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Sandoval-Castellanos E, Hare AJ, Lin AT, Dimopoulos EA, Daly KG, Geiger S, Mullin VE, Wiechmann I, Mattiangeli V, Lühken G, Zinovieva NA, Zidarov P, Çakırlar C, Stoddart S, Orton D, Bulatović J, Mashkour M, Sauer EW, Horwitz LK, Horejs B, Atici L, Özkaya V, Mullville J, Parker Pearson M, Mainland I, Card N, Brown L, Sharples N, Griffiths D, Allen D, Arbuckle B, Abell JT, Duru G, Mentzer SM, Munro ND, Uzdurum M, Gülçur S, Buitenhuis H, Gladyr E, Stiner MC, Pöllath N, Özbaşaran M, Krebs S, Burger J, Frantz L, Medugorac I, Bradley DG, Peters J. Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep ( Ovis aries). SCIENCE ADVANCES 2024; 10:eadj0954. [PMID: 38608027 PMCID: PMC11014441 DOI: 10.1126/sciadv.adj0954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.
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Affiliation(s)
- Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Andrew J. Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Audrey T. Lin
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560 USA
| | - Evangelos A. Dimopoulos
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sheila Geiger
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Ingrid Wiechmann
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University of Gießen, Ludwigstr. 21, 35390 Gießen, Germany
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Petar Zidarov
- Institute of Prehistory, Early History and Medieval Archaeology, Tübingen University, Tübingen, Germany
| | - Canan Çakırlar
- Institute of Archaeology, University of Groningen, 9712 ER Groningen, Netherlands
| | - Simon Stoddart
- Magdalene College, University of Cambridge, Cambridge CB3 0AG, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Jelena Bulatović
- Department of Historical Studies, University of Gothenburg, BOX 200, 40530 Gothenburg, Sweden
| | - Marjan Mashkour
- Unité Archéozoologie, Archéobotanique, Sociétés Pratiques et Environnements (AASPE), CNRS, Muséum National d’Histoire Naturelle, 75020 Paris, France
| | - Eberhard W. Sauer
- School of History, Classics and Archaeology, University of Edinburgh, Old Medical School, Teviot Place, Edinburgh EH8 9AG, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Barbara Horejs
- OeAI, Austrian Academy of Sciences and HEAS, University of Vienna, Vienna, Austria
| | - Levent Atici
- Department of Anthropology, University of Nevada, Las Vegas, NV 89154, USA
| | - Vecihi Özkaya
- Department of Archaeology, Dicle University, Diyarbakir, Türkiye
| | - Jacqui Mullville
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | | | - Ingrid Mainland
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | - Nick Card
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | | | - Niall Sharples
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | - David Griffiths
- University of Oxford, OUDCE, Rewley House, Oxford OX1 2JA, UK
| | - David Allen
- Hampshire Cultural Trust, Chilcomb House, Winchester, SO23 8RB, UK
| | - Benjamin Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan T. Abell
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Güneş Duru
- Department of Archaeology, Mimar Sinan Fine Arts University, 34381 Şişli/İstanbul, Türkiye
| | - Susan M. Mentzer
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Department of Geosciences, Tübingen University, 72074 Tübingen, Germany
| | - Natalie D. Munro
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA
| | - Melis Uzdurum
- Department of Archaeology, Ondokuz Mayıs University, 55270 Atakum/Samsun, Türkiye
| | - Sevil Gülçur
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | | | - Elena Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Mary C. Stiner
- School of Anthropology, University of Arizona, Tucson, AZ 85721, USA
| | - Nadja Pöllath
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Mihriban Özbaşaran
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Joachim Burger
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
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2
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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3
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Human-Plant Coevolution: A modelling framework for theory-building on the origins of agriculture. PLoS One 2022; 17:e0260904. [PMID: 36070287 PMCID: PMC9451104 DOI: 10.1371/journal.pone.0260904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
The domestication of plants and the origin of agricultural societies has been the focus of much theoretical discussion on why, how, when, and where these happened. The ‘when’ and ‘where’ have been substantially addressed by different branches of archaeology, thanks to advances in methodology and the broadening of the geographical and chronological scope of evidence. However, the ‘why’ and ‘how’ have lagged behind, holding on to relatively old models with limited explanatory power. Armed with the evidence now available, we can return to theory by revisiting the mechanisms allegedly involved, disentangling their connection to the diversity of trajectories, and identifying the weight and role of the parameters involved. We present the Human-Plant Coevolution (HPC) model, which represents the dynamics of coevolution between a human and a plant population. The model consists of an ecological positive feedback system (mutualism), which can be reinforced by positive evolutionary feedback (coevolution). The model formulation is the result of wiring together relatively simple simulation models of population ecology and evolution, through a computational implementation in R. The HPC model captures a variety of potential scenarios, though which conditions are linked to the degree and timing of population change and the intensity of selective pressures. Our results confirm that the possible trajectories leading to neolithisation are diverse and involve multiple factors. However, simulations also show how some of those factors are entangled, what are their effects on human and plant populations under different conditions, and what might be the main causes fostering agriculture and domestication.
