1
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Lopez B, Stajic J, Jiang D, Szuromi P, Aldenderfer M, Grocholski B, Seale M, Malo C, Ross SH, Ash C, Hurtley SM, Nusinovich Y, Funk MA, Yeston JS, VanHook AM, Isles HM. In Science Journals. Science 2024; 384:43-45. [PMID: 38574135 DOI: 10.1126/science.adp5706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Highlights from the Science family of journals.
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2
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Vignieri S, Lavine MS, Yeston JS, Suleymanov Y, Olingy C, Ash C, Matsiko A, Smith HJ, Alderton G, Nusinovich Y, Funk MA, Seale M, Jiang D, Ross SH, Hallberg DL, Aldenderfer M, Foley JF, Shilatifard A. In Science Journals. Science 2024; 383:715-717. [PMID: 38359142 DOI: 10.1126/science.ado6282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Highlights from the Science family of journals.
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3
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Lopez B, Smith KT, Maroso M, Jiang D, Yeston JS, Neuhofer D, Aldenderfer M, Lavine MS, Funk MA, Nusinovich Y, Uzogara E, Kelly PN, Ross SH, Ferrarelli LK. In Science Journals. Science 2023; 381:1297-1299. [PMID: 37733847 DOI: 10.1126/science.adk9202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Highlights from the Science family of journals.
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4
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Aldenderfer M. Challenging "counterestablishment" archaeology: What really matters. Sci Adv 2023; 9:eadj8096. [PMID: 37531434 PMCID: PMC10396311 DOI: 10.1126/sciadv.adj8096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Affiliation(s)
- Mark Aldenderfer
- Deputy Editor, Science Advances, Department of Anthropology and Heritage Studies, University of California, Merced, Merced, CA, USA.
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5
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Aldenderfer M, Ferrarelli LK, Stajic J, Uzogara E, Stern P, Kelly PN, Funk MA, Hurtley SM, Vignieri S, Lavine MS, Olingy C, Fogg CN, Liu LN. In Science Journals. Science 2023; 381:409-411. [PMID: 37499035 DOI: 10.1126/science.add3468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Highlights from the Science family of journals.
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6
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Lopez B, Vignieri S, Aldenderfer M, Ferrarelli LK, Kelly PN, Scanlon ST, Smith KT, Smith HJ, Lavine MS, Nusinovich Y, Fogg CN, Xia F. In Science Journals. Science 2023; 380:168-170. [PMID: 37053339 DOI: 10.1126/science.adi2034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Highlights from the Science family of journals.
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7
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Wang H, Yang MA, Wangdue S, Lu H, Chen H, Li L, Dong G, Tsring T, Yuan H, He W, Ding M, Wu X, Li S, Tashi N, Yang T, Yang F, Tong Y, Chen Z, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang Z, Gao Y, Zhang M, Wang X, Zhang C, Yuan K, Ko AMS, Aldenderfer M, Gao X, Xu S, Fu Q. Human genetic history on the Tibetan Plateau in the past 5100 years. Sci Adv 2023; 9:eadd5582. [PMID: 36930720 PMCID: PMC10022901 DOI: 10.1126/sciadv.add5582] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Using genome-wide data of 89 ancient individuals dated to 5100 to 100 years before the present (B.P.) from 29 sites across the Tibetan Plateau, we found plateau-specific ancestry across plateau populations, with substantial genetic structure indicating high differentiation before 2500 B.P. Northeastern plateau populations rapidly showed admixture associated with millet farmers by 4700 B.P. in the Gonghe Basin. High genetic similarity on the southern and southwestern plateau showed population expansion along the Yarlung Tsangpo River since 3400 years ago. Central and southeastern plateau populations revealed extensive genetic admixture within the plateau historically, with substantial ancestry related to that found in southern and southwestern plateau populations. Over the past ~700 years, substantial gene flow from lowland East Asia further shaped the genetic landscape of present-day plateau populations. The high-altitude adaptive EPAS1 allele was found in plateau populations as early as in a 5100-year-old individual and showed a sharp increase over the past 2800 years.
