Ice Sheet (CIS) during the Late Wisconsin Fraser Glaciation in four subregions of the north Pacific coast of North America. The results show archaeological sites occur after glacial maxima and are generally consistent with the age of other securely dated earliest sites in southern North America. They also highlight gaps in the vertebrate chronologies around CIS maxima in each of the subregions that point to species redistributions and extirpations and signal times of low potential for human settlement and subsistence in a key portion of the proposed coastal migration route. This study, therefore, defines new age constraints for human coastal migration theories in the peopling of the Americas debate.
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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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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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5
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Jose-Abrego A, Roman S, Laguna-Meraz S, Rebello-Pinho JR, Justo Arevalo S, Panduro A. Tracing the evolutionary history of hepatitis B virus genotype H endemic to Mexico. Front Microbiol 2023; 14:1180931. [PMID: 37293217 PMCID: PMC10244555 DOI: 10.3389/fmicb.2023.1180931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023] Open
Abstract
Hepatitis B virus (HBV) spreads efficiently among all human populations worldwide. HBV is classified into ten genotypes (A to J) with their geographic distribution and clinical features. In Mexico, HBV genotype H is the leading cause of hepatitis B and has been detected in indigenous populations, suggesting that HBV genotype H may be native to Mexico. However, little is known about the evolutionary history of HBV genotype H. Thus, we aimed to determine the age of HBV genotype H in Mexico using molecular dating techniques. Ninety-two HBV sequences of the reverse transcriptase (RT) domain of the polymerase gene (~1,251 bp) were analyzed; 48 were genotype H, 43 were genotype F, and the oldest HBV sequence from America was included as the root. All sequences were aligned, and the most recent common ancestor (TMRCA) time was calculated using the Bayesian Skyline Evolutionary Analysis. Our results estimate a TMRCA for the genotype H in Mexico of 2070.9 (667.5-4489.2) years before the present (YBP). We identified four major diversification events in genotype H, named H1, H2, H3, and H4. The TMRCA of H1 was 1213.0 (253.3-2638.3) YBP, followed by H2 1175.5 (557.5-2424.2) YBP, H3 949.6 (279.3-2105.0) YBP, and H4 1230.5 (336.3, 2756.7) YBP. We estimated that genotype H diverged from its sister genotype F around 8140.8 (1867.5-18012.8) YBP. In conclusion, this study found that genotype H in Mexico has an estimated age of 2070.9 (667.5-4489.2) YBP and has experienced at least four major diversification events since then.
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Affiliation(s)
- Alexis Jose-Abrego
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde", Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde", Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Saul Laguna-Meraz
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde", Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
- Molecular Biology in Medicine Doctorate Program, Guadalajara, Mexico
| | - João Renato Rebello-Pinho
- Department of Gastroenterology, Institute of Tropical Medicine and School of Medicine, LIM07, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Santiago Justo Arevalo
- Faculty of Biological Sciences, Ricardo Palma University, Lima, Peru
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Arturo Panduro
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde", Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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6
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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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7
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da Silva Coelho FA, Gill S, Tomlin CM, Papavassiliou M, Farley SD, Cook JA, Sonsthagen SA, Sage GK, Heaton TH, Talbot SL, Lindqvist C. Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska. Mol Ecol 2023. [PMID: 37096383 DOI: 10.1111/mec.16960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.