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4
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Ding YM, Cao Y, Zhang WP, Chen J, Liu J, Li P, Renner SS, Zhang DY, Bai WN. Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication. Genome Biol 2022; 23:145. [PMID: 35787713 PMCID: PMC9254524 DOI: 10.1186/s13059-022-02720-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/25/2022] [Indexed: 12/05/2022] Open
Abstract
Background Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them. Results We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern J. regia and its ancestor into J. sigillata, including the shell-thickness gene. Within J. regia, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline. Conclusions Both J. regia and J. sigillata appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02720-z.
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Affiliation(s)
- Ya-Mei Ding
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yu Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jun Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.,China National Botanical Garden, Beijing, 100093, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Pan Li
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO, 63130, USA.
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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5
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Wang MS, Zhang JJ, Guo X, Li M, Meyer R, Ashari H, Zheng ZQ, Wang S, Peng MS, Jiang Y, Thakur M, Suwannapoom C, Esmailizadeh A, Hirimuthugoda NY, Zein MSA, Kusza S, Kharrati-Koopaee H, Zeng L, Wang YM, Yin TT, Yang MM, Li ML, Lu XM, Lasagna E, Ceccobelli S, Gunwardana HGTN, Senasig TM, Feng SH, Zhang H, Bhuiyan AKFH, Khan MS, Silva GLLP, Thuy LT, Mwai OA, Ibrahim MNM, Zhang G, Qu KX, Hanotte O, Shapiro B, Bosse M, Wu DD, Han JL, Zhang YP. Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biol 2021; 19:118. [PMID: 34130700 PMCID: PMC8207802 DOI: 10.1186/s12915-021-01052-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/19/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. RESULTS We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. CONCLUSION This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.
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Affiliation(s)
- Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Rachel Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hidayat Ashari
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Bogor, 16911, Indonesia.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Zhu-Qing Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Mukesh Thakur
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Chatmongkon Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, Phayao, 56000, Thailand.,Unit of Excellence on Biodiversity and Natural Resources Management, University of Phayao, Phayao, 56000, Thailand
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Department of Animal Science, Shahid Bahonar University of Kerman, P.O. Box 76169133, Kerman, Iran
| | - Nalini Yasoda Hirimuthugoda
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Faculty of Agriculture, University of Ruhuna, Matara, Sri Lanka
| | - Moch Syamsul Arifin Zein
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Bogor, 16911, Indonesia
| | - Szilvia Kusza
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, H-4032, Hungary
| | - Hamed Kharrati-Koopaee
- Department of Animal Science, Shahid Bahonar University of Kerman, P.O. Box 76169133, Kerman, Iran.,Institute of Biotechnology, School of Agriculture, Shiraz University, P.O. Box 1585, Shiraz, Iran
| | - Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yun-Mei Wang
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xue-Mei Lu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentarie Ambientali, University of Perugia, 06123, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentarie Ambientali, University of Perugia, 06123, Perugia, Italy
| | | | | | - Shao-Hong Feng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Hao Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Ministry of Agriculture of China, Beijing, 100193, China
| | | | | | | | - Le Thi Thuy
- National Institute of Animal Husbandry, Hanoi, Vietnam
| | - Okeyo A Mwai
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | | | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-1870, Copenhagen, Denmark
| | - Kai-Xing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,Livestock Genetics Program, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Beth Shapiro
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mirte Bosse
- Wageningen University & Research - Animal Breeding and Genomics, 6708 PB, Wageningen, The Netherlands.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China.
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China. .,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China. .,State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, 650091, China.
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6
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Blischak PD, Barker MS, Gutenkunst RN. Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data. Mol Biol Evol 2021; 37:2124-2136. [PMID: 32068861 DOI: 10.1093/molbev/msaa042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 01/04/2023] Open
Abstract
Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model's ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.
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Affiliation(s)
- Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.,Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
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7
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Loog L. Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories. Philos Trans R Soc Lond B Biol Sci 2020; 376:20190719. [PMID: 33250022 DOI: 10.1098/rstb.2019.0719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.
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Affiliation(s)
- Liisa Loog
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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8
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White DM, Huang JP, Jara-Muñoz OA, MadriñáN S, Ree RH, Mason-Gamer RJ. The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes. Syst Biol 2020; 70:1-13. [PMID: 32979264 PMCID: PMC7744036 DOI: 10.1093/sysbio/syaa074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 11/21/2022] Open
Abstract
Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.]