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Affiliation(s)
- Hongru Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Melinda A. Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- Department of Biology, University of Richmond, Richmond, VA 23173, USA
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Hongliang Lu
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi’an 710069, China
| | - Linhui Li
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Guanghui Dong
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Haibing Yuan
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Manyu Ding
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Shuai Li
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tsho Yang
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Feng Yang
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Yuanhong He
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Zhaoxia Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yang Gao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming Zhang
- School of Cultural Heritage, Northwest University, Xi’an 710069, China
| | - Xiaoji Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, Merced, CA 95343, USA
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Qi Zhi Institute, Shanghai 200232, China
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8
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Brand JE, Suleymanov Y, Hines PJ, Fogg CN, Osborne IS, Hurtley SM, Kelly PN, Grocholski B, Vignieri S, Jiang D, Smith HJ, Wong W, Aldenderfer M, Ray LB. In Science Journals. Science 2022. [DOI: 10.1126/science.adg0305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Highlights from the
Science
family of journals
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9
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Smith HJ, Szuromi P, Jiang D, Stern P, Aldenderfer M, VanHook AM, Hines PJ, Lopez B, Alderton G, Ray LB, Stajic J, Nusinovich Y, Vignieri S, Goldberger J, Erkes DA, Hallberg DL. In Science Journals. Science 2022. [PMID: 36137021 DOI: 10.1126/science.ade9599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Highlights from the Science family of journals.
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10
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Lopez B, Vinson V, Suleymanov Y, Osborne IS, Lavine MS, Foley JF, Aldenderfer M, Jiang D, Hines PJ, Yeston J, Vignieri S, Grocholski B, Erkes DA, Norton M. In Science Journals. Science 2022. [PMID: 35951679 DOI: 10.1126/science.ade3192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Highlights from the Science family of journals.
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11
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Aldenderfer M, Lavine MS, Grocholski B, Yeston J, Purnell BA, Stern P, Hallberg DL, Smith HJ, Sugden AM, Scanlon ST, Ray LB, Szuromi P, Foley JF, Williams I. In Science Journals. Science 2022; 376:258-260. [PMID: 35420941 DOI: 10.1126/science.abq4270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Highlights from the Science family of journals.
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12
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Liu CC, Witonsky D, Gosling A, Lee JH, Ringbauer H, Hagan R, Patel N, Stahl R, Novembre J, Aldenderfer M, Warinner C, Di Rienzo A, Jeong C. Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors. Nat Commun 2022; 13:1203. [PMID: 35260549 PMCID: PMC8904508 DOI: 10.1038/s41467-022-28827-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.
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Affiliation(s)
- Chi-Chun Liu
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Anna Gosling
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
| | - Ju Hyeon Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Harald Ringbauer
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Richard Hagan
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.,Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Nisha Patel
- Department of Plant and Microbiology, University of Oklahoma, Norman, OK, 73019, USA.,Kintai Therapeutics, Cambridge, MA, 02139, USA
| | - Raphaela Stahl
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, CA, 95343, USA.
| | - Christina Warinner
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. .,Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA.
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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13
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Aldenderfer M. Exile from the Grasslands: Tibetan Herders and Chinese Development Projects. Jarmila Ptáčková. Seattle: University of Washington Press, 2020, 188 pp. $30.00, cloth. ISBN 9780295748191. Journal of Anthropological Research 2022. [DOI: 10.1086/717822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Ferrarelli LK, Ray LB, Kelly PN, Jiang D, Ash C, Lavine MS, Aldenderfer M, Hurtley SM, Scanlon ST, Stern P, Grocholski B, Zahn LM, Smith OM, Olingy C. In Science Journals. Science 2022; 375:625-627. [PMID: 35143318 DOI: 10.1126/science.ada0909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Highlights from the Science family of journals.