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Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | | | - Sean D Farley
- Alaska Department of Fish and Game, Anchorage, Alaska, USA
| | - Joseph A Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Sarah A Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, University of Nebraska-Lincoln, School of Natural Resources, Lincoln, Nebraska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, South Dakota, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
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8
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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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9
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Yurchenko AA, Naumenko AN, Artemov GN, Karagodin DA, Hodge JM, Velichevskaya AI, Kokhanenko AA, Bondarenko SM, Abai MR, Kamali M, Gordeev MI, Moskaev AV, Caputo B, Aghayan SA, Baricheva EM, Stegniy VN, Sharakhova MV, Sharakhov IV. Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group. BMC Biol 2023; 21:63. [PMID: 37032389 PMCID: PMC10084679 DOI: 10.1186/s12915-023-01538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/08/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Phylogenetic analyses of closely related species of mosquitoes are important for better understanding the evolution of traits contributing to transmission of vector-borne diseases. Six out of 41 dominant malaria vectors of the genus Anopheles in the world belong to the Maculipennis Group, which is subdivided into two Nearctic subgroups (Freeborni and Quadrimaculatus) and one Palearctic (Maculipennis) subgroup. Although previous studies considered the Nearctic subgroups as ancestral, details about their relationship with the Palearctic subgroup, and their migration times and routes from North America to Eurasia remain controversial. The Palearctic species An. beklemishevi is currently included in the Nearctic Quadrimaculatus subgroup adding to the uncertainties in mosquito systematics. RESULTS To reconstruct historic relationships in the Maculipennis Group, we conducted a phylogenomic analysis of 11 Palearctic and 2 Nearctic species based on sequences of 1271 orthologous genes. The analysis indicated that the Palearctic species An. beklemishevi clusters together with other Eurasian species and represents a basal lineage among them. Also, An. beklemishevi is related more closely to An. freeborni, which inhabits the Western United States, rather than to An. quadrimaculatus, a species from the Eastern United States. The time-calibrated tree suggests a migration of mosquitoes in the Maculipennis Group from North America to Eurasia about 20-25 million years ago through the Bering Land Bridge. A Hybridcheck analysis demonstrated highly significant signatures of introgression events between allopatric species An. labranchiae and An. beklemishevi. The analysis also identified ancestral introgression events between An. sacharovi and its Nearctic relative An. freeborni despite their current geographic isolation. The reconstructed phylogeny suggests that vector competence and the ability to enter complete diapause during winter evolved independently in different lineages of the Maculipennis Group. CONCLUSIONS Our phylogenomic analyses reveal migration routes and adaptive radiation timing of Holarctic malaria vectors and strongly support the inclusion of An. beklemishevi into the Maculipennis Subgroup. Detailed knowledge of the evolutionary history of the Maculipennis Subgroup provides a framework for examining the genomic changes related to ecological adaptation and susceptibility to human pathogens. These genomic variations may inform researchers about similar changes in the future providing insights into the patterns of disease transmission in Eurasia.
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Affiliation(s)
- Andrey A Yurchenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Kurchatov Genomics Center, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
- Current Address: INSERM U981, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Anastasia N Naumenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Gleb N Artemov
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Dmitry A Karagodin
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - James M Hodge
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Alena I Velichevskaya
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Alina A Kokhanenko
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Semen M Bondarenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Mohammad R Abai
- Department of Medical Entomology and Vector Control, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Kamali
- Department of Medical Entomology and Parasitology, Tarbiat Modares University, Tehran, Iran
| | - Mikhail I Gordeev
- Department of General Biology and Ecology, State University of Education, Mytishchi, Russia
| | - Anton V Moskaev
- Department of General Biology and Ecology, State University of Education, Mytishchi, Russia
| | - Beniamino Caputo
- Dipartimento Di Sanità Pubblica E Malattie Infettive, Università Sapienza, Rome, Italy
| | - Sargis A Aghayan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
- Department of Zoology, Yerevan State University, Yerevan, Armenia
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Vladimir N Stegniy
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Maria V Sharakhova
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia.
| | - Igor V Sharakhov
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia.
