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Pezo-Lanfranco L, Mut P, Chávez J, Fossile T, Colonese AC, Fernandes R. South American Archaeological Isotopic Database, a regional-scale multi-isotope data compendium for research. Sci Data 2024; 11:336. [PMID: 38575659 PMCID: PMC10995213 DOI: 10.1038/s41597-024-03148-9] [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: 11/10/2023] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
The South American Archaeological Isotopic Database (SAAID) is a comprehensive open-access resource that aggregates all available bioarchaeological stable and radiogenic isotope measurements, encompassing data from human individuals, animals, and plants across South America. Resulting from a collaborative effort of scholars who work with stable isotopes in this region, SAAID contains 53,781 isotopic measurements across 24,507 entries from individuals/specimens spanning over 12,000 years. SAAID includes valuable contextual information on archaeological samples and respective sites, such as chronology, geographical region, biome, and spatial coordinates, biological details like estimated sex and age for human individuals, and taxonomic description for fauna and flora. SAAID is hosted at the PACHAMAMA community within the Pandora data platform and the CORA repository to facilitate easy access. Because of its rich data structure, SAAID is particularly well-suited for conducting spatiotemporal meta-analyses. It serves as a valuable tool for addressing a variety of research topics, including the spread, adoption, and consumption intensification of food items, paleo-environmental reconstruction, as well as the exploration of mobility patterns across extensive geographic regions.
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Affiliation(s)
- Luis Pezo-Lanfranco
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
- Department of Prehistory, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
| | - Patricia Mut
- Departamento de Antropología Biológica, Universidad de la República, Montevideo, Uruguay
| | - Juan Chávez
- Department of Anthropology, University of California, Riverside, USA
- Observatorio de Patrimonio Cultural y Arqueológico - Instituto de Investigaciones Antropológicas y Arqueológicas, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Thiago Fossile
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Department of Prehistory, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - André Carlo Colonese
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Department of Prehistory, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany.
- Faculty of Archaeology, University of Warsaw, Warsaw, Poland.
- Arne Faculty of Arts, Masaryk University, Brno, Czech Republic.
- Climate Change and History Research Initiative, Princeton University, Princeton, USA.
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Shadik CR, Bush MB, Valencia BG, Rozas-Davila A, Plekhov D, Breininger RD, Davin C, Benko L, Peterson LC, VanValkenburgh P. The Evolution of Agrarian Landscapes in the Tropical Andes. PLANTS (BASEL, SWITZERLAND) 2024; 13:1019. [PMID: 38611550 PMCID: PMC11013201 DOI: 10.3390/plants13071019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
Changes in land-use practices have been a central element of human adaptation to Holocene climate change. Many practices that result in the short-term stabilization of socio-natural systems, however, have longer-term, unanticipated consequences that present cascading challenges for human subsistence strategies and opportunities for subsequent adaptations. Investigating complex sequences of interaction between climate change and human land-use in the past-rather than short-term causes and effects-is therefore essential for understanding processes of adaptation and change, but this approach has been stymied by a lack of suitably-scaled paleoecological data. Through a high-resolution paleoecological analysis, we provide a 7000-year history of changing climate and land management around Lake Acopia in the Andes of southern Peru. We identify evidence of the onset of pastoralism, maize cultivation, and possibly cultivation of quinoa and potatoes to form a complex agrarian landscape by c. 4300 years ago. Cumulative interactive climate-cultivation effects resulting in erosion ended abruptly c. 2300 years ago. After this time, reduced sedimentation rates are attributed to the construction and use of agricultural terraces within the catchment of the lake. These results provide new insights into the role of humans in the manufacture of Andean landscapes and the incremental, adaptive processes through which land-use practices take shape.
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Affiliation(s)
- Courtney R. Shadik
- Institute of Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA (A.R.-D.); (L.B.)
| | - Mark B. Bush
- Institute of Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA (A.R.-D.); (L.B.)
| | - Bryan G. Valencia
- Facultad de Ciencias de La Tierra y Agua, Universidad Regional Amazónica Ikiam, Tena 150150, Ecuador;
| | - Angela Rozas-Davila
- Institute of Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA (A.R.-D.); (L.B.)
| | - Daniel Plekhov
- Department of Anthropology, Portland State University, Portland, OR 97201, USA;
| | - Robert D. Breininger
- Institute of Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA (A.R.-D.); (L.B.)
| | - Claire Davin
- Department of Mathematics, University of Richmond, Richmond, VA 23173, USA;
| | - Lindsay Benko
- Institute of Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA (A.R.-D.); (L.B.)
| | - Larry C. Peterson
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, USA;
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3
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Lawrence ES, Gu W, Bohlender RJ, Anza-Ramirez C, Cole AM, Yu JJ, Hu H, Heinrich EC, O’Brien KA, Vasquez CA, Cowan QT, Bruck PT, Mercader K, Alotaibi M, Long T, Hall JE, Moya EA, Bauk MA, Reeves JJ, Kong MC, Salem RM, Vizcardo-Galindo G, Macarlupu JL, Figueroa-Mujíca R, Bermudez D, Corante N, Gaio E, Fox KP, Salomaa V, Havulinna AS, Murray AJ, Malhotra A, Powel FL, Jain M, Komor AC, Cavalleri GL, Huff CD, Villafuerte FC, Simonson TS. Functional EPAS1/ HIF2A missense variant is associated with hematocrit in Andean highlanders. SCIENCE ADVANCES 2024; 10:eadj5661. [PMID: 38335297 PMCID: PMC10857371 DOI: 10.1126/sciadv.adj5661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories.
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Affiliation(s)
- Elijah S. Lawrence
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cecilia Anza-Ramirez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Amy M. Cole
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - James J. Yu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erica C. Heinrich
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Katie A. O’Brien
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Carlos A. Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T. Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Patrick T. Bruck
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Kysha Mercader
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Tao Long
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - James E. Hall
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marco A. Bauk
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer J. Reeves
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mitchell C. Kong
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Rany M. Salem
- Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gustavo Vizcardo-Galindo
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jose-Luis Macarlupu
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Rómulo Figueroa-Mujíca
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Daniela Bermudez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Noemi Corante
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Eduardo Gaio
- Laboratório de Fisiologia Respiratória, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Keolu P. Fox
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM-HiLIFE), Helsinki, Finland
| | - Andrew J. Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frank L. Powel
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mohit Jain
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco C. Villafuerte
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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4
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Chen JC, Aldenderfer MS, Eerkens JW, Langlie BS, Viviano Llave C, Watson JT, Haas R. Stable isotope chemistry reveals plant-dominant diet among early foragers on the Andean Altiplano, 9.0-6.5 cal. ka. PLoS One 2024; 19:e0296420. [PMID: 38265974 PMCID: PMC10807835 DOI: 10.1371/journal.pone.0296420] [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: 07/18/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024] Open
Abstract
Current models of early human subsistence economies suggest a focus on large mammal hunting. To evaluate this hypothesis, we examine human bone stable isotope chemistry of 24 individuals from the early Holocene sites of Wilamaya Patjxa (9.0-8.7 cal. ka) and Soro Mik'aya Patjxa (8.0-6.5 cal. ka) located at 3800 meters above sea level on the Andean Altiplano, Peru. Contrary to expectation, Bayesian mixing models based on the isotope chemistry reveal that plants dominated the diet, comprising 70-95% of the average diet. Paleoethnobotanical data further show that tubers may have been the most prominent subsistence resource. These findings update our understanding of earliest forager economies and the pathway to agricultural economies in the Andean highlands. The findings furthermore suggest that the initial subsistence economies of early human populations adapting to new landscapes may have been more plant oriented than current models suggest.
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Affiliation(s)
- Jennifer C. Chen
- Department of Anthropology, The Pennsylvania State University, State College, PA, United States of America
| | - Mark S. Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, CA, United States of America
| | - Jelmer W. Eerkens
- Department of Anthropology, University of California Davis, Davis, CA, United States of America
| | - BrieAnna S. Langlie
- Department of Anthropology, Binghamton University, Binghamton, NY, United States of America
| | | | - James T. Watson
- Arizona State Museum and School of Anthropology, University of Arizona, Tucson, AZ, United States of America
| | - Randall Haas
- Department of Anthropology, University of Wyoming, Laramie, WY, United States of America
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5
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Zhao Y, Xiong W, Li C, Zhao R, Lu H, Song S, Zhou Y, Hu Y, Shi B, Ge J. Hypoxia-induced signaling in the cardiovascular system: pathogenesis and therapeutic targets. Signal Transduct Target Ther 2023; 8:431. [PMID: 37981648 PMCID: PMC10658171 DOI: 10.1038/s41392-023-01652-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 11/21/2023] Open
Abstract
Hypoxia, characterized by reduced oxygen concentration, is a significant stressor that affects the survival of aerobic species and plays a prominent role in cardiovascular diseases. From the research history and milestone events related to hypoxia in cardiovascular development and diseases, The "hypoxia-inducible factors (HIFs) switch" can be observed from both temporal and spatial perspectives, encompassing the occurrence and progression of hypoxia (gradual decline in oxygen concentration), the acute and chronic manifestations of hypoxia, and the geographical characteristics of hypoxia (natural selection at high altitudes). Furthermore, hypoxia signaling pathways are associated with natural rhythms, such as diurnal and hibernation processes. In addition to innate factors and natural selection, it has been found that epigenetics, as a postnatal factor, profoundly influences the hypoxic response and progression within the cardiovascular system. Within this intricate process, interactions between different tissues and organs within the cardiovascular system and other systems in the context of hypoxia signaling pathways have been established. Thus, it is the time to summarize and to construct a multi-level regulatory framework of hypoxia signaling and mechanisms in cardiovascular diseases for developing more therapeutic targets and make reasonable advancements in clinical research, including FDA-approved drugs and ongoing clinical trials, to guide future clinical practice in the field of hypoxia signaling in cardiovascular diseases.
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Affiliation(s)
- Yongchao Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Weidong Xiong
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China
| | - Chaofu Li
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Ranzun Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Hao Lu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Shuai Song
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - You Zhou
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Yiqing Hu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
| | - Bei Shi
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
| | - Junbo Ge
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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Niclou A, Sarma M, Levy S, Ocobock C. To the extreme! How biological anthropology can inform exercise physiology in extreme environments. Comp Biochem Physiol A Mol Integr Physiol 2023; 284:111476. [PMID: 37423419 DOI: 10.1016/j.cbpa.2023.111476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
The fields of biological anthropology and exercise physiology are closely related and can provide mutually beneficial insights into human performance. These fields often use similar methods and are both interested in how humans function, perform, and respond in extreme environments. However, these two fields have different perspectives, ask different questions, and work within different theoretical frameworks and timescales. Biological anthropologists and exercise physiologists can greatly benefit from working together when examining human adaptation, acclimatization, and athletic performance in the extremes of heat, cold, and high-altitude. Here we review the adaptations and acclimatizations in these three different extreme environments. We then examine how this work has informed and built upon exercise physiology research on human performance. Finally, we present an agenda for moving forward, hopefully, with these two fields working more closely together to produce innovative research that improves our holistic understanding of human performance capacities informed by evolutionary theory, modern human acclimatization, and the desire to produce immediate and direct benefits.
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Affiliation(s)
- Alexandra Niclou
- Pennington Biomedical Research Center, Baton Rouge, LA, United States of America. https://twitter.com/fiat_luxandra
| | - Mallika Sarma
- Human Space Flight Lab, Johns Hopkins School of Medicine, Baltimore, MD, United States of America. https://twitter.com/skyy_mal
| | - Stephanie Levy
- Department of Anthropology, CUNY Hunter College, New York, NY, United States of America; New York Consortium in Evolutionary Primatology, New York, NY, United States of America. https://twitter.com/slevyscience
| | - Cara Ocobock
- University of Notre Dame Department of Anthropology, Notre Dame, IN, United States of America; Eck Institute for Global Health, Institute for Educational Initiatives, University of Notre Dame, United States of America.