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Affiliation(s)
- Dawson M White
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.,Grainger Bioinformatics Center, The Field Museum, Chicago, IL 60605, USA
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Santiago MadriñáN
- Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.,Jardín Botánico de Cartagena "Guillermo Piñeres", Turbaco, Bolívar, Colombia
| | - Richard H Ree
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL 60605, USA
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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9
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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10
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Richerson PJ. An integrated bayesian theory of phenotypic flexibility. Behav Processes 2019; 161:54-64. [DOI: 10.1016/j.beproc.2018.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/02/2018] [Accepted: 02/02/2018] [Indexed: 12/28/2022]
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11
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Hunt HV, Rudzinski A, Jiang H, Wang R, Thomas MG, Jones MK. Genetic evidence for a western Chinese origin of broomcorn millet ( Panicum miliaceum). THE HOLOCENE 2018; 28:1968-1978. [PMID: 30542237 PMCID: PMC6236650 DOI: 10.1177/0959683618798116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/27/2018] [Indexed: 05/10/2023]
Abstract
Broomcorn millet (Panicum miliaceum) is a key domesticated cereal that has been associated with the north China centre of agricultural origins. Early archaeobotanical evidence for this crop has generated two major debates. First, its contested presence in pre-7000 cal. BP sites in eastern Europe has admitted the possibility of a western origin. Second, its occurrence in the 7th and 8th millennia cal. BP in diverse regions of northern China is consistent with several possible origin foci, associated with different Neolithic cultures. We used microsatellite and granule-bound starch synthase I (GBSSI) genotype data from 341 landrace samples across Eurasia, including 195 newly genotyped samples from China, to address these questions. A spatially explicit discriminative modelling approach favours an eastern Eurasian origin for the expansion of broomcorn millet. This is consistent with recent archaeobotanical and chronological re-evaluations, and stable isotopic data. The same approach, together with the distribution of GBSSI alleles, is also suggestive that the origin of broomcorn millet expansion was in western China. This second unexpected finding stimulates new questions regarding the ecology of wild millet and vegetation dynamics in China prior to the mid-Holocene domestication of millet. The chronological relationship between population expansion and domestication is unclear, but our analyses are consistent with the western Loess Plateau being at least one region of primary domestication of broomcorn millet. Patterns of genetic variation indicate that this region was the source of populations to the west in Eurasia, which broomcorn probably reached via the Inner Asia Mountain Corridor from the 3rd millennium BC. A secondary westward expansion along the steppe may have taken place from the 2nd millennium BC.
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Affiliation(s)
- Harriet V Hunt
- McDonald Institute for Archaeological
Research, University of Cambridge, UK
| | - Anna Rudzinski
- Research Department of Genetics,
Evolution and Environment, University College London, UK
| | - Hongen Jiang
- Department of Archaeology and
Anthropology, University of Chinese Academy of Sciences, China
| | - Ruiyun Wang
- College of Agriculture, Shanxi
Agricultural University, China
- Institute of Crop Germplasm Resources of
Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and
Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key
Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, China
| | - Mark G Thomas
- Research Department of Genetics,
Evolution and Environment, University College London, UK
- UCL Genetics Institute, University
College London, UK
| | - Martin K Jones
- Department of Archaeology and
Anthropology, University of Cambridge, UK
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12
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Gaut BS, Seymour DK, Liu Q, Zhou Y. Demography and its effects on genomic variation in crop domestication. NATURE PLANTS 2018; 4:512-520. [PMID: 30061748 DOI: 10.1038/s41477-018-0210-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 05/20/2023]
Abstract
Over two thousand plant species have been modified morphologically through cultivation and human use. Here, we review three aspects of crop domestication that are currently undergoing marked revisions, due to analytical advancements and their application to whole genome resequencing (WGS) data. We begin by discussing the duration and demographic history of domestication. There has been debate as to whether domestication occurred quickly or slowly. The latter is tentatively supported both by fossil data and application of WGS data to sequentially Markovian coalescent methods that infer the history of effective population size. This history suggests the possibility of extended human impacts on domesticated lineages prior to their purposeful cultivation. We also make the point that demographic history matters, because it shapes patterns and levels of extant genetic diversity. We illustrate this point by discussing the evolutionary processes that contribute to the empirical observation that most crops examined to date have more putatively deleterious alleles than their wild relatives. These deleterious alleles may contribute to genetic load within crops and may be fitting targets for crop improvement. Finally, the same demographic factors are likely to shape the spectrum of structural variants (SVs) within crops. SVs are known to underlie many of the phenotypic changes associated with domestication and crop improvement, but we currently lack sufficient knowledge about the mechanisms that create SVs, their rates of origin, their population frequencies and their phenotypic effects.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Qingpo Liu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, China
| | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
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13
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Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie K, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y. The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. Curr Biol 2018; 28:2274-2282.e6. [PMID: 29983312 DOI: 10.1016/j.cub.2018.05.066] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/10/2018] [Accepted: 05/24/2018] [Indexed: 12/23/2022]
Abstract
African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10,000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2,000 years ago. During the last 5 centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. A gene, PROG1, associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, a shattering gene, SH5, showed selection signature during African rice domestication, but not during Asian rice domestication. Overall, our genomic data revealed a complex history of African rice domestication influenced by important climatic changes in the Saharan area, by the expansion of African agricultural society, and by recent replacement by another domesticated species.
