Zebus and Indian Wild Cattle
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Genomic Divergence of Zebu and Taurine Cattle Identified Through High-Density SNP Genotyping
Porto-Neto et al. BMC Genomics 2013, 14:876 http://www.biomedcentral.com/1471-2164/14/876 RESEARCH ARTICLE Open Access Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping Laercio R Porto-Neto1,2,6*, Tad S Sonstegard3*, George E Liu3, Derek M Bickhart3, Marcos VB Da Silva5, Marco A Machado5, Yuri T Utsunomiya4, Jose F Garcia4, Cedric Gondro2 and Curtis P Van Tassell3 Abstract Background: Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed FST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds. Results: Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of do- mestic cattle. The top 1% smoothed FST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top FST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:~50 Mb and BTA14:~25 Mb; both regions harboring candi- date genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. -
Paleogenomics of Animal Domestication
Paleogenomics of Animal Domestication Evan K. Irving-Pease, Hannah Ryan, Alexandra Jamieson, Evangelos A. Dimopoulos, Greger Larson, and Laurent A. F. Frantz Abstract Starting with dogs, over 15,000 years ago, the domestication of animals has been central in the development of modern societies. Because of its importance for a range of disciplines – including archaeology, biology and the humanities – domestication has been studied extensively. This chapter reviews how the field of paleogenomics has revolutionised, and will continue to revolutionise, our under- standing of animal domestication. We discuss how the recovery of ancient DNA from archaeological remains is allowing researchers to overcome inherent shortcom- ings arising from the analysis of modern DNA alone. In particular, we show how DNA, extracted from ancient substrates, has proven to be a crucial source of information to reconstruct the geographic and temporal origin of domestic species. We also discuss how ancient DNA is being used by geneticists and archaeologists to directly observe evolutionary changes linked to artificial and natural selection to generate a richer understanding of this fascinating process. Keywords Ancient DNA · Archaeology · Domestication · Entomology · Evolution · Genomics · Zoology E. K. Irving-Pease (*) · H. Ryan · A. Jamieson · E. A. Dimopoulos · G. Larson The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK e-mail: [email protected] L. A. F. Frantz (*) The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK School of Biological and Chemical Sciences, Queen Mary University of London, London, UK e-mail: [email protected] Charlotte Lindqvist and Om P. -
Genetics and Animal Domestication: New Windows on an Elusive Process K
Journal of Zoology. Print ISSN 0952-8369 Genetics and animal domestication: new windows on an elusive process K. Dobney1 & G. Larson2 1 Department of Archaeology, University of Durham, Durham, UK 2 Department of Zoology, Henry Wellcome Ancient Biomolecules Centre, University of Oxford, UK Keywords Abstract domestication; genetics; phylogeography; molecular clocks; paedomorphosis. Domesticated animals are universally familiar. How, when, where and why they became domesticated is less well understood. The genetic revolution of the past few Correspondence decades has facilitated novel insights into a field that previously was principally the Greger Larson, Department of Zoology, domain of archaeozoologists. Although some of the conclusions drawn from Henry Wellcome Ancient Biomolecules genetic data have proved to be contentious, many studies have significantly altered Centre, University of Oxford, South Parks or refined our understanding of past human animal relationships. This review Road OX1 3PS, UK seeks not only to discuss the wider concerns and ramifications of genetic Email: [email protected] approaches to the study of animal domestication but also to provide a broader theoretical framework for understanding the process itself. More specifically, we Received 6 July 2005; accepted 8 September discuss issues related to the terminology associated with domestication, the 2005 possibility of domestication genes, and the promise and problems of genetics to answer the fundamental questions associated with domestication. doi:10.1111/j.1469-7998.2006.00042.x Introduction Defining domestication Over the past 10 000 years, human history has been wholly Terminology typically used in domestication studies, including transformed by the domestication of plants and animals. the word ‘domestication’ itself, is often confusing and poorly Although the term ‘domestic animal’ has universal meaning, defined. -
Rethinking Dog Domestication by Integrating Genetics, Archeology, and Biogeography
Rethinking dog domestication by integrating genetics, archeology, and biogeography Greger Larsona,1, Elinor K. Karlssonb,c, Angela Perria, Matthew T. Webster d,SimonY.W.Hoe, Joris Petersf, Peter W. Stahl g, Philip J. Piperh,i, Frode Lingaasj, Merete Fredholmk, Kenine E. Comstockl, Jaime F. Modianom,n, Claude Schellingo, Alexander I. Agoulnikp, Peter A. Leegwaterq, Keith Dobneyr, Jean-Denis Vignes, Carles Vilàt, Leif Anderssond,u, and Kerstin Lindblad-Tohb,d aDurham Evolution and Ancient DNA, Department of Archaeology, University of Durham, Durham DH1 3LE, United Kingdom; bBroad Institute of MIT and Harvard, Cambridge MA 02142; cFaculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge MA 02138; dScience for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden; eSchool of Biological Sciences, University of Sydney, Sydney NSW 2006, Australia; fVeterinary Sciences Department, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University, 80539 Munich, Germany; gDepartment of Anthropology, University of Victoria, Victoria, BC, Canada V8W 2Y2; hSchool of Archaeology and Anthropology, Australian National University, Canberra, Australian Capital Territory 200, Australia; iArchaeological Studies Program, University of the Philippines, Diliman, 1101, Quezon City, Philippines; jDepartment of Basic Sciences and Aquatic Medicine, Division of Genetics, Norwegian School of Veterinary Science, -