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Jorgensen K, Song D, Weinstein J, Garcia OA, Pearson LN, Inclán M, Rivera-Chira M, León-Velarde F, Kiyamu M, Brutsaert TD, Bigham AW, Lee FS. High-Altitude Andean H194R HIF2A Allele Is a Hypomorphic Allele. Mol Biol Evol 2023; 40:msad162. [PMID: 37463421 PMCID: PMC10370452 DOI: 10.1093/molbev/msad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
For over 10,000 years, Andeans have resided at high altitude where the partial pressure of oxygen challenges human survival. Recent studies have provided evidence for positive selection acting in Andeans on the HIF2A (also known as EPAS1) locus, which encodes for a central transcription factor of the hypoxia-inducible factor pathway. However, the precise mechanism by which this allele might lead to altitude-adaptive phenotypes, if any, is unknown. By analyzing whole genome sequencing data from 46 high-coverage Peruvian Andean genomes, we confirm evidence for positive selection acting on HIF2A and a unique pattern of variation surrounding the Andean-specific single nucleotide variant (SNV), rs570553380, which encodes for an H194R amino acid substitution in HIF-2α. Genotyping the Andean-associated SNV rs570553380 in a group of 299 Peruvian Andeans from Cerro de Pasco, Peru (4,338 m), reveals a positive association with increased fraction of exhaled nitric oxide, a marker of nitric oxide biosynthesis. In vitro assays show that the H194R mutation impairs binding of HIF-2α to its heterodimeric partner, aryl hydrocarbon receptor nuclear translocator. A knockin mouse model bearing the H194R mutation in the Hif2a gene displays decreased levels of hypoxia-induced pulmonary Endothelin-1 transcripts and protection against hypoxia-induced pulmonary hypertension. We conclude the Andean H194R HIF2A allele is a hypomorphic (partial loss of function) allele.
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Affiliation(s)
- Kelsey Jorgensen
- Department of Anthropology, University of California, Los Angeles, CA, USA
| | - Daisheng Song
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julien Weinstein
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Obed A Garcia
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Laurel N Pearson
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - María Inclán
- División de. Estudios Políticos, Centro de Investigación y Docencia Económicas, Mexico City, CDMX, Mexico
| | - Maria Rivera-Chira
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Fabiola León-Velarde
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Melisa Kiyamu
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Tom D Brutsaert
- Department of Exercise Science, Syracuse University, Syracuse, NY, USA
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles, CA, USA
| | - Frank S Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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8
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Amaru R, Song J, Reading NS, Gordeuk VR, Prchal JT. "What We Know and What We Do Not Know about Evolutionary Genetic Adaptation to High Altitude Hypoxia in Andean Aymaras". Genes (Basel) 2023; 14:640. [PMID: 36980912 PMCID: PMC10048644 DOI: 10.3390/genes14030640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Three well-studied populations living at high altitudes are Tibetans, Andeans (Aymaras and Quechuas), and Ethiopians. Unlike Tibetans and Ethiopians who have similar hemoglobin (Hb) levels as individuals living at sea level, Aymara Hb levels increase when living at higher altitudes. Our previous whole genome study of Aymara people revealed several selected genes that are involved in cardiovascular functions, but their relationship with Hb levels was not elucidated. Here, we studied the frequencies of known evolutionary-selected variants in Tibetan and Aymara populations and their correlation with high Hb levels in Aymara. We genotyped 177 Aymaras at three different altitudes: 400 m (Santa Cruz), 4000 m (La Paz), and 5000 m (Chorolque), and correlated the results with the elevation of residence. Some of the Tibetan-selected variants also exist in Aymaras, but at a lower prevalence. Two of 10 Tibetan selected variants of EPAS1 were found (rs13005507 and rs142764723) and these variants did not correlate with Hb levels. Allele frequencies of 5 Aymara selected SNPs (heterozygous and homozygous) at 4000 m (rs11578671_BRINP3, rs34913965_NOS2, rs12448902_SH2B1, rs10744822_TBX5, and rs487105_PYGM) were higher compared to Europeans. The allelic frequencies of rs11578671_BRINP3, rs34913965_NOS2, and rs10744822_SH2B1 were significantly higher for Aymaras living at 5000 m than those at 400 m elevation. Variant rs11578671, close to the BRINP3 coding region, correlated with Hb levels in females. Variant rs34913965 (NOS2) correlated with leukocyte counts. Variants rs12448902 (SH2B1) and rs34913965 (NOS2) associated with higher platelet levels. The correlation of these SNPs with blood cell counts demonstrates that the selected genetic variants in Aymara influence hematopoiesis and cardiovascular effects.
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Affiliation(s)
- Ricardo Amaru
- Cell Biology Unit, School of Medicine, San Andres University, La Paz 0201, Bolivia
| | - Jihyun Song
- Division of Hematology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - N. Scott Reading
- Division of Hematology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
- Department of Pathology-ARUP Laboratories, University of Utah, Salt Lake City, UT 84132, USA
| | - Victor R. Gordeuk
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 61820, USA
| | - Josef T. Prchal
- Division of Hematology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
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9
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Joseph SK, Migliore NR, Olivieri A, Torroni A, Owings AC, DeGiorgio M, Ordóñez WG, Aguilú JO, González-Andrade F, Achilli A, Lindo J. Genomic evidence for adaptation to tuberculosis in the Andes before European contact. iScience 2023; 26:106034. [PMID: 36824277 PMCID: PMC9941198 DOI: 10.1016/j.isci.2023.106034] [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] [Received: 07/13/2022] [Revised: 11/11/2022] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
Most studies focusing on human high-altitude adaptation in the Andean highlands have thus far been focused on Peruvian populations. We present high-coverage whole genomes from Indigenous people living in the Ecuadorian highlands and perform multi-method scans to detect positive natural selection. We identified regions of the genome that show signals of strong selection to both cardiovascular and hypoxia pathways, which are distinct from those uncovered in Peruvian populations. However, the strongest signals of selection were related to regions of the genome that are involved in immune function related to tuberculosis. Given our estimated timing of this selection event, the Indigenous people of Ecuador may have adapted to Mycobacterium tuberculosis thousands of years before the arrival of Europeans. Furthermore, we detect a population collapse that coincides with the arrival of Europeans, which is more severe than other regions of the Andes, suggesting differing effects of contact across high-altitude populations.
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Affiliation(s)
- Sophie K. Joseph
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Amanda C. Owings
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | | | | | - Fabricio González-Andrade
- Translational Medicine Unit, Central University of Ecuador, Faculty of Medical Sciences, Iquique N14-121 y Sodiro-Itchimbia, Sector El Dorado, 170403 Quito, Ecuador,Corresponding author
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia 27100, Italy,Corresponding author
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA,Corresponding author
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10
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Zila-Velasque JP, Grados-Espinoza P, Morán-Mariños C, Morales Pocco KO, Capcha-Jimenez US, Ortiz-Benique ZN. Adaptation and altitude sickness: A 40-year bibliometric analysis and collaborative networks. Front Public Health 2023; 11:1069212. [PMID: 36935697 PMCID: PMC10018125 DOI: 10.3389/fpubh.2023.1069212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction We analyze the scientific production and collaboration networks of studies based on adaptation and altitude diseases in the period 1980-2020. Methods The publications were extracted from journals indexed in Scopus. The bibliometric analysis was used to analyze the scientific production, including the number of annual publications, the documents, and the characteristics of the publications. With the VOSviewer software, the analysis of collaborative networks, productivity of the countries, as well as the analysis of the co-occurrence of keywords were visualized. Results 15,240 documents were registered, of which 3,985 documents were analyzed. A significant trend was observed in the number of publications (R 2: 0.9847; P: < 0.001), with annual growth of 4.6%. The largest number of publications were original articles (77.8%), these published more frequently in the journal "Altitude Medicine and Biology". The largest number of countries were from Europe and Asia; however, the largest collaboration network was with the United States. Of the countries with high altitudes, China and Peru ranked first in scientific productivity. The research priorities were on the adaptation mechanism (37.1%), mainly anoxia and respiratory function. Acute mountain sickness (18.4%) and pulmonary edema (14.7%) were the most reported diseases. Of the top 10 institutions, "University of Colorado" and "Universidad Peruana Cayetano Heredia" contributed more than 100 publications. Conclusions Scientific production on adaptation and altitude illnesses continues to grow. The United States and United Kingdom present collaborative networks with high-altitude countries. The research is aimed at studying the mechanisms of adaptation to altitude and acute mountain sickness.
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Affiliation(s)
- J. Pierre Zila-Velasque
- Red Latinoamericana de Medicina en la Altitud e Investigación, Pasco, Peru
- Facultad de Medicina Humana, Universidad Nacional Daniel Alcides Carrión, Pasco, Peru
- Unidad de Investigación en Bibliometría, Vicerrectorado de Investigación, Universidad San Ignacio de Loyola, Lima, Peru
| | - Pamela Grados-Espinoza
- Red Latinoamericana de Medicina en la Altitud e Investigación, Pasco, Peru
- Facultad de Medicina Humana, Universidad Nacional Daniel Alcides Carrión, Pasco, Peru
| | - Cristian Morán-Mariños
- Unidad de Investigación en Bibliometría, Vicerrectorado de Investigación, Universidad San Ignacio de Loyola, Lima, Peru
- Servicio de Neumología, Hospital Nacional Dos de Mayo, Lima, Peru
- Red de Eficacia Clinica y Sanitaria (REDECS), Lima, Peru
- *Correspondence: Cristian Morán-Mariños
| | - Kevin O. Morales Pocco
- Red Latinoamericana de Medicina en la Altitud e Investigación, Pasco, Peru
- Universidad Nacional del Altiplano Puno, Puno, Peru
- Asociación Científica de Estudiantes de Medicina – UNAP, Puno, Peru
| | - Uriel S. Capcha-Jimenez
- Red Latinoamericana de Medicina en la Altitud e Investigación, Pasco, Peru
- Facultad de Medicina, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Sociedad Científica de San Fernando, Lima, Peru
| | - Zhamanda N. Ortiz-Benique
- Red Latinoamericana de Medicina en la Altitud e Investigación, Pasco, Peru
- Facultad de Medicina, Universidad Nacional de San Agustín, Arequipa, Peru
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11
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Yu JJ, Non AL, Heinrich EC, Gu W, Alcock J, Moya EA, Lawrence ES, Tift MS, O'Brien KA, Storz JF, Signore AV, Khudyakov JI, Milsom WK, Wilson SM, Beall CM, Villafuerte FC, Stobdan T, Julian CG, Moore LG, Fuster MM, Stokes JA, Milner R, West JB, Zhang J, Shyy JY, Childebayeva A, Vázquez-Medina JP, Pham LV, Mesarwi OA, Hall JE, Cheviron ZA, Sieker J, Blood AB, Yuan JX, Scott GR, Rana BK, Ponganis PJ, Malhotra A, Powell FL, Simonson TS. Time Domains of Hypoxia Responses and -Omics Insights. Front Physiol 2022; 13:885295. [PMID: 36035495 PMCID: PMC9400701 DOI: 10.3389/fphys.2022.885295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context of high-altitude exposure, cardiopulmonary disease, and sleep apnea), and how findings from each of these fields inform the other and lead to promising new directions in basic and clinical hypoxia research.