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Affiliation(s)
- Philippe Cubry
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Christine Tranchant-Dubreuil
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; SouthGreen Development Platform, Agropolis Campus, Montpellier, France
| | - Anne-Céline Thuillet
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Cécile Monat
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; SouthGreen Development Platform, Agropolis Campus, Montpellier, France
| | | | - Karine Labadie
- CEA, Institut de Biologie François Jacob, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France; CNRS, UMR 8030, CP5706, Evry, France; Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Corinne Cruaud
- CEA, Institut de Biologie François Jacob, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France; CNRS, UMR 8030, CP5706, Evry, France; Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Stefan Engelen
- CEA, Institut de Biologie François Jacob, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France; CNRS, UMR 8030, CP5706, Evry, France; Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Nora Scarcelli
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Bénédicte Rhoné
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Lyon, France
| | - Concetta Burgarella
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | | | - Pierre Larmande
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; SouthGreen Development Platform, Agropolis Campus, Montpellier, France; Institut de Biologie Computationnelle (IBC), Université Montpellier 2, 860 Rue St Priest, 34095 Montpellier Cedex 5, France
| | - Patrick Wincker
- CEA, Institut de Biologie François Jacob, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France; CNRS, UMR 8030, CP5706, Evry, France; Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Olivier François
- Université Grenoble-Alpes, CNRS, UMR 5525 TIMC-IMAG, 38042 Grenoble, France
| | - François Sabot
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; SouthGreen Development Platform, Agropolis Campus, Montpellier, France; Université de Montpellier, Place Eugène Bataillon, 34000 Montpellier, France.
| | - Yves Vigouroux
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; Université de Montpellier, Place Eugène Bataillon, 34000 Montpellier, France.
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14
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. ANNALS OF BOTANY 2018; 121:385-403. [PMID: 29293871 PMCID: PMC5838823 DOI: 10.1093/aob/mcx145] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
| | - Jean-Frédéric Terral
- ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
- International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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15
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Equifinality in empirical studies of cultural transmission. Behav Processes 2018; 161:129-138. [PMID: 29369783 DOI: 10.1016/j.beproc.2018.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 02/07/2023]
Abstract
Cultural systems exhibit equifinal behavior - a single final state may be arrived at via different mechanisms and/or from different initial states. Potential for equifinality exists in all empirical studies of cultural transmission including controlled experiments, observational field research, and computational simulations. Acknowledging and anticipating the existence of equifinality is important in empirical studies of social learning and cultural evolution; it helps us understand the limitations of analytical approaches and can improve our ability to predict the dynamics of cultural transmission. Here, I illustrate and discuss examples of equifinality in studies of social learning, and how certain experimental designs might be prone to it. I then review examples of equifinality discussed in the social learning literature, namely the use of s-shaped diffusion curves to discern individual from social learning and operational definitions and analytical approaches used in studies of conformist transmission. While equifinality exists to some extent in all studies of social learning, I make suggestions for how to address instances of it, with an emphasis on using data simulation and methodological verification alongside modern statistical approaches that emphasize prediction and model comparison. In cases where evaluated learning mechanisms are equifinal due to non-methodological factors, I suggest that this is not always a problem if it helps us predict cultural change. In some cases, equifinal learning mechanisms might offer insight into how both individual learning, social learning strategies and other endogenous social factors might by important in structuring cultural dynamics and within- and between-group heterogeneity.
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17
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Chacón-Sánchez MI, Martínez-Castillo J. Testing Domestication Scenarios of Lima Bean ( Phaseolus lunatus L.) in Mesoamerica: Insights from Genome-Wide Genetic Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:1551. [PMID: 28955351 PMCID: PMC5601060 DOI: 10.3389/fpls.2017.01551] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/24/2017] [Indexed: 05/03/2023]
Abstract
Plant domestication can be seen as a long-term process that involves a complex interplay among demographic processes and evolutionary forces. Previous studies have suggested two domestication scenarios for Lima bean in Mesoamerica: two separate domestication events, one from gene pool MI in central-western Mexico and another one from gene pool MII in the area Guatemala-Costa Rica, or a single domestication from gene pool MI in central-western Mexico followed by post-domestication gene flow with wild populations. In this study we evaluated the genetic structure of the wild gene pool and tested these two competing domestication scenarios of Lima bean in Mesoamerica by applying an ABC approach to a set of genome-wide SNP markers. The results confirm the existence of three gene pools in wild Lima bean, two Mesoamerican gene pools (MI and MII) and the Andean gene pool (AI), and suggest the existence of another gene pool in central Colombia. The results indicate that although both domestication scenarios may be supported by genetic data, higher statistical support was given to the single domestication scenario in central-western Mexico followed by admixture with wild populations. Domestication would have involved strong founder effects reflected in loss of genetic diversity and increased LD levels in landraces. Genomic regions affected by selection were detected and these may harbor candidate genes related to domestication.