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15
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Smith HJ, Funk MA, Jiang D, Stajic J, Szuromi P, Ash C, Hines PJ, Ferrarelli LK, Alderton G, Scanlon ST, Rai TS, Yeston J, Osborne IS, Olingy C, Malo CS, Aldenderfer M. In Science Journals. Science 2021; 374:574-576. [PMID: 34709894 DOI: 10.1126/science.acx9415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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16
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17
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Aldenderfer M, Funk MA, Maroso M, Sugden AM, Osborne IS, Hines PJ, Lavine MS, Szuromi P, Alderton G, Zahn LM, Stajic J, Purnell BA, VanHook AM, Isles HM, Ash C. In Science Journals. Science 2021; 373:1485-1487. [PMID: 34554777 DOI: 10.1126/science.acx9133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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18
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Smith HJ, Hurtley SM, Lavine MS, Yeston J, Vignieri S, Zahn LM, Ferrarelli LK, Aldenderfer M, Alderton G, Funk MA, Scanlon ST, Hines PJ, Vinson V, Jiang D, Stajic J, Grocholski B, Kelly PN, Malo CS, Williams I. In Science Journals. Science 2021. [DOI: 10.1126/science.acx8941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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19
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Aldenderfer M. Insights into the Roman diet from Herculaneum. Science 2021. [DOI: 10.1126/science.373.6558.977-h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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20
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Alderton G, Grocholski B, Hines PJ, Osborne IS, Ferrarelli LK, Smith OM, Vignieri S, Szuromi P, Olingy C, Vinson V, Lavine MS, Zahn LM, Aldenderfer M, Ash C. This Week in Science. Science 2021. [DOI: 10.1126/science.2021.372.6542.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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21
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Aldenderfer M. Human impact on landscapes in early Africa. Science 2021. [DOI: 10.1126/science.372.6542.584-g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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22
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Aldenderfer M. Sounds from a Paleolithic seashell horn. Science 2021. [DOI: 10.1126/science.371.6530.687-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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23
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Stajic J, Aldenderfer M, Grocholski B, Rai TS, Vinson V, VanHook AM, Alderton G, Ash C, Funk MA, Malo CS, Zahn LM, Purnell BA, Williams I, Jiang D, Smith KT, Stern P. This Week in Science. Science 2021. [DOI: 10.1126/science.2021.371.6530.twis] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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24
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Stajic J, Yeston J, Alderton G, Ray LB, Ferrarelli LK, Ash C, Zahn LM, Nusinovich Y, Scanlon ST, Vinson V, Hines PJ, Jiang D, Vignieri S, Aldenderfer M, Olingy C, Szuromi P. This Week in Science. Science 2021. [DOI: 10.1126/science.2021.371.6526.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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25
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Aldenderfer M. Early cave art from Sulawesi. Science 2021. [DOI: 10.1126/science.371.6526.248-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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26
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Aldenderfer M. A woman hunter in the early Andes. Science 2020. [DOI: 10.1126/science.370.6517.677-g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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27
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Zahn LM, Osborne IS, Ash C, Smith HJ, Charneski CA, VanHook AM, Smith KT, Lavine MS, Alderton G, Vinson V, Aldenderfer M, Szuromi P, Vignieri S, Rai TS, Williams I. This Week in Science. Science 2020. [DOI: 10.1126/science.2020.370.6517.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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28
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Ash C, Aldenderfer M, Wong W, Grocholski B, Osborne IS, Zahn LM, Olingy C, Kelly PN, Szuromi P, Alderton G, Vignieri S, Hines PJ, Lavine MS, Norton M, Funk MA, Yeston J. This Week in Science. Science 2020. [DOI: 10.1126/science.2020.370.6516.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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29
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Aldenderfer M. Temporal changes in body temperature. Science 2020. [DOI: 10.1126/science.370.6516.543-h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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30