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Affiliation(s)
- James J. Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Amy L. Non
- Department of Anthropology, Division of Social Sciences, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Amy L. Non, Tatum S. Simonson,
| | - Erica C. Heinrich
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, United States
| | - Wanjun Gu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, MX, United States
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Elijah S. Lawrence
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Michael S. Tift
- Department of Biology and Marine Biology, College of Arts and Sciences, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Katie A. O'Brien
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Department of Physiology, Development and Neuroscience, Faculty of Biology, School of Biological Sciences, University of Cambridge, Cambridge, ENG, United Kingdom
| | - Jay F. Storz
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Anthony V. Signore
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Jane I. Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, United States
| | | | - Sean M. Wilson
- Lawrence D. Longo, MD Center for Perinatal Biology, Loma Linda, CA, United States
| | | | | | | | - Colleen G. Julian
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lorna G. Moore
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Aurora, CO, United States
| | - Mark M. Fuster
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jennifer A. Stokes
- Department of Kinesiology, Southwestern University, Georgetown, TX, United States
| | - Richard Milner
- San Diego Biomedical Research Institute, San Diego, CA, United States
| | - John B. West
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jiao Zhang
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - John Y. Shyy
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - José Pablo Vázquez-Medina
- Department of Integrative Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States
| | - Luu V. Pham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Omar A. Mesarwi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - James E. Hall
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Zachary A. Cheviron
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT, United States
| | - Jeremy Sieker
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Arlin B. Blood
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Jason X. Yuan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Graham R. Scott
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Brinda K. Rana
- Moores Cancer Center, UC San Diego, La Jolla, CA, United States,Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - Paul J. Ponganis
- Center for Marine Biotechnology and Biomedicine, La Jolla, CA, United States
| | - Atul Malhotra
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Frank L. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Amy L. Non, Tatum S. Simonson,
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12
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Bush MB, Rozas-Davila A, Raczka M, Nascimento M, Valencia B, Sales RK, McMichael CNH, Gosling WD. A palaeoecological perspective on the transformation of the tropical Andes by early human activity. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200497. [PMID: 35249394 PMCID: PMC8899620 DOI: 10.1098/rstb.2020.0497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Palaeoecological records suggest that humans have been in the Andes since at least 14 000 years ago. Early human impacts on Andean ecosystems included an increase in fire activity and the extinction of the Pleistocene megafauna. These changes in Andean ecosystems coincided with rapid climate change as species were migrating upslope in response to deglacial warming. Microrefugia probably played a vital role in the speed and genetic composition of that migration. The period from ca 14 500 to 12 500 years ago was when novel combinations of plant species appeared to form no-analogue assemblages in the Andes. By 12 000 years ago most areas in what are today the Andean grasslands were being burned and modified by human activity. As the vegetation of these highland settings has been modified by human activity for the entirety of the Holocene, they should be regarded as long-term manufactutred landscapes. The sharp tree lines separating Andean forests from grasslands that we see today were probably also created by repeated burning and owe their position more to human-induced fire than climatic constraints. In areas that were readly penetrated by humans on the forested slopes of the Andes, substantial modification and settlement had occurred by the mid-Holocene. In hard-to-reach areas, however, the amount of human modification may always have been minimal, and these slopes can be considered as being close to natural in their vegetation. This article is part of the theme issue 'Tropical forests in the deep human past'.
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Affiliation(s)
- M B Bush
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - A Rozas-Davila
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - M Raczka
- Department of Geography and Environmental Science, University of Reading, Whiteknights, Reading, Berkshire RG6 6AH, UK
| | - M Nascimento
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, Netherlands
| | - B Valencia
- Facultad de Ciencias de la Tierra y Agua, Ciencias de la Tierra y Clima, Universidad Regional Amazónica Ikiam, Tena, Ecuador
| | - R K Sales
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - C N H McMichael
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, Netherlands
| | - W D Gosling
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, Netherlands
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13
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Sales RK, McMichael CNH, Flantua SGA, Hagemans K, Zondervan JR, González-Arango C, Church WB, Bush MB. Potential distributions of pre-Columbian people in Tropical Andean landscapes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200502. [PMID: 35249384 PMCID: PMC8899625 DOI: 10.1098/rstb.2020.0502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Much has yet to be learned of the spatial patterning of pre-Columbian people across the Tropical Andes. Using compiled archaeological data and a suite of environmental variables, we generate an ensemble species distribution model (SDM) that incorporates general additive models, random forest models and Maxent models to reconstruct spatial patterns of pre-Columbian people that inhabited the Tropical Andes east of the continental divide, within the modern countries of Bolivia, Peru and Ecuador. Within this region, here referred to as the eastern Andean flank, elevation, mean annual cloud frequency, distance to rivers and precipitation of the driest quarter are the environmental variables most closely related to human occupancy. Our model indicates that 11.04% of our study area (65 368 km2) was likely occupied by pre-Columbian people. Our model shows that 30 of 351 forest inventory plots, which are used to generate ecological understanding of Andean ecosystems, were likely occupied in the pre-Columbian period. In previously occupied sites, successional trajectories may still be shaping forest dynamics, and those forests may still be recovering from the ecological legacy of pre-Columbian impacts. Our ensemble SDM links palaeo- and neo-ecology and can also be used to guide both future archaeological and ecological studies. This article is part of the theme issue 'Tropical forests in the deep human past'.
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Affiliation(s)
- Rachel K Sales
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Crystal N H McMichael
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Suzette G A Flantua
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Department of Biological Sciences, University of Bergen, PO Box 7803, Bergen, Norway
| | - Kimberley Hagemans
- Department of Physical Geography, Faculty of Geosciences, Utrecht University, Princetonlaan 8a, 3584 CB, Utrecht, The Netherlands
| | - Jesse R Zondervan
- School of Geography, Earth, and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, UK.,Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | | | - Warren B Church
- Department of Earth and Space Sciences, Columbus State University, Columbus, GA 31907, USA
| | - Mark B Bush
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA
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14
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Beckman EJ, Martins F, Suzuki TA, Bi K, Keeble S, Good JM, Chavez AS, Ballinger MA, Agwamba K, Nachman MW. The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America. Genetics 2022; 220:iyab226. [PMID: 34897431 PMCID: PMC9097263 DOI: 10.1093/genetics/iyab226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/04/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely nonoverlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans.
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Affiliation(s)
- Elizabeth J Beckman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Felipe Martins
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Taichi A Suzuki
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
- Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Evolution, Ecology, and Organismal Biology and the Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Mallory A Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kennedy Agwamba
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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15
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Kun Á. Is there still evolution in the human population? Biol Futur 2022; 73:359-374. [PMID: 36592324 PMCID: PMC9806833 DOI: 10.1007/s42977-022-00146-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/08/2022] [Indexed: 01/03/2023]
Abstract
It is often claimed that humanity has stopped evolving because modern medicine erased all selection on survival. Even if that would be true, and it is not, there would be other mechanisms of evolution which could still led to changes in allelic frequencies. Here I show, by applying basic evolutionary genetics knowledge, that we expect humanity to evolve. The results from genome sequencing projects have repeatedly affirmed that there are still recent signs of selection in our genomes. I give some examples of such adaptation. Then I briefly discuss what our evolutionary future has in store for us.
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Affiliation(s)
- Ádám Kun
- grid.5591.80000 0001 2294 6276Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary ,Parmenides Center for the Conceptual Foundations of Science, Pöcking, Germany ,grid.481817.3Institute of Evolution, Centre for Ecological Research, Budapest, Hungary ,grid.5018.c0000 0001 2149 4407MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary ,grid.5018.c0000 0001 2149 4407MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary
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16
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Basak N, Thangaraj K. High-altitude adaptation: Role of genetic and epigenetic factors. J Biosci 2021. [DOI: 10.1007/s12038-021-00228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Jiang X, He Y, Shen Q, Duan L, Yuan Y, Tang L, Shi Y, Liu B, Zhai H, Shi P, Yang C, Chen Y. RETSAT Mutation Selected for Hypoxia Adaptation Inhibits Tumor Growth. Front Cell Dev Biol 2021; 9:744992. [PMID: 34805153 PMCID: PMC8601408 DOI: 10.3389/fcell.2021.744992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/18/2021] [Indexed: 12/14/2022] Open
Abstract
Hypoxia occurs not only in natural environments including high altitude, underground burrows and deep sea, but also in human pathological conditions, such as hypoxic solid tumors. It has been well documented that hypoxia related signaling pathway is associated with a poor clinical outcome. Our group has recently identified multiple novel genes critical for solid tumor growth comparing the genome-wide convergent/parallel sequence evolution of highland mammals. Among them, a single mutation on the retinol saturase gene (RETSAT) containing amino acid switch from glutamine (Q) to arginine (R) at the position 247 was identified. Here, we demonstrate that RETSAT is mostly downregulated in multiple types of human cancers, whose lower expression correlates with worse clinical outcome. We show that higher expression of RETSAT is positively associated with immune infiltration in different human cancers. Furthermore, we identify that the promoter region of RETSAT is highly methylated, which leads to its decreased expressions in tumor tissues comparing to normal tissues. Furthermore, we show that RETSAT knockdown promotes, while its overexpression inhibits, the cell proliferation ability of mouse embryonic fibroblasts (MEFs) and B16 in vitro. In addition, the mice carrying homozygous Q247R mutation (RETSATR/R) is more resistant to xenograft tumor formation, as well as DMBA/TPA induced cutaneous keratinocyte carcinoma formation, compared to littermate wild-type (RETSATQ/Q) mice. Mechanistic study uncovers that the oncogenic factor, the prolyl isomerase (PPIase) Pin1 and its related downstream signaling pathway, were both markedly repressed in the mutant mice compared to the wild-type mice. In summary, these results suggest that interdisciplinary study between evolution and tumor biology can facilitate identification of novel molecular events essential for hypoxic solid tumor growth in the future.
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Affiliation(s)
- Xiulin Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yaomei He
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Qiushuo Shen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Lincan Duan
- The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yixiao Yuan
- The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lin Tang
- The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yulin Shi
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Baiyang Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Haoqing Zhai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Cuiping Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yongbin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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18
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Gangwar A, Paul S, Arya A, Ahmad Y, Bhargava K. Altitude acclimatization via hypoxia-mediated oxidative eustress involves interplay of protein nitrosylation and carbonylation: A redoxomics perspective. Life Sci 2021; 296:120021. [PMID: 34626604 DOI: 10.1016/j.lfs.2021.120021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 12/17/2022]
Abstract
AIM Hypoxia is an important feature of multiple diseases like cancer and obesity and also an environmental stressor to high altitude travelers. Emerging research suggests the importance of redox signaling in physiological responses transforming the notion of oxidative stress into eustress and distress. However, the behavior of redox protein post-translational modifications (PTMs), and their correlation with stress acclimatization in humans remains sketchy. Scant information exists about modifications in redoxome during physiological exposure to environmental hypoxia. In this study, we investigated redox PTMs, nitrosylation and carbonylation, in context of extended environmental hypoxia exposure. METHODS The volunteers were confirmed to be free of any medical conditions and matched for age and weight. The human global redoxome and the affected networks were investigated using TMT-labeled quantitative proteo-bioinformatics and biochemical assays. The percolator PSM algorithm was used for peptide-spectrum match (PSM) validation in database searches. The FDR for peptide matches was set to 0.01. 1-way ANOVA and Tukey's Multiple Comparison test were used for biochemical assays. p-value<0.05 was considered statistically significant. Three independent experiments (biological replicates) were performed. Results were presented as Mean ± standard error of mean (SEM). KEY FINDINGS This investigation revealed direct and indirect interplay between nitrosylation and carbonylation especially within coagulation and inflammation networks; interlinked redox signaling (via nitrosylation‑carbonylation); and novel nitrosylation and carbonylation sites in individual proteins. SIGNIFICANCE This study elucidates the role of redox PTMs in hypoxia signaling favoring tolerance and survival. Also, we demonstrated direct and indirect interplay between nitrosylation and carbonylation is crucial to extended hypoxia tolerance.
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Affiliation(s)
- Anamika Gangwar
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India
| | - Subhojit Paul
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India
| | - Aditya Arya
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India
| | - Yasmin Ahmad
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India.
| | - Kalpana Bhargava
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India.