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10
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Lesnek AJ. Windows of opportunity for the peopling of the Americas. Proc Natl Acad Sci U S A 2023; 120:e2300979120. [PMID: 36848550 PMCID: PMC10013856 DOI: 10.1073/pnas.2300979120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Affiliation(s)
- Alia J. Lesnek
- School of Earth and Environmental Sciences, Queens College, City University of New York, Flushing, NY11367
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11
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Ice and ocean constraints on early human migrations into North America along the Pacific coast. Proc Natl Acad Sci U S A 2023; 120:e2208738120. [PMID: 36745804 PMCID: PMC9963817 DOI: 10.1073/pnas.2208738120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Founding populations of the first Americans likely occupied parts of Beringia during the Last Glacial Maximum (LGM). The timing, pathways, and modes of their southward transit remain unknown, but blockage of the interior route by North American ice sheets between ~26 and 14 cal kyr BP (ka) favors a coastal route during this period. Using models and paleoceanographic data from the North Pacific, we identify climatically favorable intervals when humans could have plausibly traversed the Cordilleran coastal corridor during the terminal Pleistocene. Model simulations suggest that northward coastal currents strengthened during the LGM and at times of enhanced freshwater input, making southward transit by boat more difficult. Repeated Cordilleran glacial-calving events would have further challenged coastal transit on land and at sea. Following these events, ice-free coastal areas opened and seasonal sea ice was present along the Alaskan margin until at least 15 ka. Given evidence for humans south of the ice sheets by 16 ka and possibly earlier, we posit that early people may have taken advantage of winter sea ice that connected islands and coastal refugia. Marine ice-edge habitats offer a rich food supply and traversing coastal sea ice could have mitigated the difficulty of traveling southward in watercraft or on land over glaciers. We identify 24.5 to 22 ka and 16.4 to 14.8 ka as environmentally favorable time periods for coastal migration, when climate conditions provided both winter sea ice and ice-free summer conditions that facilitated year-round marine resource diversity and multiple modes of mobility along the North Pacific coast.
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12
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Van Gijn R, Norder S, Arias L, Emlen NQ, Azevedo MCBC, Caine A, Dunn S, Howard A, Julmi N, Krasnoukhova O, Stoneking M, Wiegertjes J. The social lives of isolates (and small language families): the case of the Northwest Amazon. Interface Focus 2023; 13:20220054. [PMID: 36655194 PMCID: PMC9732644 DOI: 10.1098/rsfs.2022.0054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
The Americas are home to patches of extraordinary linguistic (genealogical) diversity. These high-diversity areas are particularly unexpected given the recent population of the Americas. In this paper, we zoom in on one such area, the Northwest Amazon, and address the question of how the diversity in this area has persisted to the present. We contrast two hypotheses that claim opposite mechanisms for the maintenance of diversity: the isolation hypothesis suggests that isolation facilitates the preservation of diversity, while the integration hypothesis proposes that conscious identity preservation in combination with contact drives diversity maintenance. We test predictions for both hypotheses across four disciplines: biogeography, cultural anthropology, population genetics and linguistics. Our results show signs of both isolation and integration, but they mainly suggest considerable diversity in how groups of speakers have interacted with their surroundings.
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Affiliation(s)
- Rik Van Gijn
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands
| | - Sietze Norder
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands,Copernicus Institute of Sustainable Development, Environmental Science Group, Utrecht University, Utrecht 3584 CB, The Netherlands
| | - Leonardo Arias
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands,Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Nicholas Q. Emlen
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands,University of Groningen, Campus Fryslân 8911 CE, The Netherlands
| | | | - Allison Caine
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands,Department of Anthropology, University of Wyoming, 82071, Laramie, WY, USA
| | - Saskia Dunn
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands
| | - Austin Howard
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands
| | - Nora Julmi
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands
| | - Olga Krasnoukhova
- Leiden University Centre for Linguistics, Leiden 2311 BE, The Netherlands
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig 04103, Germany,Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Villeurbanne, France
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13
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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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14
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Salis AT, Bray SCE, Lee MSY, Heiniger H, Barnett R, Burns JA, Doronichev V, Fedje D, Golovanova L, Harington CR, Hockett B, Kosintsev P, Lai X, Mackie Q, Vasiliev S, Weinstock J, Yamaguchi N, Meachen JA, Cooper A, Mitchell KJ. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge. Mol Ecol 2022; 31:6407-6421. [PMID: 34748674 DOI: 10.1111/mec.16267] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