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Aldenderfer M. New insights into Clovis-era archaeology. Science 2020. [DOI: 10.1126/science.370.6515.418-k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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31
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Aldenderfer M, Smith HJ, Grocholski B, Williams I, Zahn LM, Vignieri S, Szuromi P, Alderton G, Vinson V, Lavine MS, Ash C, Wong W, Lee MM, Osborne IS, Purnell BA, Hines PJ, Maroso M, Yeston J. This Week in Science. Science 2020. [DOI: 10.1126/science.2020.370.6515.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Vignieri S, Hines PJ, Fogg CN, Foley JF, Kelly PN, Ash C, Purnell BA, Vinson V, Aldenderfer M, Szuromi P, Smith HJ, Osborne IS, Scanlon ST, Suleymanov Y, Charneski CA, Smith KT, Alderton G. This Week in Science. Science 2020. [DOI: 10.1126/science.2020.369.6510.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Aldenderfer M. Horses were not domesticated in Anatolia. Science 2020. [DOI: 10.1126/science.369.6510.1443-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Aldenderfer M. Caring for Glaciers: Land, Animals, and Humanity in the Himalayas. Karine Gagné. Seattle: University of Washington Press, 2019, 258 pp. $30.00, paper. ISBN 9780295744001. Journal of Anthropological Research 2020. [DOI: 10.1086/708416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Aldenderfer M, Szuromi P, Smith HJ, Zahn LM, Ash C, Alderton G, Hines PJ, Grocholski B, Hurtley SM, VanHook AM, Stajic J, Vinson V, Kelly PN, Sugden AM, Czajka C, Yeston J, Purnell BA, Balasubramani A, Smith KT. This Week in Science. Science 2020. [DOI: 10.1126/science.2020.369.6503.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Aldenderfer M. Source of Stonehenge's sarsens. Science 2020. [DOI: 10.1126/science.369.6503.519-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Aldenderfer M. Timing the rise of maize in Mesoamerica. Science 2020. [DOI: 10.1126/science.368.6495.1076-g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Alderton G, Yeston J, Osborne IS, Stern P, Grocholski B, Aldenderfer M, Smith HJ, Ash C, Pujanandez L, Kiberstis PA, Scanlon ST, Williams I, Wong W, Mao S, Purnell BA, Stajic J, Funk MA, Sugden AM. This Week in Science. Science 2020. [DOI: 10.1126/science.2020.368.6495.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Stephens L, Fuller D, Boivin N, Rick T, Gauthier N, Kay A, Marwick B, Armstrong CG, Barton CM, Denham T, Douglass K, Driver J, Janz L, Roberts P, Rogers JD, Thakar H, Altaweel M, Johnson AL, Sampietro Vattuone MM, Aldenderfer M, Archila S, Artioli G, Bale MT, Beach T, Borrell F, Braje T, Buckland PI, Jiménez Cano NG, Capriles JM, Diez Castillo A, Çilingiroğlu Ç, Negus Cleary M, Conolly J, Coutros PR, Covey RA, Cremaschi M, Crowther A, Der L, di Lernia S, Doershuk JF, Doolittle WE, Edwards KJ, Erlandson JM, Evans D, Fairbairn A, Faulkner P, Feinman G, Fernandes R, Fitzpatrick SM, Fyfe R, Garcea E, Goldstein S, Goodman RC, Dalpoim Guedes J, Herrmann J, Hiscock P, Hommel P, Horsburgh KA, Hritz C, Ives JW, Junno A, Kahn JG, Kaufman B, Kearns C, Kidder TR, Lanoë F, Lawrence D, Lee GA, Levin MJ, Lindskoug HB, López-Sáez JA, Macrae S, Marchant R, Marston JM, McClure S, McCoy MD, Miller AV, Morrison M, Motuzaite Matuzeviciute G, Müller J, Nayak A, Noerwidi S, Peres TM, Peterson CE, Proctor L, Randall AR, Renette S, Robbins Schug G, Ryzewski K, Saini R, Scheinsohn V, Schmidt P, Sebillaud P, Seitsonen O, Simpson IA, Sołtysiak A, Speakman RJ, Spengler RN, Steffen ML, Storozum MJ, Strickland KM, Thompson J, Thurston TL, Ulm S, Ustunkaya MC, Welker MH, West C, Williams PR, Wright DK, Wright N, Zahir M, Zerboni A, Beaudoin E, Munevar Garcia S, Powell J, Thornton A, Kaplan JO, Gaillard MJ, Klein Goldewijk K, Ellis E. Archaeological assessment reveals Earth’s early transformation through land use. Science 2019; 365:897-902. [DOI: 10.1126/science.aax1192] [Citation(s) in RCA: 237] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022]
Abstract
Environmentally transformative human use of land accelerated with the emergence of agriculture, but the extent, trajectory, and implications of these early changes are not well understood. An empirical global assessment of land use from 10,000 years before the present (yr B.P.) to 1850 CE reveals a planet largely transformed by hunter-gatherers, farmers, and pastoralists by 3000 years ago, considerably earlier than the dates in the land-use reconstructions commonly used by Earth scientists. Synthesis of knowledge contributed by more than 250 archaeologists highlighted gaps in archaeological expertise and data quality, which peaked for 2000 yr B.P. and in traditionally studied and wealthier regions. Archaeological reconstruction of global land-use history illuminates the deep roots of Earth’s transformation and challenges the emerging Anthropocene paradigm that large-scale anthropogenic global environmental change is mostly a recent phenomenon.