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Affiliation(s)
- María I. Chacón-Sánchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
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18
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Gillreath-Brown A, Bocinsky RK. A Dialogue Between Empirical and Model-Based Agricultural Studies in Archaeology. J ETHNOBIOL 2017. [DOI: 10.2993/0278-0771-37.2.167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Pankin A, von Korff M. Co-evolution of methods and thoughts in cereal domestication studies: a tale of barley (Hordeum vulgare). CURRENT OPINION IN PLANT BIOLOGY 2017; 36:15-21. [PMID: 28011443 DOI: 10.1016/j.pbi.2016.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/20/2016] [Accepted: 12/02/2016] [Indexed: 05/02/2023]
Abstract
Five major cereals such as wheat, rice, maize, barley and sorghum were among the first Neolithic crops that facilitated the establishment of the early agricultural societies. Since then they have remained the staple source of calories for the majority of the human population. Ample archaeological and molecular evidence has provided important insights into the domestication history of cereals but the debates on the origin of cereal crops are still far from resolved. Here, we review the recent advances in applying genome sequencing technologies for deciphering the history of cereal domestication. As a model example, we demonstrate that the evolution of thoughts on barley domestication closely followed the development of views on the rise of agriculture in the Near East in general and greatly accelerated with the advent of the genomic technologies and resources available for barley research.
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Affiliation(s)
- Artem Pankin
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225 Düsseldorf, Germany.
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225 Düsseldorf, Germany.
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20
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d'Alpoim Guedes JA, Crabtree SA, Bocinsky RK, Kohler TA. Twenty-first century approaches to ancient problems: Climate and society. Proc Natl Acad Sci U S A 2016; 113:14483-14491. [PMID: 27956613 PMCID: PMC5187725 DOI: 10.1073/pnas.1616188113] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
By documenting how humans adapted to changes in their environment that are often much greater than those experienced in the instrumental record, archaeology provides our only deep-time laboratory for highlighting the circumstances under which humans managed or failed to find to adaptive solutions to changing climate, not just over a few generations but over the longue durée Patterning between climate-mediated environmental change and change in human societies has, however, been murky because of low spatial and temporal resolution in available datasets, and because of failure to model the effects of climate change on local resources important to human societies. In this paper we review recent advances in computational modeling that, in conjunction with improving data, address these limitations. These advances include network analysis, niche and species distribution modeling, and agent-based modeling. These studies demonstrate the utility of deep-time modeling for calibrating our understanding of how climate is influencing societies today and may in the future.
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Affiliation(s)
| | - Stefani A Crabtree
- Department of Anthropology, Washington State University, Pullman, WA 99163
- Université de Franche-Comté, Maison des Sciences de l'Homme et de l'Environnement C. N. Ledoux (MSHE), 25030 Besançon Cedex, France
| | - R Kyle Bocinsky
- Department of Anthropology, Washington State University, Pullman, WA 99163
- Crow Canyon Archaeological Center, Cortez, CO 81321
| | - Timothy A Kohler
- Department of Anthropology, Washington State University, Pullman, WA 99163
- Crow Canyon Archaeological Center, Cortez, CO 81321
- Santa Fe Institute, Santa Fe, NM 87501
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21
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Cultural group selection follows Darwin's classic syllogism for the operation of selection. Behav Brain Sci 2016; 39:e58. [PMID: 27561598 DOI: 10.1017/s0140525x15000606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The main objective of our target article was to sketch the empirical case for the importance of selection at the level of groups on cultural variation. Such variation is massive in humans, but modest or absent in other species. Group selection processes acting on this variation is a framework for developing explanations of the unusual level of cooperation between non-relatives found in our species. Our case for cultural group selection (CGS) followed Darwin's classic syllogism regarding natural selection: If variation exists at the level of groups, if this variation is heritable, and if it plays a role in the success or failure of competing groups, then selection will operate at the level of groups. We outlined the relevant domains where such evidence can be sought and characterized the main conclusions of work in those domains. Most commentators agree that CGS plays some role in human evolution, although some were considerably more skeptical. Some contributed additional empirical cases. Some raised issues of the scope of CGS explanations versus competing ones.