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19
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Jacovas VC, Michita RT, Bisso-Machado R, Reales G, Tarazona-Santos EM, Sandoval JR, Salazar-Granara A, Chies JAB, Bortolini MC. HLA-G 3'UTR haplotype frequencies in highland and lowland South Native American populations. Hum Immunol 2021; 83:27-38. [PMID: 34563386 DOI: 10.1016/j.humimm.2021.09.002] [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: 03/18/2021] [Revised: 08/09/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022]
Abstract
Human Leukocyte Antigen (HLA)-G participates in several biological processes, including reproduction, vascular remodeling, immune tolerance, and hypoxia response. HLA-G is a potential candidate gene for high altitude adaptation since its expression is modulated in both micro and macro environment under hypoxia and constant cellular stress. Besides the promoter region, the HLA-G 3'untranslated region (UTR) influences HLA-G expression patterns through several post-transcriptional mechanisms. Currently, the 3'UTR genetic diversity in terms of altitude adaptation of Native American populations is still unexplored, particularly at high altitude ecoregions. Here, we evaluated 288 Native Americans from 9 communities located in the Andes [highland (HL); ≥2,500 m (range = 2,838-4,433 m)] and 8 populations located in lowland (LL) regions [<2,500 m (range = 80-431 m); Amazonian tropical forest, Brazilian central plateau, and Chaco] of South America. In total, nine polymorphic sites and ten haplotypes were observed. The most frequent haplotypes (UTR-1, UTR-2, and UTR-3) accounted for ∼ 77% of haplotypes found in LL, while in the HL, the same haplotypes reach ∼ 93%. Also, a remarkable high frequency of putative ancestral UTR-5 haplotype was observed in LL (21.5%), while in HL UTR-2 reaches up to 47%. Further, UTR-2 frequency positively correlates with altitude-related variables, while a negative correlation for UTR-5 was observed. From an evolutionary perspective, we observed a tendency towards balancing selection in HL and LL populations thus suggesting that haplotypes of ancient and more derived alleles may have been co-opted for relatively recent adaptations such as those experienced by modern humans in the highland and lowland of South America. We also discuss how long-term balancing selection can be a reservoir of genetic variants that can be positively selected. Finally, our study provides some pieces of evidence that HLA-G 3'UTR haplotypes may have contributed to high altitude adaptation in the Andes.
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Affiliation(s)
- Vanessa Cristina Jacovas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rafael Tomoya Michita
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Human Molecular Genetics Laboratory, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, Brazil
| | - Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Guillermo Reales
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Eduardo M Tarazona-Santos
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - José Raul Sandoval
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | | | - José Artur Bogo Chies
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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20
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The History and Driving Force for Prehistoric Human Expansion Upward to the Hinterland of the Tibetan Plateau Post–Last Glacial Maximum. SUSTAINABILITY 2021. [DOI: 10.3390/su13137065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The timing and motivation of prehistoric human expansion into the hinterland of the Tibetan Plateau (TP) is a widely debated scientific issue. Recent archaeological studies have brought forward predictions of the earliest human occupation of the TP to the late–Middle Pleistocene. However, massive human occupation of the TP did not appear until the termination of the Last Glacial Maximum (LGM). The spatio-temporal distribution of prehistoric hunter-gatherers on the TP varies significantly before the permanent occupation after 3600 BP (before present). Here, we report on environmental-archaeological evidence from the Canxionggashuo (CXGS) site in Yushu Prefecture, which provides information that is key to understanding the dynamics of post-LGM human occupation on the TP. Radiocarbon dating has revealed two occupation periods of the CXGS site at 8600–7100 cal (calibrated years) BP and 2400–2100 cal BP. The charcoal concentration in cultural layers correlates well with paleo–human activities. Hunter-gatherers expanded westwards from the northeastern margin of the TP to the hinterland of the TP during the warming period of the early–middle Holocene (~11,500–6000 BP). However, these groups retreated during the middle–late Holocene (~6000–3600 BP) under a cooling-drying climate. Prehistoric humans finally occupied the hinterland of the TP permanently after 3600 BP, with an enhanced cold-adaptive lifestyle, although the climate was still deteriorating.
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21
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García A, Nores R, Motti JMB, Pauro M, Luisi P, Bravi CM, Fabra M, Gosling AL, Kardailsky O, Boocock J, Solé-Morata N, Matisoo-Smith EA, Comas D, Demarchi DA. Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America. Hum Mol Genet 2021; 30:1200-1217. [PMID: 33856032 DOI: 10.1093/hmg/ddab105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/15/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.
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Affiliation(s)
- Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Rodrigo Nores
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Josefina M B Motti
- FACSO (NEIPHPA), Universidad Nacional del Centro de la Provincia de Buenos Aires, CONICET, Quequén 7631, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET, CICPBA, Universidad Nacional de La Plata, La Plata 1906, Argentina
| | - Mariana Fabra
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Anna L Gosling
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - James Boocock
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
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22
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Storz JF. High-Altitude Adaptation: Mechanistic Insights from Integrated Genomics and Physiology. Mol Biol Evol 2021; 38:2677-2691. [PMID: 33751123 PMCID: PMC8233491 DOI: 10.1093/molbev/msab064] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Population genomic analyses of high-altitude humans and other vertebrates have identified numerous candidate genes for hypoxia adaptation, and the physiological pathways implicated by such analyses suggest testable hypotheses about underlying mechanisms. Studies of highland natives that integrate genomic data with experimental measures of physiological performance capacities and subordinate traits are revealing associations between genotypes (e.g., hypoxia-inducible factor gene variants) and hypoxia-responsive phenotypes. The subsequent search for causal mechanisms is complicated by the fact that observed genotypic associations with hypoxia-induced phenotypes may reflect second-order consequences of selection-mediated changes in other (unmeasured) traits that are coupled with the focal trait via feedback regulation. Manipulative experiments to decipher circuits of feedback control and patterns of phenotypic integration can help identify causal relationships that underlie observed genotype–phenotype associations. Such experiments are critical for correct inferences about phenotypic targets of selection and mechanisms of adaptation.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
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23
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Lindo J, DeGiorgio M. Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics. Genes (Basel) 2021; 12:360. [PMID: 33801556 PMCID: PMC8001801 DOI: 10.3390/genes12030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/03/2022] Open
Abstract
The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.
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Affiliation(s)
- John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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24
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Arima H, Nakano M, Koirala S, Ito H, Pandey BD, Pandey K, Wada T, Yamamoto T. Unique hemoglobin dynamics in female Tibetan highlanders. Trop Med Health 2021; 49:2. [PMID: 33397517 PMCID: PMC7780399 DOI: 10.1186/s41182-020-00289-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tibetan highlanders have adapted to hypoxic environments through the development of unique mechanisms that suppress an increase in hemoglobin (Hb) concentration even in high-altitude areas. Hb concentrations generally decrease with increasing age. However, in the highlands, chronic altitude sickness is known to occur in the elderly population. To investigate how aging in a hypoxic environment affects Hb levels in Tibetan highlanders, we focused on the Mustang people, who live above 3500 m. We tried to clarify the pure relationship between aging and Hb levels in a hypoxic environment. RESULTS We found that the Hb concentration increased with increasing age in females but not in males. Multivariate analysis showed that age, pulse pressure, the poverty index, and vascular diameter were strongly correlated with the Hb concentration. CONCLUSIONS We found unique Hb dynamics among female Tibetan highlanders. As seen in these Hb dynamics, there may be sex-based differences in the adaptive mechanism in Tibetan highlanders.
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Affiliation(s)
- Hiroaki Arima
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masayuki Nakano
- Department of Nutrition, Faculty of Health Sciences, Kochi Gakuen University, Kochi, Japan
| | | | - Hiromu Ito
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Basu Dev Pandey
- Everest International Clinic and Research Center, Kathmandu, Nepal.,Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal
| | - Kishor Pandey
- Everest International Clinic and Research Center, Kathmandu, Nepal.,Nepal Academy of Science and Technology, Lalitpur, Nepal
| | - Takayuki Wada
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Graduate School of Human Life Science, Osaka City University, Osaka, Japan
| | - Taro Yamamoto
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan. .,Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan. .,Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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25
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Effect of EGLN1 Genetic Polymorphisms on Hemoglobin Concentration in Andean Highlanders. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3436581. [PMID: 33282944 PMCID: PMC7686849 DOI: 10.1155/2020/3436581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/03/2020] [Accepted: 10/15/2020] [Indexed: 11/20/2022]
Abstract
The physiological characteristics of Andean natives living at high altitudes have been investigated extensively, with many studies reporting that Andean highlanders have a higher hemoglobin (Hb) concentration than other highlander populations. It has previously been reported that positive natural selection has acted independently on the egl-9 family hypoxia inducible factor 1 (EGLN1) gene in Tibetan and Andean highlanders and is related to Hb concentration in Tibetans. However, no study has yet revealed the genetic determinants of Hb concentration in Andeans even though several single-nucleotide polymorphisms (SNPs) in EGLN1 have previously been examined. Therefore, we explored the relationship between hematological measurements and tag SNPs designed to cover the whole EGLN1 genomic region in Andean highlanders living in Bolivia. Our findings indicated that haplotype frequencies estimated from the EGLN1 SNPs were significantly correlated with Hb concentration in the Bolivian highlanders. Moreover, we found that an Andean-dominant haplotype related to high Hb level may have expanded rapidly in ancestral Andean highlander populations. Analysis of genotype data in an ~436.3 kb genomic region containing EGLN1 using public databases indicated that the population structure based on EGLN1 genetic markers in Andean highlanders was largely different from that in other human populations. This finding may be related to an intrinsic or adaptive physiological characteristic of Andean highlanders. In conclusion, the high Hb concentrations in Andean highlanders can be partly characterized by EGLN1 genetic variants.
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Karakostis FA, Reyes-Centeno H, Franken M, Hotz G, Rademaker K, Harvati K. Biocultural evidence of precise manual activities in an Early Holocene individual of the high-altitude Peruvian Andes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 174:35-48. [PMID: 33191560 DOI: 10.1002/ajpa.24160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/12/2020] [Accepted: 10/02/2020] [Indexed: 01/02/2023]
Abstract
OBJECTIVES Cuncaicha, a rockshelter site in the southern Peruvian Andes, has yielded archaeological evidence for human occupation at high elevation (4,480 masl) during the Terminal Pleistocene (12,500-11,200 cal BP), Early Holocene (9,500-9,000 cal BP), and later periods. One of the excavated human burials (Feature 15-06), corresponding to a middle-aged female dated to ~8,500 cal BP, exhibits skeletal osteoarthritic lesions previously proposed to reflect habitual loading and specialized crafting labor. Three small tools found in association with this burial are hypothesized to be associated with precise manual dexterity. MATERIALS AND METHODS Here, we tested this functional hypothesis through the application of a novel multivariate methodology for the three-dimensional analysis of muscle attachment surfaces (entheses). This original approach has been recently validated on both lifelong-documented anthropological samples as well as experimental studies in nonhuman laboratory samples. Additionally, we analyzed the three-dimensional entheseal shape and resulting moment arms for muscle opponens pollicis. RESULTS Results show that Cuncaicha individual 15-06 shows a distinctive entheseal pattern associated with habitual precision grasping via thumb-index finger coordination, which is shared exclusively with documented long-term precision workers from recent historical collections. The separate geometric morphometric analysis revealed that the individual's opponens pollicis enthesis presents a highly projecting morphology, which was found to strongly correlate with long joint moment arms (a fundamental component of force-producing capacity), closely resembling the form of Paleolithic hunter-gatherers from diverse geo-chronological contexts of Eurasia and North Africa. DISCUSSION Overall, our findings provide the first biocultural evidence to confirm that the lifestyle of some of the earliest Andean inhabitants relied on habitual and forceful precision grasping tasks.