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Affiliation(s)
- Alexander T Salis
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Sarah C E Bray
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Registry of Senior Australians (ROSA), South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia.,South Australian Museum, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ross Barnett
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James A Burns
- Curator Emeritus, Royal Alberta Museum, Edmonton, Alberta, Canada
| | | | - Daryl Fedje
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | | | - C Richard Harington
- Curator Emeritus and Research Associate, Research Division (Paleobiology), Canadian Museum of Nature, Ottawa, Canada
| | - Bryan Hockett
- US Department of Interior, Bureau of Land Management, Nevada State Office, Reno, Nevada, USA
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Department of History, Ural Federal University, Yekaterinburg, Russia
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Quentin Mackie
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | - Sergei Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Russia
| | - Jacobo Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, UK
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Julie A Meachen
- Anatomy Department, Des Moines University, Des Moines, Iowa, USA
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Zoology, Otago Palaeogenetics Laboratory, University of Otago, Dunedin, New Zealand
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15
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Du J, Mix AC, Haley BA, Belanger CL, Sharon. Volcanic trigger of ocean deoxygenation during Cordilleran ice sheet retreat. Nature 2022; 611:74-80. [DOI: 10.1038/s41586-022-05267-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/23/2022] [Indexed: 11/06/2022]
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16
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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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17
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Pacheco C, Stronen AV, Jędrzejewska B, Plis K, Okhlopkov IM, Mamaev NV, Drovetski SV, Godinho R. Demography and evolutionary history of grey wolf populations around the Bering Strait. Mol Ecol 2022; 31:4851-4865. [PMID: 35822863 PMCID: PMC9545117 DOI: 10.1111/mec.16613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.
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Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Sergei V Drovetski
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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18
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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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19
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Bennett MR, Bustos D, Pigati JS, Springer KB, Urban TM, Holliday VT, Reynolds SC, Budka M, Honke JS, Hudson AM, Fenerty B, Connelly C, Martinez PJ, Santucci VL, Odess D. Evidence of humans in North America during the Last Glacial Maximum. Science 2021; 373:1528-1531. [PMID: 34554787 DOI: 10.1126/science.abg7586] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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)
- Matthew R Bennett
- Institute for Studies in Landscapes and Human Evolution, Bournemouth University, Poole, BH12 5BB, UK
| | - David Bustos
- National Park Service, White Sands National Park, P.O. Box 1086, Holloman AFB, NM 88330, USA
| | - Jeffrey S Pigati
- US Geological Survey, Denver Federal Center, Box 25046, MS 980, Denver, CO 80225, USA
| | - Kathleen B Springer
- US Geological Survey, Denver Federal Center, Box 25046, MS 980, Denver, CO 80225, USA
| | - Thomas M Urban
- Department of Classics and Cornell Tree Ring Laboratory, Cornell University, Ithaca, NY 14853, USA
| | - Vance T Holliday
- School of Anthropology, P.O. Box 210030, University of Arizona, Tucson, AZ 85721-0030, USA.,Department of Geosciences, University of Arizona, Tucson, AZ 85721-0030, USA
| | - Sally C Reynolds
- Institute for Studies in Landscapes and Human Evolution, Bournemouth University, Poole, BH12 5BB, UK
| | - Marcin Budka
- Institute for Studies in Landscapes and Human Evolution, Bournemouth University, Poole, BH12 5BB, UK
| | - Jeffrey S Honke
- US Geological Survey, Denver Federal Center, Box 25046, MS 980, Denver, CO 80225, USA
| | - Adam M Hudson
- US Geological Survey, Denver Federal Center, Box 25046, MS 980, Denver, CO 80225, USA
| | - Brendan Fenerty
- Department of Geosciences, University of Arizona, Tucson, AZ 85721-0030, USA
| | - Clare Connelly
- National Park Service, White Sands National Park, P.O. Box 1086, Holloman AFB, NM 88330, USA
| | - Patrick J Martinez
- National Park Service, White Sands National Park, P.O. Box 1086, Holloman AFB, NM 88330, USA
| | - Vincent L Santucci
- National Park Service, Geologic Resources Division, 1849 C Street NW, Washington, DC 20240, USA
| | - Daniel Odess
- National Park Service, Cultural Resources Directorate, Washington, DC 20240, USA
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20
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Willerslev E, Meltzer DJ. Peopling of the Americas as inferred from ancient genomics. Nature 2021; 594:356-364. [PMID: 34135521 DOI: 10.1038/s41586-021-03499-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.