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22
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MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 2016; 5:329-351. [PMID: 27813680 DOI: 10.1146/annurev-animal-022516-022747] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.
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Affiliation(s)
- David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland; .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; .,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 31000 Toulouse, France
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23
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Perry GLW, Wainwright J, Etherington TR, Wilmshurst JM. Experimental Simulation: Using Generative Modeling and Palaeoecological Data to Understand Human-Environment Interactions. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00109] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Decroocq S, Cornille A, Tricon D, Babayeva S, Chague A, Eyquard JP, Karychev R, Dolgikh S, Kostritsyna T, Liu S, Liu W, Geng W, Liao K, Asma BM, Akparov Z, Giraud T, Decroocq V. New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance. Mol Ecol 2016; 25:4712-29. [PMID: 27480465 DOI: 10.1111/mec.13772] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/14/2016] [Accepted: 07/25/2016] [Indexed: 12/01/2022]
Abstract
Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.
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Affiliation(s)
- Stéphane Decroocq
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Amandine Cornille
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala, Sweden
| | - David Tricon
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Sevda Babayeva
- Genetic Resources Institute of ANAS, Azadlig ave. 155, AZ1106, Baku, Azerbaijan
| | - Aurélie Chague
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Jean-Philippe Eyquard
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Raul Karychev
- Kazakh Research Institute of Horticulture and Viticulture, 238-a Gagarin Avenue, 480060, Almaty, Kazakhstan
| | - Svetlana Dolgikh
- Kazakh Research Institute of Horticulture and Viticulture, 238-a Gagarin Avenue, 480060, Almaty, Kazakhstan
| | - Tatiana Kostritsyna
- Botanical Garden of National Academy of Sciences, Akhunbaeva street 1a, 720064, Bishkek, Kyrgyzstan
| | - Shuo Liu
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.,Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou City, Liaoning, 115009, China
| | - Weisheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou City, Liaoning, 115009, China
| | - Wenjuan Geng
- College of Horticulture & Forestry Sciences, Xinjiang Agricultural University, 311 NongDaDong Road, 830052, Urumqi City, Xinjiang, China
| | - Kang Liao
- College of Horticulture & Forestry Sciences, Xinjiang Agricultural University, 311 NongDaDong Road, 830052, Urumqi City, Xinjiang, China
| | - Bayram M Asma
- Department of Horticulture, Inonu University, Malatya, 44210, Turkey
| | - Zeynal Akparov
- Genetic Resources Institute of ANAS, Azadlig ave. 155, AZ1106, Baku, Azerbaijan
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France.
| | - Véronique Decroocq
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France. .,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.
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25
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Shepherd LD, de Lange PJ, Cox S, McLenachan PA, Roskruge NR, Lockhart PJ. Evidence of a Strong Domestication Bottleneck in the Recently Cultivated New Zealand Endemic Root Crop, Arthropodium cirratum (Asparagaceae). PLoS One 2016; 11:e0152455. [PMID: 27011209 PMCID: PMC4806853 DOI: 10.1371/journal.pone.0152455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/15/2016] [Indexed: 11/18/2022] Open
Abstract
We use chloroplast DNA sequencing to examine aspects of the pre-European Māori cultivation of an endemic New Zealand root crop, Arthropodium cirratum (rengarenga). Researching the early stages of domestication is not possible for the majority of crops, because their cultivation began many thousands of years ago and/or they have been substantially altered by modern breeding methods. We found high levels of genetic variation and structuring characterised the natural distribution of A. cirratum, while the translocated populations only retained low levels of this diversity, indicating a strong bottleneck even at the early stages of this species’ cultivation. The high structuring detected at four chloroplast loci within the natural A. cirratum range enabled the putative source(s) of the translocated populations to be identified as most likely located in the eastern Bay of Plenty/East Cape region. The high structuring within A. cirratum also has implications for the conservation of genetic diversity within this species, which has undergone recent declines in both its natural and translocated ranges.