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Affiliation(s)
- Fotios Alexandros Karakostis
- Paleoanthropology, Senckenberg Centre for Human Evolution and Palaeoenvironment, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Hugo Reyes-Centeno
- DFG (Deutsche Forschungsgemeinschaft) Center for Advanced Studies "Words, Bones, Genes, Tools," Eberhard Karls University of Tübingen, Tübingen, Germany.,Department of Anthropology, University of Kentucky, Lexington, Kentucky, USA.,William S. Webb Museum of Anthropology, University of Kentucky, Lexington, Kentucky, USA
| | - Michael Franken
- State Office for Cultural Heritage Baden-Württemberg, Osteology, Konstanz, Germany
| | - Gerhard Hotz
- Anthropological Collection, Natural History Museum of Basel, Basel, Switzerland.,Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
| | - Kurt Rademaker
- Department of Anthropology, College of Social Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Katerina Harvati
- Paleoanthropology, Senckenberg Centre for Human Evolution and Palaeoenvironment, Department of Geosciences, University of Tübingen, Tübingen, Germany.,DFG (Deutsche Forschungsgemeinschaft) Center for Advanced Studies "Words, Bones, Genes, Tools," Eberhard Karls University of Tübingen, Tübingen, Germany
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Haas R, Watson J, Buonasera T, Southon J, Chen JC, Noe S, Smith K, Llave CV, Eerkens J, Parker G. Female hunters of the early Americas. SCIENCE ADVANCES 2020; 6:6/45/eabd0310. [PMID: 33148651 PMCID: PMC7673694 DOI: 10.1126/sciadv.abd0310] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Sexual division of labor with females as gatherers and males as hunters is a major empirical regularity of hunter-gatherer ethnography, suggesting an ancestral behavioral pattern. We present an archeological discovery and meta-analysis that challenge the man-the-hunter hypothesis. Excavations at the Andean highland site of Wilamaya Patjxa reveal a 9000-year-old human burial (WMP6) associated with a hunting toolkit of stone projectile points and animal processing tools. Osteological, proteomic, and isotopic analyses indicate that this early hunter was a young adult female who subsisted on terrestrial plants and animals. Analysis of Late Pleistocene and Early Holocene burial practices throughout the Americas situate WMP6 as the earliest and most secure hunter burial in a sample that includes 10 other females in statistical parity with early male hunter burials. The findings are consistent with nongendered labor practices in which early hunter-gatherer females were big-game hunters.
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Affiliation(s)
- Randall Haas
- Department of Anthropology, University of California Davis, One Shields Ave., Davis, CA 95616, USA.
- Collasuyo Archaeological Research Institute, Jiron Nicaragua 199, Puno, Puno, Peru
| | - James Watson
- Arizona State Museum, The University of Arizona, 1013 E. University Blvd., Tucson, AZ 85721, USA
- School of Anthropology, The University of Arizona, 1009 E. South Campus Drive, Tucson, AZ 85721, USA
| | - Tammy Buonasera
- Department of Anthropology, University of California Davis, One Shields Ave., Davis, CA 95616, USA
- Department of Environmental Toxicology, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - John Southon
- W.M. Keck Carbon Cycle Accelerator Mass Spectrometer Facility, University of California Irvine, B321 Croul Hall, Irvine, CA 92697, USA
| | - Jennifer C Chen
- Department of Anthropology, Penn State University, 410 Carpenter Building, University Park, PA 16802, USA
| | - Sarah Noe
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Kevin Smith
- Department of Anthropology, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Carlos Viviano Llave
- Collasuyo Archaeological Research Institute, Jiron Nicaragua 199, Puno, Puno, Peru
| | - Jelmer Eerkens
- Department of Anthropology, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Glendon Parker
- Department of Environmental Toxicology, University of California Davis, One Shields Ave., Davis, CA 95616, USA
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Pamenter ME, Hall JE, Tanabe Y, Simonson TS. Cross-Species Insights Into Genomic Adaptations to Hypoxia. Front Genet 2020; 11:743. [PMID: 32849780 PMCID: PMC7387696 DOI: 10.3389/fgene.2020.00743] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Over millions of years, vertebrate species populated vast environments spanning the globe. Among the most challenging habitats encountered were those with limited availability of oxygen, yet many animal and human populations inhabit and perform life cycle functions and/or daily activities in varying degrees of hypoxia today. Of particular interest are species that inhabit high-altitude niches, which experience chronic hypobaric hypoxia throughout their lives. Physiological and molecular aspects of adaptation to hypoxia have long been the focus of high-altitude populations and, within the past decade, genomic information has become increasingly accessible. These data provide an opportunity to search for common genetic signatures of selection across uniquely informative populations and thereby augment our understanding of the mechanisms underlying adaptations to hypoxia. In this review, we synthesize the available genomic findings across hypoxia-tolerant species to provide a comprehensive view of putatively hypoxia-adaptive genes and pathways. In many cases, adaptive signatures across species converge on the same genetic pathways or on genes themselves [i.e., the hypoxia inducible factor (HIF) pathway). However, specific variants thought to underlie function are distinct between species and populations, and, in most cases, the precise functional role of these genomic differences remains unknown. Efforts to standardize these findings and explore relationships between genotype and phenotype will provide important clues into the evolutionary and mechanistic bases of physiological adaptations to environmental hypoxia.
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Affiliation(s)
- Matthew E. Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - James E. Hall
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Yuuka Tanabe
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
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29
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Toyne JM, Turner BL. Linking isotope analysis and paleopathology: An andean perspective. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2020; 29:117-127. [PMID: 32507722 DOI: 10.1016/j.ijpp.2019.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 10/24/2019] [Accepted: 11/15/2019] [Indexed: 06/11/2023]
Abstract
This paper reviews the significant advances in isotopic investigations in Andean South America and directs scholars to explore new theoretical and analytical directions, specifically the applicability of isotope data to paleopathology. Excellent preservation and large skeletal collections of human remains make the Central Andes ideal for biogeochemical reconstructions and advancements in isotopic methods. Our aims are twofold: first, we present a meta-analysis of stable and radiogenic isotope research in the Central Andes since 1985, and highlight those that combine analyses of isotope ratios and pathological conditions. Second, we discuss useful directions for incorporating stable isotope analysis more explicitly in studies of paleopathology in the Andes more in the future. Principle research foci have described dietary variation and regional population mobility since the 1980s, where early methodological explorations identified significant trends in isotopic variation. For the years 1980-2017, we identified 96 scholarly publications through a meta-data analysis of major peer-reviewed journals, book chapters, and conference proceedings. These demonstrate specific trends in topical and methodological preferences across the Andean region and a shift from 10 publications pre-1997 to 67 in the last 10 years. However, combined isotope and paleopathology studies in this region remain sparse; given the ecological, geological, and cultural complexity of the Central Andes, analyses of pathological conditions in different regions would significantly benefit from the information on diet, mobility, and local ecology that isotope ratios provide. Isotope analysis requires destruction of archaeological tissues, and interpreting isotope data can be complex, but it can also provide unique insights into the pathogenesis of multifactorial conditions and assist differential diagnosis. Therefore, we also discuss research designs for pairing isotopic and paleopathological variables that will allow researchers to better capture disease ecologies in archaeological samples and their variation across different regions, within related sites, and within individual lifespans.
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Affiliation(s)
- J Marla Toyne
- Department of Anthropology, University of Central Florida, Orlando, FL, 32803-1631, United States.
| | - Bethany L Turner
- Department of Anthropology, Georgia State University, PO Box 3998, Atlanta, GA 30302-3998, United States.
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Nakatsuka N, Lazaridis I, Barbieri C, Skoglund P, Rohland N, Mallick S, Posth C, Harkins-Kinkaid K, Ferry M, Harney É, Michel M, Stewardson K, Novak-Forst J, Capriles JM, Durruty MA, Álvarez KA, Beresford-Jones D, Burger R, Cadwallader L, Fujita R, Isla J, Lau G, Aguirre CL, LeBlanc S, Maldonado SC, Meddens F, Messineo PG, Culleton BJ, Harper TK, Quilter J, Politis G, Rademaker K, Reindel M, Rivera M, Salazar L, Sandoval JR, Santoro CM, Scheifler N, Standen V, Barreto MI, Espinoza IF, Tomasto-Cagigao E, Valverde G, Kennett DJ, Cooper A, Krause J, Haak W, Llamas B, Reich D, Fehren-Schmitz L. A Paleogenomic Reconstruction of the Deep Population History of the Andes. Cell 2020; 181:1131-1145.e21. [PMID: 32386546 PMCID: PMC7304944 DOI: 10.1016/j.cell.2020.04.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/11/2020] [Accepted: 04/13/2020] [Indexed: 02/03/2023]
Abstract
There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA.
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chiara Barbieri
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | | | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
| | - Jannine Novak-Forst
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - José M Capriles
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Marta Alfonso Durruty
- Department of Sociology, Anthropology and Social Work, Kansas State University, Manhattan, KS 66506, USA
| | | | - David Beresford-Jones
- McDonald Institute for Archaeological Research, University of Cambridge, Downing St., Cambridge, CB2 3ER, UK
| | - Richard Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lauren Cadwallader
- Office of Scholarly Communication, Cambridge University Library, Cambridge CB3 9DR, UK
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular, Facultdad de Medicina, Universidad de San Martín de Porres, Lima 15011, Peru
| | - Johny Isla
- Peruvian Ministry of Culture, DDC Ica, Directos of the Nasca-Palpa Management Plan, Calle Juan Matta 880, Nasca 11401, Peru
| | - George Lau
- Sainsbury Research Unit, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Carlos Lémuz Aguirre
- Carrera de Arqueología, Universidad Mayor de San Andrés, Edificio Facultad de Ciencias Sociales 3er Piso, La Paz 1995, Bolivia
| | - Steven LeBlanc
- Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA
| | - Sergio Calla Maldonado
- Carrera de Arqueología, Universidad Mayor de San Andrés, Edificio Facultad de Ciencias Sociales 3er Piso, La Paz 1995, Bolivia
| | - Frank Meddens
- School of Archaeology, Geography and Environmental Sciences, University of Reading, Reading, Berkshire, RG6 6AH, UK
| | - Pablo G Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Brendan J Culleton
- Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jeffrey Quilter
- Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | - Markus Reindel
- Commission for Archaeology of Non-European Cultures, German Archaeological Institute, Berlin 14195, Germany
| | - Mario Rivera
- Universidad de Magallanes, Punta Arenas 6210427, Chile; Field Museum Natural History 1400 S Lake Shore Dr., Chicago, IL 60605, USA
| | - Lucy Salazar
- McDonald Institute for Archaeological Research, University of Cambridge, Downing St., Cambridge, CB2 3ER, UK
| | - José R Sandoval
- Centro de Genética y Biología Molecular, Facultdad de Medicina, Universidad de San Martín de Porres, Lima 15011, Peru
| | - Calogero M Santoro
- Instituto de Alta Investigation, Universidad de Tarapaca, Antafogasta 1520, Arica, 1000000, Chile
| | - Nahuel Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Vivien Standen
- Departamento de Antropología, Universidad de Tarapacá, Antafogasta 1520, Arica, 1000000, Chile
| | - Maria Ines Barreto
- Museo de Sitio Huaca Pucllana, Calle General Borgoño, Cuadra 8, Miraflores, Lima 18, Peru
| | - Isabel Flores Espinoza
- Museo de Sitio Huaca Pucllana, Calle General Borgoño, Cuadra 8, Miraflores, Lima 18, Peru
| | - Elsa Tomasto-Cagigao
- Department of Humanities, Pontifical Catholic University of Peru, San Miguel 15088, Peru
| | - Guido Valverde
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Douglas J Kennett
- Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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Ossendorf G, Groos AR, Bromm T, Tekelemariam MG, Glaser B, Lesur J, Schmidt J, Akçar N, Bekele T, Beldados A, Demissew S, Kahsay TH, Nash BP, Nauss T, Negash A, Nemomissa S, Veit H, Vogelsang R, Woldu Z, Zech W, Opgenoorth L, Miehe G. Middle Stone Age foragers resided in high elevations of the glaciated Bale Mountains, Ethiopia. Science 2020; 365:583-587. [PMID: 31395781 DOI: 10.1126/science.aaw8942] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 06/26/2019] [Indexed: 01/28/2023]
Abstract
Studies of early human settlement in alpine environments provide insights into human physiological, genetic, and cultural adaptation potentials. Although Late and even Middle Pleistocene human presence has been recently documented on the Tibetan Plateau, little is known regarding the nature and context of early persistent human settlement in high elevations. Here, we report the earliest evidence of a prehistoric high-altitude residential site. Located in Africa's largest alpine ecosystem, the repeated occupation of Fincha Habera rock shelter is dated to 47 to 31 thousand years ago. The available resources in cold and glaciated environments included the exploitation of an endemic rodent as a key food source, and this played a pivotal role in facilitating the occupation of this site by Late Pleistocene hunter-gatherers.