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Affiliation(s)
- Eske Willerslev
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Wellcome Trust Sanger Institute, Cambridge, UK.
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Anthropology, Southern Methodist University, Dallas, TX, USA.
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21
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Colella JP, Frederick LM, Talbot SL, Cook JA. Extrinsically reinforced hybrid speciation within Holarctic ermine (
Mustela
spp.) produces an insular endemic. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Jocelyn P. Colella
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- Biodiversity Institute University of Kansas Lawrence KS USA
| | - Lindsey M. Frederick
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- New Mexico Museum of Natural History and Science Albuquerque NM USA
| | | | - Joseph A. Cook
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
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22
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da Silva Coelho FA, Gill S, Tomlin CM, Heaton TH, Lindqvist C. An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas. Proc Biol Sci 2021; 288:20203103. [PMID: 33622130 PMCID: PMC7934960 DOI: 10.1098/rspb.2020.3103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ13C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs' terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages.
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Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Timothy H 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.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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23
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Walczak MH, Mix AC, Cowan EA, Fallon S, Fifield LK, Alder JR, Du J, Haley B, Hobern T, Padman J, Praetorius SK, Schmittner A, Stoner JS, Zellers SD. Phasing of millennial-scale climate variability in the Pacific and Atlantic Oceans. Science 2020; 370:716-720. [PMID: 33004677 DOI: 10.1126/science.aba7096] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 09/17/2020] [Indexed: 11/02/2022]
Abstract
New radiocarbon and sedimentological results from the Gulf of Alaska document recurrent millennial-scale episodes of reorganized Pacific Ocean ventilation synchronous with rapid Cordilleran Ice Sheet discharge, indicating close coupling of ice-ocean dynamics spanning the past 42,000 years. Ventilation of the intermediate-depth North Pacific tracks strength of the Asian monsoon, supporting a role for moisture and heat transport from low latitudes in North Pacific paleoclimate. Changes in carbon-14 age of intermediate waters are in phase with peaks in Cordilleran ice-rafted debris delivery, and both consistently precede ice discharge events from the Laurentide Ice Sheet, known as Heinrich events. This timing precludes an Atlantic trigger for Cordilleran Ice Sheet retreat and instead implicates the Pacific as an early part of a cascade of dynamic climate events with global impact.
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Affiliation(s)
- Maureen H Walczak
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA. .,Australian National University, Canberra ACT
| | - Alan C Mix
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Ellen A Cowan
- Department of Geological and Environmental Sciences, Appalachian State University, Boone, NC, USA
| | | | | | - Jay R Alder
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA.,United States Geological Survey, Corvallis, OR, USA
| | - Jianghui Du
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA.,Department of Earth Sciences, Institute of Geochemistry and Petrology, ETH Zurich, Zurich, Switzerland
| | - Brian Haley
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Tim Hobern
- Australian National University, Canberra ACT
| | - June Padman
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | | | - Andreas Schmittner
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Joseph S Stoner
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
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24
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Abstract
The global spread of parasites is unquestionably linked with human activities. Migration in all its different forms played a major role in the introduction of parasites into new areas. In ancient times, mass migrations were the main causes for the spread of parasites while in the recent past and present, emigration, immigration, displacement, external and internal migration, and labor migration were the reasons for the dispersal of parasites. With the advent of seagoing ships, long-distance trading became another important mode of spreading parasites. This review summarizes the spread of parasites using notable examples. In addition, the different hypotheses explaining the arrival of Plasmodium vivax and soil-transmitted helminths in pre-Columbian America are also discussed.