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Affiliation(s)
- Mark Aldenderfer
- John D. and Catherine T. MacArthur Foundation Distinguished Professor of Anthropology, University of California, Merced, CA 95343, USA
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41
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Ziesemer KA, Ramos-Madrigal J, Mann AE, Brandt BW, Sankaranarayanan K, Ozga AT, Hoogland M, Hofman CA, Salazar-García DC, Frohlich B, Milner GR, Stone AC, Aldenderfer M, Lewis CM, Hofman CL, Warinner C, Schroeder H. The efficacy of whole human genome capture on ancient dental calculus and dentin. Am J Phys Anthropol 2018; 168:496-509. [PMID: 30586168 PMCID: PMC6519167 DOI: 10.1002/ajpa.23763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/09/2018] [Accepted: 11/10/2018] [Indexed: 12/28/2022]
Abstract
Objectives Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Materials and methods Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing. Results Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four‐fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on‐target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum‐level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off‐target sequences in human genome‐enriched calculus libraries may still be useful for oral microbiome reconstruction. Discussion While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.
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Affiliation(s)
| | | | - Allison E Mann
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma
| | - Andrew T Ozga
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute for Human Origins, Arizona State University, Tempe, Arizona.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Domingo C Salazar-García
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | | | - George R Milner
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute for Human Origins, Arizona State University, Tempe, Arizona.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, California
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Corinne L Hofman
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Christina Warinner
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hannes Schroeder
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Aldenderfer M. Stress in Neanderthal children. Science 2018. [DOI: 10.1126/science.362.6414.554-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Smith HJ, Aldenderfer M, Stern P, Smith OM, Hurtley SM, Osborne IS, Kiberstis PA, Szuromi P, Wong W, Grocholski B, Ash C, Mao S, Scanlon ST, Fogg CN, Yeston J. This Week in Science. Science 2018. [DOI: 10.1126/science.2018.362.6414.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Stern P, Mao S, Balasubramani A, Osborne IS, Yeston J, Zahn LM, Szuromi P, Nusinovich Y, Aldenderfer M, Wong W, Purnell BA, Ash C, Vignieri S. This Week in Science. Science 2018. [DOI: 10.1126/science.2018.362.6413.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Aldenderfer M. Pre-Clovis projectile points in North America. Science 2018. [DOI: 10.1126/science.362.6413.415-f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Osborne IS, Fahrenkamp-Uppenbrink J, Yeston J, Purnell BA, Vignieri S, Smith HJ, Williams I, Hurtley SM, Hines PJ, Maroso M, Wong W, Kiberstis PA, Vinson V, Szuromi P, Aldenderfer M, Smith KT, Sugden AM, Lavine MS. This Week in Science. Science 2018. [DOI: 10.1126/science.2018.361.6406.twis] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Aldenderfer M. Organization of historical cemeteries. Science 2018. [DOI: 10.1126/science.361.6406.987-g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Yeston J, Grocholski B, Hurtley SM, Vignieri S, Zahn LM, Osborne IS, Ray LB, Aldenderfer M, Stajic J, Kelly PN, Fogg CN, Vinson V, Pujanandez L, Stern P. This Week in Science. Science 2018. [DOI: 10.1126/science.2018.361.6402.twis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Aldenderfer M. Peopling the Americas: Which way? Science 2018. [DOI: 10.1126/science.361.6402.564-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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