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Affiliation(s)
- Götz Ossendorf
- Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany.
| | | | - Tobias Bromm
- Department of Soil Biogeochemistry, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Bruno Glaser
- Department of Soil Biogeochemistry, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
| | - Joséphine Lesur
- MNHN/CNRS-UMR 7209 Archaeozoology, Archaeobotany Laboratory (AASPE), Paris, France
| | - Joachim Schmidt
- Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Naki Akçar
- Institute of Geological Sciences, University of Bern, Bern, Switzerland
| | - Tamrat Bekele
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alemseged Beldados
- Department of Archaeology and Heritage Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Barbara P Nash
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, USA
| | - Thomas Nauss
- Faculty of Geography, Philipps University Marburg, Marburg, Germany
| | - Agazi Negash
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Heinz Veit
- Institute of Geography, University of Bern, Bern, Switzerland
| | - Ralf Vogelsang
- Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany
| | - Zerihun Woldu
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wolfgang Zech
- Institute of Soil Science and Soil Geography, University of Bayreuth, Bayreuth, Germany
| | - Lars Opgenoorth
- Department of Ecology, Philipps University Marburg, Marburg, Germany.,Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Georg Miehe
- Faculty of Geography, Philipps University Marburg, Marburg, Germany
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Barbieri C, Barquera R, Arias L, Sandoval JR, Acosta O, Zurita C, Aguilar-Campos A, Tito-Álvarez AM, Serrano-Osuna R, Gray RD, Mafessoni F, Heggarty P, Shimizu KK, Fujita R, Stoneking M, Pugach I, Fehren-Schmitz L. The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast. Mol Biol Evol 2020; 36:2698-2713. [PMID: 31350885 PMCID: PMC6878948 DOI: 10.1093/molbev/msz174] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.
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Affiliation(s)
- Chiara Barbieri
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - José R Sandoval
- Centro de Investigación de Genética y Biología Molecular (CIGBM), Universidad de San Martín de Porres, Lima, Peru
| | - Oscar Acosta
- Centro de Investigación de Genética y Biología Molecular (CIGBM), Universidad de San Martín de Porres, Lima, Peru
| | - Camilo Zurita
- Cátedra de Inmunología, Facultad de Medicina, Universidad Central del Ecuador, Quito, Ecuador.,Zurita & Zurita Laboratorios, Unidad de Investigaciones en Biomedicina, Quito, Ecuador
| | - Abraham Aguilar-Campos
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Ana M Tito-Álvarez
- Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador
| | - Ricardo Serrano-Osuna
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Russell D Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paul Heggarty
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Ricardo Fujita
- Centro de Investigación de Genética y Biología Molecular (CIGBM), Universidad de San Martín de Porres, Lima, Peru
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, Santa Cruz, CA.,Genomics Institute, University of California, Santa Cruz, CA
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Accinelli RA, Leon-Abarca JA. Age and altitude of residence determine anemia prevalence in Peruvian 6 to 35 months old children. PLoS One 2020; 15:e0226846. [PMID: 31940318 PMCID: PMC6961872 DOI: 10.1371/journal.pone.0226846] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/05/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A Demographic and Family Health Survey (ENDES, for Encuesta Demográfica y de Salud Familiar in Spanish) is carried out annually in Peru. Based on it, the anemia prevalence was 43.6% in 2016 and 43.8% in 2017 using the WHO cutoff value of 11 g/dL and the altitude-correction equation. OBJECTIVE To assess factors contributing to anemia and to determine its prevalence in Peruvian children 6 to 35 months old. METHODS We used the MEASURE DHS-based ENDES survey to obtain representative data for11364 children from 6 to 35 months old on hemoglobin and health determinants. To evaluate normal hemoglobin levels, we used the original WHO criterion of the 5th percentile in children without chronic malnutrition and then applied it to the overall population. Relationships between hemoglobin and altitude levels, usage of cleaning methods to sanitize water safe to drink, usage of solid fuels and poverty status were tested using methodology for complex survey data. Percentile curves were made for altitude intervals by plotting hemoglobin compared to age. The new anemia rates are presented in graphs by Peruvian political regions according to the degree of public health significance. RESULTS Hemoglobin increased as age and altitude of residence increased. Using the 5th percentile, anemia prevalence was 7.3% in 2016 and 2017. Children from low altitudes had higher anemia prevalence (8.5%) than those from high altitudes (1.2%, p<0.0001). In the rainforest area of Peru, anemia prevalence was highest (13.5%), while in the highlands it was lowest (3.3%, p<0.0001). With access to safe drinking water and without chronic malnutrition, anemia rates could be reduced in the rainforest by 45% and 33%, respectively. CONCLUSION Anemia prevalence in Peruvian children from 6 to 35 months old was 7.3% in 2016 and 2017.
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Affiliation(s)
- Roberto Alfonso Accinelli
- Instituto de Investigaciones de la Altura, Universidad Peruana Cayetano Heredia, Lima, Perú
- Facultad de Medicina Alberto Hurtado, Universidad Peruana Cayetano Heredia, Lima, Perú
- Hospital Cayetano Heredia, Lima, Perú
| | - Juan Alonso Leon-Abarca
- Instituto de Investigaciones de la Altura, Universidad Peruana Cayetano Heredia, Lima, Perú
- Facultad de Medicina Alberto Hurtado, Universidad Peruana Cayetano Heredia, Lima, Perú
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Menéndez LP, Rademaker K, Harvati K. Revisiting East–West Skull Patterns and the Role of Random Factors in South America: Cranial Reconstruction and Morphometric Analysis of the Facial Skeleton from Cuncaicha Rockshelter (Southern Peru). ACTA ACUST UNITED AC 2019. [DOI: 10.1080/20555563.2019.1703167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lumila Paula Menéndez
- Konrad Lorenz Institute, Klosterneuburg, Austria, and DFG Centre for Advanced Studies “Words, Bones, Genes, Tools”, University of Tübingen, Tübingen, Germany
| | | | - Katerina Harvati
- Paleoanthropology, Senckenberg Centre for Human Evolution and Paleoenvironment, and DFG Centre for Advanced Studies “Words, Bones, Genes, Tools”, University of Tübingen, Tübingen, Germany
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36
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Julian CG. An Aptitude for Altitude: Are Epigenomic Processes Involved? Front Physiol 2019; 10:1397. [PMID: 31824328 PMCID: PMC6883803 DOI: 10.3389/fphys.2019.01397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/29/2019] [Indexed: 12/30/2022] Open
Abstract
In recent years, high-throughput genomic technologies and computational advancements have invigorated efforts to identify the molecular mechanisms regulating human adaptation to high altitude. Although exceptional progress regarding the identification of genomic regions showing evidence of recent positive selection has been made, many of the key “hypoxia tolerant” phenotypes of highland populations have not yet been linked to putative adaptive genetic variants. As a result, fundamental questions regarding the biological processes by which such adaptations are acquired remain unanswered. This Mini Review discusses the hypothesis that the epigenome works in coordination with underlying genomic sequence to govern adaptation to the chronic hypoxia of high altitude by influencing adaptive capacity and phenotypic variation under conditions of environmental hypoxia. Efforts to unravel the complex interactions between the genome, epigenome, and environmental exposures are essential to more fully appreciate the mechanisms underlying human adaptation to hypoxia.
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Affiliation(s)
- Colleen G Julian
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
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37
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Association of EGLN1 gene with high aerobic capacity of Peruvian Quechua at high altitude. Proc Natl Acad Sci U S A 2019; 116:24006-24011. [PMID: 31712437 DOI: 10.1073/pnas.1906171116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Highland native Andeans have resided at altitude for millennia. They display high aerobic capacity (VO2max) at altitude, which may be a reflection of genetic adaptation to hypoxia. Previous genomewide (GW) scans for natural selection have nominated Egl-9 homolog 1 gene (EGLN1) as a candidate gene. The encoded protein, EGLN1/PHD2, is an O2 sensor that controls levels of the Hypoxia Inducible Factor-α (HIF-α), which regulates the cellular response to hypoxia. From GW association and analysis of covariance performed on a total sample of 429 Peruvian Quechua and 94 US lowland referents, we identified 5 EGLN1 SNPs associated with higher VO2max (L⋅min-1 and mL⋅min-1⋅kg-1) in hypoxia (rs1769793, rs2064766, rs2437150, rs2491403, rs479200). For 4 of these SNPs, Quechua had the highest frequency of the advantageous (high VO2max) allele compared with 25 diverse lowland comparison populations from the 1000 Genomes Project. Genotype effects were substantial, with high versus low VO2max genotype categories differing by ∼11% (e.g., for rs1769793 SNP genotype TT = 34.2 mL⋅min-1⋅kg-1 vs. CC = 30.5 mL⋅min-1⋅kg-1). To guard against spurious association, we controlled for population stratification. Findings were replicated for EGLN1 SNP rs1769793 in an independent Andean sample collected in 2002. These findings contextualize previous reports of natural selection at EGLN1 in Andeans, and support the hypothesis that natural selection has increased the frequency of an EGLN1 causal variant that enhances O2 delivery or use during exercise at altitude in Peruvian Quechua.
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38
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Gazal S, Espinoza JR, Austerlitz F, Marchant D, Macarlupu JL, Rodriguez J, Ju-Preciado H, Rivera-Chira M, Hermine O, Leon-Velarde F, Villafuerte FC, Richalet JP, Gouya L. The Genetic Architecture of Chronic Mountain Sickness in Peru. Front Genet 2019; 10:690. [PMID: 31417607 PMCID: PMC6682665 DOI: 10.3389/fgene.2019.00690] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/02/2019] [Indexed: 12/23/2022] Open
Abstract
Chronic mountain sickness (CMS) is a pathological condition resulting from chronic exposure to high-altitude hypoxia. While its prevalence is high in native Andeans (>10%), little is known about the genetic architecture of this disease. Here, we performed the largest genome-wide association study (GWAS) of CMS (166 CMS patients and 146 controls living at 4,380 m in Peru) to detect genetic variants associated with CMS. We highlighted four new candidate loci, including the first CMS-associated variant reaching GWAS statistical significance (rs7304081; P = 4.58 × 10−9). By looking at differentially expressed genes between CMS patients and controls around these four loci, we suggested AEBP2, CAST, and MCTP2 as candidate CMS causal genes. None of the candidate loci were under strong natural selection, consistent with the observation that CMS affects fitness mainly after the reproductive years. Overall, our results reveal new insights on the genetic architecture of CMS and do not provide evidence that CMS-associated variants are linked to a strong ongoing adaptation to high altitude.