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Affiliation(s)
- Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- * E-mail:
| | - Peter J. de Lange
- Science and Capability Group, Terrestrial Ecosystems, Department of Conservation, Newton, Auckland, New Zealand
| | - Simon Cox
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Nick R. Roskruge
- Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Peter J. Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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26
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Zhang Y, Lu Y, Yindee M, Li K, Kuo H, Ju Y, Ye S, Faruque MO, Li Q, Wang Y, Cuong VC, Pham LD, Bouahom B, Yang B, Liang X, Cai Z, Vankan D, Manatchaiworakul W, Kowlim N, Duangchantrasiri S, Wajjwalku W, Colenbrander B, Zhang Y, Beerli P, Lenstra JA, Barker JSF. Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Mol Ecol 2016; 25:1530-50. [DOI: 10.1111/mec.13518] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/30/2015] [Accepted: 12/10/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Yi Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yongfang Lu
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Marnoch Yindee
- Department of Clinical Science and Public Health Faculty of Veterinary Science Mahidol University Kanchanaburi Campus Kanchanaburi 71150 Thailand
| | - Kuan‐Yi Li
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Hsiao‐Yun Kuo
- Livestock Research Institute Council of Agriculture Tainan 71246 Taiwan
| | - Yu‐Ten Ju
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Shaohui Ye
- College of Animal Science and Technology Yunnan Agricultural University Kunming 650201 China
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics Bangladesh Agricultural University Mymensingh 2202 Bangladesh
| | - Qiang Li
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Vu Chi Cuong
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Lan Doan Pham
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Bounthong Bouahom
- National Agriculture and Forestry Research Institute P.O. Box 811 Vientiane Capital Lao P.D.R
| | - Bingzhuang Yang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Xianwei Liang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Zhihua Cai
- College of Animal Science Anhui Science and Technology University Fengyang 233100 China
| | - Dianne Vankan
- The School of Veterinary Science University of Queensland, Gatton Campus Gatton Qld 4343 Australia
| | - Wallaya Manatchaiworakul
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Nonglid Kowlim
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Somphot Duangchantrasiri
- Khao‐Nang‐Ram Wildlife Research Station Department of National Parks Wildlife and Plant Conservation Bangkok 10900 Thailand
| | - Worawidh Wajjwalku
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Ben Colenbrander
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - Yuan Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Peter Beerli
- Department of Scientific Computing Florida State University Tallahassee FL 32306‐4120 USA
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - J. Stuart F. Barker
- School of Environmental and Rural Science University of New England Armidale NSW 2351 Australia
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27
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Besnard G, Rubio de Casas R. Single vs multiple independent olive domestications: the jury is (still) out. THE NEW PHYTOLOGIST 2016; 209:466-70. [PMID: 26555218 DOI: 10.1111/nph.13518] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, 31062, Toulouse Cedex 9, France
| | - Rafael Rubio de Casas
- Estación Experimental de Zonas Áridas, EEZA-CSIC, Carretera de Sacramento s/n, 04120, Almería, Spain
- UMR 5175 CEFE-Centre d'Ecologie Fonctionnelle et Evolutive (CNRS), 1919 Route de Mende, 34293, Montpellier Cedex 05, France
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28
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Xue AT, Hickerson MJ. The aggregate site frequency spectrum for comparative population genomic inference. Mol Ecol 2015; 24:6223-40. [PMID: 26769405 PMCID: PMC4717917 DOI: 10.1111/mec.13447] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to perform complex demographic inference at unprecedented resolution across assemblages of nonmodel species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) data sets collected from multiple, co-distributed species for assemblage-level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multispecies demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a data set consisting of five populations of the threespine stickleback (Gasterosteus aculeatus). Corroborating what is generally understood about the recent postglacial origins of these populations, the joint aSFS/hABC analysis strongly suggests that the stickleback data are most consistent with synchronous expansion after the Last Glacial Maximum (posterior probability = 0.99). The aSFS will have general application for multilevel statistical frameworks to test models involving assemblages and/or communities, and as large-scale SNP data from nonmodel species become routine, the aSFS expands the potential for powerful next-generation comparative population genomic inference.
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Affiliation(s)
- Alexander T. Xue
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and Behavior, City College and Graduate Center of City University of New York, 160 Convent Avenue, Marshak Science Building, Room 526, New York, NY 10031
| | - Michael J. Hickerson
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and Behavior, City College and Graduate Center of City University of New York, 160 Convent Avenue, Marshak Science Building, Room 526, New York, NY 10031
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29
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Transition to farming more likely for small, conservative groups with property rights, but increased productivity is not essential. Proc Natl Acad Sci U S A 2015; 112:14218-23. [PMID: 26578766 DOI: 10.1073/pnas.1511870112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Theories for the origins of agriculture are still debated, with a range of different explanations offered. Computational models can be used to test these theories and explore new hypotheses; Bowles and Choi [Bowles S, Choi J-K (2013) Proc Natl Acad Sci USA 110(22):8830-8835] have developed one such model. Their model shows the coevolution of farming and farming-friendly property rights, and by including climate variability, replicates the timings for the emergence of these events seen in the archaeological record. Because the processes modeled occurred a long time ago, it can be difficult to justify exact parameter values; hence, we propose a fitting to idealized outcomes (FIO) method to explore the model's parameter space in more detail. We have replicated the model of Bowles and Choi, and used the FIO method to identify complexities and interactions of the model previously unidentified. Our results indicate that the key parameters for the emergence of farming are group structuring, group size, conservatism, and farming-friendly property rights (lending further support to Bowles and Choi's original proposal). We also find that although advantageous, it is not essential that farming productivity be greater than foraging productivity for farming to emerge. In addition, we highlight how model behaviors can be missed when gauging parameter sensitivity via a fix-all-but-one variation approach.