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Affiliation(s)
- Dietmar Steverding
- Bob Champion Research and Education Building, Norwich Medical School, University of East Anglia , Norwich, UK
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25
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The timing and effect of the earliest human arrivals in North America. Nature 2020; 584:93-97. [PMID: 32699413 DOI: 10.1038/s41586-020-2491-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
Abstract
The peopling of the Americas marks a major expansion of humans across the planet. However, questions regarding the timing and mechanisms of this dispersal remain, and the previously accepted model (termed 'Clovis-first')-suggesting that the first inhabitants of the Americas were linked with the Clovis tradition, a complex marked by distinctive fluted lithic points1-has been effectively refuted. Here we analyse chronometric data from 42 North American and Beringian archaeological sites using a Bayesian age modelling approach, and use the resulting chronological framework to elucidate spatiotemporal patterns of human dispersal. We then integrate these patterns with the available genetic and climatic evidence. The data obtained show that humans were probably present before, during and immediately after the Last Glacial Maximum (about 26.5-19 thousand years ago)2,3 but that more widespread occupation began during a period of abrupt warming, Greenland Interstadial 1 (about 14.7-12.9 thousand years before AD 2000)4. We also identify the near-synchronous commencement of Beringian, Clovis and Western Stemmed cultural traditions, and an overlap of each with the last dates for the appearance of 18 now-extinct faunal genera. Our analysis suggests that the widespread expansion of humans through North America was a key factor in the extinction of large terrestrial mammals.
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26
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Waters MR. Late Pleistocene exploration and settlement of the Americas by modern humans. SCIENCE (NEW YORK, N.Y.) 2020; 365:365/6449/eaat5447. [PMID: 31296740 DOI: 10.1126/science.aat5447] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
North and South America were the last continents to be explored and settled by modern humans at the end of the Pleistocene. Genetic data, derived from contemporary populations and ancient individuals, show that the first Americans originated from Asia and after several population splits moved south of the continental ice sheets that covered Canada sometime between ~17.5 and ~14.6 thousand years (ka) ago. Archaeological evidence shows that geographically dispersed populations lived successfully, using biface, blade, and osseous technologies, in multiple places in North and South America between ~15.5 and ~14 ka ago. Regional archaeological complexes emerged by at least ~13 ka ago in North America and ~12.9 ka ago in South America. Current genetic and archaeological data do not support an earlier (pre-17.5 ka ago) occupation of the Americas.
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Affiliation(s)
- Michael R Waters
- Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, College Station, TX 77843, USA
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27
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Davis LG, Madsen DB, Becerra-Valdivia L, Higham T, Sisson DA, Skinner SM, Stueber D, Nyers AJ, Keen-Zebert A, Neudorf C, Cheyney M, Izuho M, Iizuka F, Burns SR, Epps CW, Willis SC, Buvit I. Late Upper Paleolithic occupation at Cooper's Ferry, Idaho, USA, ~16,000 years ago. Science 2020; 365:891-897. [PMID: 31467216 DOI: 10.1126/science.aax9830] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 08/01/2019] [Indexed: 01/17/2023]
Abstract
Radiocarbon dating of the earliest occupational phases at the Cooper's Ferry site in western Idaho indicates that people repeatedly occupied the Columbia River basin, starting between 16,560 and 15,280 calibrated years before the present (cal yr B.P.). Artifacts from these early occupations indicate the use of unfluted stemmed projectile point technologies before the appearance of the Clovis Paleoindian tradition and support early cultural connections with northeastern Asian Upper Paleolithic archaeological traditions. The Cooper's Ferry site was initially occupied during a time that predates the opening of an ice-free corridor (≤14,800 cal yr B.P.), which supports the hypothesis that initial human migration into the Americas occurred via a Pacific coastal route.
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Affiliation(s)
- Loren G Davis
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR 97331, USA.