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Affiliation(s)
- Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,INSERM, Infection, Antimicrobials, Modelling, Evolution (IAME), UMR 1137, Paris, France.,Plateforme de génomique constitutionnelle du GHU Nord, Assistance Publique des Hôpitaux de Paris (APHP), Hôpital Bichat, Paris, France
| | - Jose R Espinoza
- Laboratorio de Biotecnología Molecular-LID, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Frédéric Austerlitz
- UMR CNRS 7206 Eco-Anthropologie et Ethnobiologie, Musée de l'Homme, Paris, France
| | - Dominique Marchant
- Université Paris 13, Sorbonne Paris Cité, INSERM UMR 1272 Hypoxie et Poumon, Bobigny, France
| | - Jose Luis Macarlupu
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jorge Rodriguez
- Laboratorio de Biotecnología Molecular-LID, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Hugo Ju-Preciado
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Maria Rivera-Chira
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Olivier Hermine
- Université Paris Descartes, Institut National de la Santé et de la Recherche Médicale Unité 1163, Centre National de la Recherche Scientifique, Equipes de Recherche Labellisées 8254, Institut Imagine, Paris, France.,Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France
| | - Fabiola Leon-Velarde
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Francisco C Villafuerte
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jean-Paul Richalet
- Université Paris 13, Sorbonne Paris Cité, INSERM UMR 1272 Hypoxie et Poumon, Bobigny, France.,Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France
| | - Laurent Gouya
- Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France.,Université Paris Diderot, INSERM U1149, Hème, fer et pathologies inflammatoires, Assistance Publique des Hôpitaux de Paris (APHP), Hôpital Louis Mourier, Paris, France
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39
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Prufer KM, Alsgaard AV, Robinson M, Meredith CR, Culleton BJ, Dennehy T, Magee S, Huckell BB, Stemp WJ, Awe JJ, Capriles JM, Kennett DJ. Linking late Paleoindian stone tool technologies and populations in North, Central and South America. PLoS One 2019; 14:e0219812. [PMID: 31318917 PMCID: PMC6638942 DOI: 10.1371/journal.pone.0219812] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 06/29/2019] [Indexed: 01/20/2023] Open
Abstract
From the perspective of Central and South America, the peopling of the New World was a complex process lasting thousands of years and involving multiple waves of Pleistocene and early Holocene period immigrants entering into the neotropics. These Paleoindian colonists initially brought with them technologies developed for adaptation to environments and resources found in North America. As the ice age ended across the New World people adapted more generalized stone tools to exploit changing environments and resources. In the neotropics these changes would have been pronounced as patchy forests and grasslands gave way to broadleaf tropical forests. We document a late Pleistocene/early Holocene stone tool tradition from Belize, located in southern Mesoamerica. This represents the first endogenous Paleoindian stone tool technocomplex recovered from well dated stratigraphic contexts for Mesoamerica. Previously designated Lowe, these artifacts share multiple features with contemporary North and South American Paleoindian tool types. Once hafted, these bifaces appear to have served multiple functions for cutting, hooking, thrusting, or throwing. The tools were developed at a time of technological regionalization reflecting the diverse demands of a period of pronounced environmental change and population movement. Combined stratigraphic, technological, and population paleogenetic data suggests that there were strong ties between lowland neotropic regions at the onset of the Holocene.
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Affiliation(s)
- Keith M. Prufer
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico United States of America
- Center for Stable Isotopes, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Asia V. Alsgaard
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico United States of America
| | - Mark Robinson
- Department of Archaeology, Exeter University, Exeter, United Kingdom
| | - Clayton R. Meredith
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico United States of America
| | - Brendan J. Culleton
- Institute of Energy and the Environment, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Timothy Dennehy
- School of Human Evolution, Arizona State University, Tempe, Arizona, United States of America
| | - Shelby Magee
- SWCA Environmental Consultants, Carlsbad, New Mexico, United States of America
| | - Bruce B. Huckell
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico United States of America
| | - W. James Stemp
- Department of Sociology, Anthropology and Criminology, Keene State College, Keene, New Hampshire, United States of America
| | - Jaime J. Awe
- Department of Anthropology, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jose M. Capriles
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Douglas J. Kennett
- Department of Anthropology, University of California at Santa Barbara, Santa Barbara, California, United States of America
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40
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Zhang XL, Ha BB, Wang SJ, Chen ZJ, Ge JY, Long H, He W, Da W, Nian XM, Yi MJ, Zhou XY, Zhang PQ, Jin YS, Bar-Yosef O, Olsen JW, Gao X. The earliest human occupation of the high-altitude Tibetan Plateau 40 thousand to 30 thousand years ago. Science 2019; 362:1049-1051. [PMID: 30498126 DOI: 10.1126/science.aat8824] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 10/10/2018] [Indexed: 02/04/2023]
Abstract
The Tibetan Plateau is the highest and one of the most demanding environments ever inhabited by humans. We investigated the timing and mechanisms of its initial colonization at the Nwya Devu site, located nearly 4600 meters above sea level. This site, dating from 40,000 to 30,000 years ago, is the highest Paleolithic archaeological site yet identified globally. Nwya Devu has yielded an abundant blade tool assemblage, indicating hitherto-unknown capacities for the survival of modern humans who camped in this environment. This site deepens the history of the peopling of the "roof of the world" and the antiquity of human high-altitude occupations more generally.
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Affiliation(s)
- X L Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - B B Ha
- Tibetan Cultural Relics Conservation Institute, Lhasa 850000, Tibet Autonomous Region, China
| | - S J Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Z J Chen
- Tibetan Cultural Relics Conservation Institute, Lhasa 850000, Tibet Autonomous Region, China
| | - J Y Ge
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. .,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - H Long
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - W He
- Tibetan Cultural Relics Conservation Institute, Lhasa 850000, Tibet Autonomous Region, China
| | - W Da
- Nagqu Prefecture Cultural Relics Bureau, Nagqu 852000, Tibet Autonomous Region, China
| | - X M Nian
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - M J Yi
- School of History, Renmin University of China, Beijing 100872, China
| | - X Y Zhou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - P Q Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Y S Jin
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - O Bar-Yosef
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - J W Olsen
- School of Anthropology, University of Arizona, Tucson, AZ 85721, USA.,Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - X Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. .,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
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41
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Human Genetic Adaptation to High Altitude: Evidence from the Andes. Genes (Basel) 2019; 10:genes10020150. [PMID: 30781443 PMCID: PMC6410003 DOI: 10.3390/genes10020150] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/29/2019] [Accepted: 02/11/2019] [Indexed: 12/31/2022] Open
Abstract
Whether Andean populations are genetically adapted to high altitudes has long been of interest. Initial studies focused on physiological changes in the O₂ transport system that occur with acclimatization in newcomers and their comparison with those of long-resident Andeans. These as well as more recent studies indicate that Andeans have somewhat larger lung volumes, narrower alveolar to arterial O₂ gradients, slightly less hypoxic pulmonary vasoconstrictor response, greater uterine artery blood flow during pregnancy, and increased cardiac O2 utilization, which overall suggests greater efficiency of O₂ transfer and utilization. More recent single nucleotide polymorphism and whole-genome sequencing studies indicate that multiple gene regions have undergone recent positive selection in Andeans. These include genes involved in the regulation of vascular control, metabolic hemostasis, and erythropoiesis. However, fundamental questions remain regarding the functional links between these adaptive genomic signals and the unique physiological attributes of highland Andeans. Well-designed physiological and genome association studies are needed to address such questions. It will be especially important to incorporate the role of epigenetic processes (i.e.; non-sequence-based features of the genome) that are vital for transcriptional responses to hypoxia and are potentially heritable across generations. In short, further exploration of the interaction among genetic, epigenetic, and environmental factors in shaping patterns of adaptation to high altitude promises to improve the understanding of the mechanisms underlying human adaptive potential and clarify its implications for human health.
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42
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Méndez C, Nuevo Delaunay A, Seguel R, Maldonado A, Murillo I, Jackson D, Aspillaga E, Izaurieta R, Méndez V, Fernández M. Late Pleistocene to early Holocene high-quality quartz crystal procurement from the Valiente quarry workshop site (32°S, Chile, South America). PLoS One 2018; 13:e0208062. [PMID: 30496241 PMCID: PMC6264839 DOI: 10.1371/journal.pone.0208062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/09/2018] [Indexed: 11/18/2022] Open
Abstract
The procurement of high-quality lithic resources is amongst the most indicative processes of decision-making in the archaeology of early human groups peopling the Americas. Directly dated deposits from quarry workshops have been absent of the late Pleistocene record of South America. We present the results of the excavations of a high-quality translucent quartz crystal workshop that yielded radiocarbon-dated coherently layered stratigraphic deposits that shed light into the behavior of the initial stages of lithic procurement. Based on a detailed analysis of the context of the Valiente site (32° S, Chile, South America), we discuss the stages of bifacial production of point technology. The deposit produced evidence of cumulative occupations over the period between 12,630 and 11,320 calibrated years before present. This ~1,300-year span is coincidental with a major environmental step-wise drying trend as indicated by the local and regional pollen records. Furthermore, it is synchronous to the process in which natural landscapes became the earliest taskscapes in the region, thereby encompassing major cultural changes related to the organization of the land use. These results are discussed in the frame of contemporaneous archaeological data to discuss specific aspects of technology and decision-making of the earliest settlers of South America.
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Affiliation(s)
- César Méndez
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Aisén, Chile
- * E-mail:
| | - Amalia Nuevo Delaunay
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Aisén, Chile
| | - Roxana Seguel
- Centro Nacional de Conservación y Restauración, Servicio Nacional del Patrimonio Cultural, Santiago, Región Metropolitana, Chile
| | - Antonio Maldonado
- Centro de Estudios Avanzados en Zonas Áridas, Universidad de La Serena, La Serena, Coquimbo, Chile
| | - Ismael Murillo
- Servicio Nacional de Geología y Minería, Providencia, Santiago, Región Metropolitana, Chile
| | - Douglas Jackson
- Sociedad Malacológica de Chile, Santiago, Región Metropolitana, Chile
| | - Eugenio Aspillaga
- Departamento de Antropología, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Roberto Izaurieta
- Departamento de Antropología, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Víctor Méndez
- Independent researcher, Santiago, Región Metropolitana, Chile
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43
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Posth C, Nakatsuka N, Lazaridis I, Skoglund P, Mallick S, Lamnidis TC, Rohland N, Nägele K, Adamski N, Bertolini E, Broomandkhoshbacht N, Cooper A, Culleton BJ, Ferraz T, Ferry M, Furtwängler A, Haak W, Harkins K, Harper TK, Hünemeier T, Lawson AM, Llamas B, Michel M, Nelson E, Oppenheimer J, Patterson N, Schiffels S, Sedig J, Stewardson K, Talamo S, Wang CC, Hublin JJ, Hubbe M, Harvati K, Nuevo Delaunay A, Beier J, Francken M, Kaulicke P, Reyes-Centeno H, Rademaker K, Trask WR, Robinson M, Gutierrez SM, Prufer KM, Salazar-García DC, Chim EN, Müller Plumm Gomes L, Alves ML, Liryo A, Inglez M, Oliveira RE, Bernardo DV, Barioni A, Wesolowski V, Scheifler NA, Rivera MA, Plens CR, Messineo PG, Figuti L, Corach D, Scabuzzo C, Eggers S, DeBlasis P, Reindel M, Méndez C, Politis G, Tomasto-Cagigao E, Kennett DJ, Strauss A, Fehren-Schmitz L, Krause J, Reich D. Reconstructing the Deep Population History of Central and South America. Cell 2018; 175:1185-1197.e22. [PMID: 30415837 PMCID: PMC6327247 DOI: 10.1016/j.cell.2018.10.027] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/15/2018] [Accepted: 10/11/2018] [Indexed: 01/16/2023]
Abstract
We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.
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Affiliation(s)
- Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany.
| | - Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA.