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30
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Wright D. The Genetic Architecture of Domestication in Animals. Bioinform Biol Insights 2015; 9:11-20. [PMID: 26512200 PMCID: PMC4603525 DOI: 10.4137/bbi.s28902] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/24/2015] [Accepted: 08/26/2015] [Indexed: 12/12/2022] Open
Abstract
Domestication has been essential to the progress of human civilization, and the process itself has fascinated biologists for hundreds of years. Domestication has led to a series of remarkable changes in a variety of plants and animals, in what is termed the “domestication phenotype.” In domesticated animals, this general phenotype typically consists of similar changes in tameness, behavior, size/morphology, color, brain composition, and adrenal gland size. This domestication phenotype is seen in a range of different animals. However, the genetic basis of these associated changes is still puzzling. The genes for these different traits tend to be grouped together in clusters in the genome, though it is still not clear whether these clusters represent pleiotropic effects, or are in fact linked clusters. This review focuses on what is currently known about the genetic architecture of domesticated animal species, if genes of large effect (often referred to as major genes) are prevalent in driving the domestication phenotype, and whether pleiotropy can explain the loci underpinning these diverse traits being colocated.
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Affiliation(s)
- Dominic Wright
- IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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31
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Diez CM, Trujillo I, Martinez-Urdiroz N, Barranco D, Rallo L, Marfil P, Gaut BS. Olive domestication and diversification in the Mediterranean Basin. THE NEW PHYTOLOGIST 2015; 206:436-447. [PMID: 25420413 DOI: 10.1111/nph.13181] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/06/2014] [Indexed: 05/02/2023]
Abstract
Olive (Olea europaea ssp. europaea) is the most important oil fruit crop in temperate areas, but the origin of the cultivated olive remains unclear. The existence of one or several domestication events in the Mediterranean Basin (MB) is still debated. We analyzed a dataset of 387 cultivated and wild accessions that were genotyped at 25 simple-sequence repeat (SSR) loci. The sample represented genetic diversity at the geographic extremes of the MB. We inferred relationships among samples and also applied approximate Bayesian computation to estimate the most probable demographic model of our samples. Cultivated olives clustered into three different gene pools (Q1, Q2 and Q3), corresponding loosely to the west, central and eastern MB, respectively. Q1 consisted primarily of accessions from southern Spain, retained the fingerprint of a genetic bottleneck, and was closely related to accessions from the eastern MB. Q2 showed signs of recent admixture with wild olives and may derive from a local domestication event in the central MB. Overall our results suggest that admixture shaped olive germplasm and perhaps also local domestication events.
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Affiliation(s)
- Concepcion M Diez
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, 92697, USA
| | - Isabel Trujillo
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
| | - Nieves Martinez-Urdiroz
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
| | - Diego Barranco
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
| | - Luis Rallo
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
| | - Pedro Marfil
- Departamento de Historia del Arte, Arqueología y Música. Facultad de Filosofía y Letras, Universidad de Córdoba, Plaza del Cardenal Salazar 3, 14071, Córdoba, Spain
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, 92697, USA
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32
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Dussert Y, Snirc A, Robert T. Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet. Mol Ecol 2015; 24:1387-402. [PMID: 25705965 DOI: 10.1111/mec.13119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 02/04/2023]
Abstract
Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early- and late-flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early- and late-flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation-by-distance pattern. Conversely, our data brought evidence for two well-differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.
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Affiliation(s)
- Y Dussert
- Ecologie, Systématique et Evolution, UMR 8079 CNRS, Université Paris-Sud, 91405, Orsay, France; Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, 75252, Paris Cedex 05, France
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33
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Larson G, Fuller DQ. The Evolution of Animal Domestication. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-110512-135813] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Greger Larson
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, United Kingdom;
| | - Dorian Q. Fuller
- Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom
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Abstract
It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.
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Evaluating the roles of directed breeding and gene flow in animal domestication. Proc Natl Acad Sci U S A 2014; 111:6153-8. [PMID: 24753599 DOI: 10.1073/pnas.1312984110] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
For the last 150 y scholars have focused upon the roles of intentional breeding and genetic isolation as fundamental to understanding the process of animal domestication. This analysis of ethnoarchaeological, archaeological, and genetic data suggests that long-term gene flow between wild and domestic stocks was much more common than previously assumed, and that selective breeding of females was largely absent during the early phases of animal domestication. These findings challenge assumptions about severe genetic bottlenecks during domestication, expectations regarding monophyletic origins, and interpretations of multiple domestications. The findings also raise new questions regarding ways in which behavioral and phenotypic domestication traits were developed and maintained.
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