| | - David B Madsen
- Texas Archeological Research Laboratory, University of Texas, Austin, TX 78758, USA
| | - Lorena Becerra-Valdivia
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, School of Archaeology, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, School of Archaeology, 1 South Parks Road, Oxford OX1 3TG, UK
| | - David A Sisson
- Bureau of Land Management, Cottonwood Field Office, 2 Butte Drive, Cottonwood, ID 83522, USA
| | - Sarah M Skinner
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR 97331, USA
| | - Daniel Stueber
- University of Victoria, Department of Anthropology, P.O. Box 1700 STN CSC, Victoria, BC V8W 2Y2, Canada
| | | | - Amanda Keen-Zebert
- Division of Earth and Ecosystem Sciences, Desert Research Institute, 2215 Raggio Parkway, Reno, NV 89512, USA
| | - Christina Neudorf
- Division of Earth and Ecosystem Sciences, Desert Research Institute, 2215 Raggio Parkway, Reno, NV 89512, USA
| | - Melissa Cheyney
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR 97331, USA
| | - Masami Izuho
- Tokyo Metropolitan University, Faculty of Humanities and Social Sciences, 1-1 Minami-Osawa, Hachioji-shi, Tokyo, Japan 192-0397
| | - Fumie Iizuka
- Tokyo Metropolitan University, Faculty of Humanities and Social Sciences, 1-1 Minami-Osawa, Hachioji-shi, Tokyo, Japan 192-0397.,School of Social Sciences, Humanities and Arts, University of California, Merced, Merced, CA, USA
| | - Samuel R Burns
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR 97331, USA
| | - Clinton W Epps
- Oregon State University, Department of Fisheries and Wildlife, 104 Nash Hall, Corvallis, OR 97331, USA
| | - Samuel C Willis
- Oregon Parks and Recreation Department, Stewardship Section, 725 Summer Street, NE, Suite C, Salem, OR 97301, USA
| | - Ian Buvit
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR 97331, USA
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28
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Sawyer YE, MacDonald SO, Lessa EP, Cook JA. Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska. Ecol Evol 2019; 9:1777-1797. [PMID: 30847072 PMCID: PMC6392352 DOI: 10.1002/ece3.4861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Although islands are of long-standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high-latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for three mammals co-distributed along the North Pacific Coast. We examined variation in mitochondrial and nuclear loci for long-tailed voles (Microtus longicaudus), northwestern deermice (Peromyscus keeni), and dusky shrews (Sorex monticola), and then tested hypotheses derived from Species Distribution Models, reconstructions of paleoshorelines, and island area and isolation. In all three species, we identified paleoendemic clades that likely originated in coastal refugia, a finding consistent with other paleoendemic lineages identified in the region such as ermine. Although there is spatial concordance at the regional level for endemism, finer scale spatial and temporal patterns are less clearly defined. Demographic expansion across the region for these distinctive clades is also evident and highlights the dynamic history of Late Quaternary contraction and expansion that characterizes high-latitude species.
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Affiliation(s)
- Yadéeh E. Sawyer
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Stephen O. MacDonald
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Facultad de CienciasUniversidad de la RepúblicaMontevideoUruguay
| | - Joseph A. Cook
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
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29
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Grugni V, Raveane A, Ongaro L, Battaglia V, Trombetta B, Colombo G, Capodiferro MR, Olivieri A, Achilli A, Perego UA, Motta J, Tribaldos M, Woodward SR, Ferretti L, Cruciani F, Torroni A, Semino O. Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas. BMC Biol 2019; 17:3. [PMID: 30674303 PMCID: PMC6345020 DOI: 10.1186/s12915-018-0622-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two well-differentiated components originated and subsequently mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analysis of the Y-chromosome haplogroup Q, which is the only Pan-American haplogroup and accounts for virtually all Native American Y chromosomes in Mesoamerica and South America. RESULTS Our analyses of 1.5 Mb of 152 Y chromosomes, 34 re-sequenced in this work, support a "coastal and inland routes scenario" for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand years ago (kya), followed by a period of constant population size from 8 to 3 kya, after which a secondary sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainly revealed by haplogroup Q-Z780, suggest an entrance in South America prior to 15 kya. During the global constant population size phase, local South American hints of growth were registered by different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steady population growth and a single cohesive culture diffusion as it occurred in Europe. CONCLUSIONS We established and dated a detailed haplogroup Q phylogeny that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ugo A Perego
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Jorge Motta
- Secretaría Nacional de Ciencia, Tecnología e Innovación (SENACYT), Panama City, Panama
| | - Maribel Tribaldos
- Department of Health Technology Assessment and Economic Evaluation, Panama City, Panama
| | | | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.