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Francis Crick Institute, London NW1 1AT, UK
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia 27100, Italy
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Brendan J Culleton
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Kelly Harkins
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Jakob Sedig
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology and Ethnology, Xiamen University, Xiamen 361005, China
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Mark Hubbe
- Department of Anthropology, The Ohio State University, Columbus, OH 43210, USA; Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Región de Antofagasta, Antofagasta CP 1410000, Chile
| | - Katerina Harvati
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany
| | | | - Judith Beier
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany
| | - Michael Francken
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany
| | - Peter Kaulicke
- Pontifical Catholic University of Peru, San Miguel, Lima 32, Peru
| | - Hugo Reyes-Centeno
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | - Willa R Trask
- Central Identification Laboratory, Defense POW/MIA Accounting Agency, Department of Defense, Joint Base Pearl Harbor-Hickam, HI 96853, USA
| | - Mark Robinson
- Department of Archaeology, Exeter University, Exeter EX4 4QJ, UK
| | | | - Keith M Prufer
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA; Center for Stable Isotopes, University of New Mexico, Albuquerque, NM 87131, USA
| | - Domingo C Salazar-García
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany; Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | - Eliane N Chim
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | | | - Marcony L Alves
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Andersen Liryo
- Museu Nacional da Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil
| | - Mariana Inglez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Rodrigo E Oliveira
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Departamento de Estomatologia, Faculdade de Odontologia, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Danilo V Bernardo
- Laboratório de Estudos em Antropologia Biológica, Bioarqueologia e Evolução Humana, Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande, Rio Grande do Sul 96203-900, Brazil
| | - Alberto Barioni
- Faculdade de Filosofia Ciencias e Letras, Universidade de São Paulo, São Paulo 05508-080, Brazil
| | - Veronica Wesolowski
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Nahuel A Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Mario A Rivera
- Comité Chileno del Consejo Internacional de Monumentos y Sitios, Santiago 8320000, Chile; Field Museum of Natural History, Chicago, IL 60605, USA; Universidad de Magallanes, Punta Arenas 6200000, Chile
| | - Claudia R Plens
- Escola De Filosofia, Letras E Ciências Humanas, Universidade Federal de São Paulo, São Paulo 07252-312, Brazil
| | - Pablo G Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Levy Figuti
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires y CONICET, Ciudad Autonoma de Buenos Aires, Junin 954, Argentina
| | - Clara Scabuzzo
- CONICET-División Arqueología, Facultad de Ciencias Naturales y Museo, La Plata 1900, Argentina
| | - Sabine Eggers
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Naturhistorisches Museum Wien, Vienna 1010, Austria
| | - Paulo DeBlasis
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Markus Reindel
- German Archaeological Institute, Commission for Archaeology of Non-European Cultures, Bonn 53173, Germany
| | - César Méndez
- Centro de Investigación en Ecosistemas de la Patagonia, Coyhaique 5951601, Chile
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | | | - Douglas J Kennett
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - André Strauss
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil; Centro de Arqueologia Annette Laming Emperaire, Miguel A Salomão, Lagoa Santa, MG 33400-000, Brazil
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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Lindo J, Haas R, Hofman C, Apata M, Moraga M, Verdugo RA, Watson JT, Viviano Llave C, Witonsky D, Beall C, Warinner C, Novembre J, Aldenderfer M, Di Rienzo A. The genetic prehistory of the Andean highlands 7000 years BP though European contact. SCIENCE ADVANCES 2018; 4:eaau4921. [PMID: 30417096 PMCID: PMC6224175 DOI: 10.1126/sciadv.aau4921] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/12/2018] [Indexed: 05/02/2023]
Abstract
The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.
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Affiliation(s)
- John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Randall Haas
- Department of Anthropology, University of California, Davis, CA 95616, USA
| | - Courtney Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | - Mario Apata
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
- Departamento de Antropología, Universidad de Chile, Santiago, Chile
| | - Ricardo A. Verdugo
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
- Departamento de Oncología Básico-Clínica, Universidad de Chile, Santiago, Chile
| | - James T. Watson
- Arizona State Museum and School of Anthropology, University of Arizona, Tucson, AZ 85721, USA
| | | | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Beall
- Department of Anthropology, Case Western University, Cleveland, OH 44106, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Mark Aldenderfer
- School of Social Sciences, Humanities, and Arts, University of California, Merced, Merced, CA 95343, USA
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
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45
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Jacovas VC, Couto-Silva CM, Nunes K, Lemes RB, de Oliveira MZ, Salzano FM, Bortolini MC, Hünemeier T. Selection scan reveals three new loci related to high altitude adaptation in Native Andeans. Sci Rep 2018; 8:12733. [PMID: 30143708 PMCID: PMC6109162 DOI: 10.1038/s41598-018-31100-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/06/2018] [Indexed: 12/16/2022] Open
Abstract
The Andean Altiplano has been occupied continuously since the late Pleistocene, ~12,000 years ago, which places the Andean natives as one of the most ancient populations living at high altitudes. In the present study, we analyzed genomic data from Native Americans living a long-time at Andean high altitude and at Amazonia and Mesoamerica lowland areas. We have identified three new candidate genes - SP100, DUOX2 and CLC - with evidence of positive selection for altitude adaptation in Andeans. These genes are involved in the TP53 pathway and are related to physiological routes important for high-altitude hypoxia response, such as those linked to increased angiogenesis, skeletal muscle adaptations, and immune functions at the fetus-maternal interface. Our results, combined with other studies, showed that Andeans have adapted to the Altiplano in different ways and using distinct molecular strategies as compared to those of other natives living at high altitudes.
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Affiliation(s)
- Vanessa C Jacovas
- Genetics Departament, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cainã M Couto-Silva
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Renan B Lemes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | | | - Francisco M Salzano
- Genetics Departament, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Cátira Bortolini
- Genetics Departament, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil.
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46
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Defining the ‘generalist specialist’ niche for Pleistocene Homo sapiens. Nat Hum Behav 2018; 2:542-550. [DOI: 10.1038/s41562-018-0394-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 06/17/2018] [Accepted: 06/19/2018] [Indexed: 12/15/2022]
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Brandini S, Bergamaschi P, Cerna MF, Gandini F, Bastaroli F, Bertolini E, Cereda C, Ferretti L, Gómez-Carballa A, Battaglia V, Salas A, Semino O, Achilli A, Olivieri A, Torroni A. The Paleo-Indian Entry into South America According to Mitogenomes. Mol Biol Evol 2018; 35:299-311. [PMID: 29099937 PMCID: PMC5850732 DOI: 10.1093/molbev/msx267] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recent and compelling archaeological evidence attests to human presence ∼14.5 ka at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 ka, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel subhaplogroups, often branching into further subclades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these subhaplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 ka comprised between 16.0 and 14.6 ka.
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Affiliation(s)
- Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Paola Bergamaschi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Servizio di Immunoematologia e Medicina Trasfusionale, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marco Fernando Cerna
- Biotechnology Laboratory, Salesian Polytechnic University of Ecuador, Quito, Ecuador
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | | | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Salas
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
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48
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Moore LG. Human Genetic Adaptation to High Altitudes: Current Status and Future Prospects. QUATERNARY INTERNATIONAL : THE JOURNAL OF THE INTERNATIONAL UNION FOR QUATERNARY RESEARCH 2017; 461:4-13. [PMID: 29375239 PMCID: PMC5784843 DOI: 10.1016/j.quaint.2016.09.045] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The question of whether human populations have adapted genetically to high altitude has been of interest since studies began there in the early 1900s. Initially there was debate as to whether genetic adaptation to high altitude has taken place based, in part, on disciplinary orientation and the sources of evidence being considered. Studies centered on short-term responses, termed acclimatization, and the developmental changes occurring across lifetimes. A paradigm shift occurred with the advent of single nucleotide polymorphism (SNP) technologies and statistical methods for detecting evidence of natural selection, resulting in an exponential rise in the number of publications reporting genetic adaptation. Reviewed here are the various kinds of evidence by which adaptation to high altitude has been assessed and which have led to widespread acceptance of the idea that genetic adaptation to high altitude has occurred. While methodological and other challenges remain for determining the specific gene or genes involved and the physiological mechanisms by which they are exerting their effects, considerable progress has been realized as shown by recent studies in Tibetans, Andeans and Ethiopians. Further advances are anticipated with the advent of new statistical methods, whole-genome sequencing and other molecular techniques for finer-scale genetic mapping, and greater intradisciplinary and interdisciplinary collaboration to identify the functional consequences of the genes or gene regions implicated and the time scales involved.
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Affiliation(s)
- Lorna G Moore
- Department of Obstetrics & Gynecology, University of Colorado Denver, Aurora CO (formerly of the Department of Anthropology, University of Colorado Denver, Denver CO)
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49
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Abstract
Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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50
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Kuzminsky SC, Reyes Báez O, Arriaza B, Méndez C, Standen VG, San Román M, Muñoz I, Durán Herrera Á, Hubbe M. Investigating cranial morphological variation of early human skeletal remains from Chile: A 3D geometric morphometric approach. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:223-237. [PMID: 29090737 DOI: 10.1002/ajpa.23344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 09/25/2017] [Accepted: 10/07/2017] [Indexed: 11/11/2022]
Abstract
OBJECTIVES Archaeological and genetic research has demonstrated that the Pacific Coast was a key route in the early colonization of South America. Research examining South American skeletons >8000 cal BP has revealed differences in cranial morphology between early and late Holocene populations, which may reflect distinct migration events and/or populations. However, genetic, cultural, and some skeletal data contradict this model. Given these discrepancies, this study examines ∼9000 years of prehistory to test the hypothesis that Early skeletons have a distinct cranial morphology from later skeletons. MATERIALS AND METHODS Using 3D digital models, craniofacial landmarks, and geometric morphometric analyses, we compared Early Holocene crania (n = 4) to later Chilean samples (n = 90) frequently absent in continental assessments of craniofacial variation. PCA, Mahalanobis distances, posterior and typicality probabilities were used to examine variation. RESULTS Two of the earliest skeletons from northern Chile show clear affinities to individuals from later sites in the same region. However, the hypothesis cannot be rejected as one Early individual from northern Chile and one individual from inland Patagonia did not always show clear affinities to coastal populations. DISCUSSION Biological affinities among northern populations and other regions of Chile align with genetic and archaeological data, supporting cultural and biological continuity along the Pacific Coast. In Patagonia, archaeological data are in accordance with skeletal differences between the Early inland steppe individual and coastal populations. This study incorporates 3D methods and skeletal datasets not widely used in assessments of biological affinity, thus contributing to a critical body of research examining the ancient population history of western South America.
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Affiliation(s)
- Susan C Kuzminsky
- Instituto de Investigaciones Arqueológicas y Museo R.P Gustavo Le Paige, Universidad Católica del Norte, Gustavo Le Paige 380, San Pedro de Atacama, Chile.,Anthropology Department, University of California, 156 High Street, Santa Cruz, California
| | - Omar Reyes Báez
- Centro de Estudios del Hombre Austral, Instituto de la Patagonia, Universidad de Magallanes, Avenida Bulnes 01890 Casilla 113D, Punta Arenas, Chile
| | - Bernardo Arriaza
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - César Méndez
- Centro de Investigación en Ecosistemas de la Patagonia, Moraleda 16, Coyhaique, Chile
| | - Vivien G Standen
- Departamento de Antropología, Universidad de Tarapacá, 18 de Septiembre 2222, Casilla 6-D, Arica, Chile
| | - Manuel San Román
- Centro de Estudios del Hombre Austral, Instituto de la Patagonia, Universidad de Magallanes, Avenida Bulnes 01890 Casilla 113D, Punta Arenas, Chile
| | - Iván Muñoz
- Departamento de Antropología, Universidad de Tarapacá, 18 de Septiembre 2222, Casilla 6-D, Arica, Chile
| | | | - Mark Hubbe
- Instituto de Investigaciones Arqueológicas y Museo R.P Gustavo Le Paige, Universidad Católica del Norte, Gustavo Le Paige 380, San Pedro de Atacama, Chile.,Department of Anthropology, 4034 Smith Laboratory, The Ohio State University, 174 W. 18th Avenue, Columbus, Ohio
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