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30
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Waters MR, Keene JL, Forman SL, Prewitt ER, Carlson DL, Wiederhold JE. Pre-Clovis projectile points at the Debra L. Friedkin site, Texas-Implications for the Late Pleistocene peopling of the Americas. SCIENCE ADVANCES 2018; 4:eaat4505. [PMID: 30397643 PMCID: PMC6200361 DOI: 10.1126/sciadv.aat4505] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/19/2018] [Indexed: 05/23/2023]
Abstract
Lanceolate projectile points of the Clovis complex and stemmed projectile points of the Western Stemmed Tradition first appeared in North America by ~13 thousand years (ka) ago. The origin, age, and chronological superposition of these stemmed and lanceolate traditions are unclear. At the Debra L. Friedkin site, Texas, below Folsom and Clovis horizons, we find stemmed projectile points dating from ~13.5 to ~15.5 ka ago, with a triangular lanceolate point form appearing ~14 ka ago. The sequential relationship of stemmed projectile points followed by lanceolate forms suggests that lanceolate points are derived from stemmed forms or that they originated from two separate migrations into the Americas.
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Affiliation(s)
- Michael R. Waters
- Center for the Study of the First Americans, Texas A&M University, College Station, TX 77843-4352, USA
- Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
- Corresponding author.
| | - Joshua L. Keene
- Center for the Study of the First Americans, Texas A&M University, College Station, TX 77843-4352, USA
- Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - Steven L. Forman
- Department of Geosciences and Institute of Archaeology, Baylor University, Waco, TX 76798, USA
| | - Elton R. Prewitt
- Texas Archeological Research Laboratory, University of Texas, Austin, TX 78712, USA
| | - David L. Carlson
- Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - James E. Wiederhold
- Center for the Study of the First Americans, Texas A&M University, College Station, TX 77843-4352, USA
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31
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Potter BA, Baichtal JF, Beaudoin AB, Fehren-Schmitz L, Haynes CV, Holliday VT, Holmes CE, Ives JW, Kelly RL, Llamas B, Malhi RS, Miller DS, Reich D, Reuther JD, Schiffels S, Surovell TA. Current evidence allows multiple models for the peopling of the Americas. SCIENCE ADVANCES 2018; 4:eaat5473. [PMID: 30101195 PMCID: PMC6082647 DOI: 10.1126/sciadv.aat5473] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/26/2018] [Indexed: 05/10/2023]
Abstract
Some recent academic and popular literature implies that the problem of the colonization of the Americas has been largely resolved in favor of one specific model: a Pacific coastal migration, dependent on high marine productivity, from the Bering Strait to South America, thousands of years before Clovis, the earliest widespread cultural manifestation south of the glacial ice. Speculations on maritime adaptations and typological links (stemmed points) across thousands of kilometers have also been advanced. A review of the current genetic, archeological, and paleoecological evidence indicates that ancestral Native American population expansion occurred after 16,000 years ago, consistent with the archeological record, particularly with the earliest securely dated sites after ~15,000 years ago. These data are largely consistent with either an inland (ice-free corridor) or Pacific coastal routes (or both), but neither can be rejected at present. Systematic archeological and paleoecological investigations, informed by geomorphology, are required to test each hypothesis.
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Affiliation(s)
- Ben A. Potter
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- Corresponding author.
| | - James F. Baichtal
- Tongass National Forest, U.S. Forest Service, Thorne Bay, AK 99919, USA
| | | | - Lars Fehren-Schmitz
- UCSC Paleogenomics Lab, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - C. Vance Haynes
- School of Anthropology and Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Vance T. Holliday
- School of Anthropology and Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Charles E. Holmes
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - John W. Ives
- Institute of Prairie Archaeology, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Robert L. Kelly
- Department of Anthropology, University of Wyoming, Laramie, WY 82071, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ripan S. Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - D. Shane Miller
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Starkville, MS 39759, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Joshua D. Reuther
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK 99775, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Todd A. Surovell
- Department of Anthropology, University of Wyoming, Laramie, WY 82071, USA
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