Detecting Sex and Selection in Ancient Cattle Remains Using
!! ! " # $ %&'%(&)% $ * +(+%(''()%(& , - ,,, .(%)/)&% ! " # $% % %&%%' ' ' ( )* + ) , -)$% %) , , . / , ( ). ) 0!1)22 ) )3,40154 566!501$ 52) . %%%% + + + ). ++ ' )* 2$0 ' 7 + )" + + ' ' ). + 4 ' ' ' '+ / + ) * ' + '' ) 5 8 ' 9 . 3 '' : + $%%%%51%%%% + + ).9 ,( + + '8 ' ' ) * + 7 )3 ,( + + + ' )* ' + +' ' 4 ) .,( 8 ! !" ! # !$ %&'( ! !)*+,-. ! ;-, $% % 3,, 26 52$ ! 3,40154 566!501$ 52 & &&& 5 $<$2 = &>> )7)> ? @ & &&& 5 $<$2 A Till mamma Art work on front page by Lotta Tomasson List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I Svensson, E.M., Axelsson, E., Vretemark, M., Makowiecki, D., Gilbert, M.T.P., Willerslev, E., Götherström, A. Insights into Y chromosomal genetic variation and effective population size in the extinct European aurochs Bos primigenius. Manuscript II Svensson, E., Götherström, A., (2008) Temporal fluctuations of Y-chromosomal variation in Bos taurus. Biology Letters, 4(6):752-754 III Svensson, E.M., Götherström, A., Vretemark, M. (2008) A DNA test for sex identification in cattle confirms osteometric results. Journal of Archaeological Science 35(4):942-946 IV Telldahl, Y., Svensson, E.M., Götherström, A., Storå, J. -
Characterisation of the Cattle, Buffalo and Chicken Populations in the Northern Vietnamese Province of Ha Giang Cécile Berthouly
Characterisation of the cattle, buffalo and chicken populations in the northern Vietnamese province of Ha Giang Cécile Berthouly To cite this version: Cécile Berthouly. Characterisation of the cattle, buffalo and chicken populations in the northern Vietnamese province of Ha Giang. Life Sciences [q-bio]. AgroParisTech, 2008. English. NNT : 2008AGPT0031. pastel-00003992 HAL Id: pastel-00003992 https://pastel.archives-ouvertes.fr/pastel-00003992 Submitted on 16 Jun 2009 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Agriculture, UFR Génétique, UMR 1236 Génétique Alimentation, Biologie, Biodiva project UR 22 Faune Sauvage Elevage et Reproduction et Diversité Animales Environnement, Santé Thesis to obtain the degree DOCTEUR D’AGROPARISTECH Field: Animal Genetics presented and defended by Cécile BERTHOULY on May 23rd, 2008 Characterisation of the cattle, buffalo and chicken populations in the Northern Vietnamese province of Ha Giang Supervisors: Jean-Charles MAILLARD and Etienne VERRIER Committee Steffen WEIGEND Senior scientist, Federal Agricultural -
Animal Domestication in the Era of Ancient Genomics Laurent Frantz, Daniel Bradley, Greger Larson, Ludovic Orlando
Animal domestication in the era of ancient genomics Laurent Frantz, Daniel Bradley, Greger Larson, Ludovic Orlando To cite this version: Laurent Frantz, Daniel Bradley, Greger Larson, Ludovic Orlando. Animal domestication in the era of ancient genomics. Nature Reviews Genetics, Nature Publishing Group, 2020, 21 (8), pp.449-460. 10.1038/s41576-020-0225-0. hal-03030302 HAL Id: hal-03030302 https://hal.archives-ouvertes.fr/hal-03030302 Submitted on 30 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Animal domestication in the era of ancient genomics Laurent A. F. Frantz1†, Daniel G. Bradley2, Greger Larson3 and Ludovic Orlando4,5† 1 School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. 2 Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland 3 The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK. 4 Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, -
Genetic Variation of Mitochondrial DNA Within Domestic Yak Populations J.F
Genetic variation of mitochondrial DNA within domestic yak populations J.F. Bailey,1 B. Healy,1 H. Jianlin,2 L. Sherchand,3 S.L. Pradhan,4 T. Tsendsuren,5 J.M. Foggin,6 C. Gaillard,7 D. Steane,8 I. Zakharov 9 and D.G. Bradley1 1. Department of Genetics, Trinity College, Dublin 2, Ireland 2. Department of Animal Science, Gansu Agricultural University, Lanzhou 730070, Gansu, P.R. China 3. Livestock Production Division, Department of Livestock Services, Harihar Bhawan, Pulchowk, Nepal 4. Resource Development Advisor, Nepal–Australia Community Resource Management Project, Kathmandu, Nepal 5. Institute of Biology, Academy of Sciences of Mongolia, Ulaan Baatar, Mongolia 6. Department of Biology, Arizona State University, Tempe, AZ 85287–1501 USA 7. Institute of Animal Breeding, University of Berne, Bremgarten-strasse 109a, CH-3012 Berne, Switzerland 8. FAO (Food and Agricultural Organization of the United Nations) Regional Office for Asia and the Pacific, 39 Phra Atit Road, Bangkok 10200, Thailand 9. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkin str., 3, 117809 GSP-1, Moscow B-333, Russia Summary Yak (Bos grunniens) are members of the Artiodactyla, family Bovidae, genus Bos. Wild yak are first observed at Pleistocene levels of the fossil record. We believed that they, together with the closely related species of Bos taurus, B. indicus and Bison bison, resulted from a rapid radiation of the genus towards the end of the Miocene. Today domestic yak live a fragile existence in a harsh environment. Their fitness for this environment is vital to their survival and to the millions of pastoralists who depend upon them. -
Comparative Genomic Evidence for Self-Domestication in Homo Sapiens
bioRxiv preprint doi: https://doi.org/10.1101/125799; this version posted April 9, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Comparative genomic evidence for self-domestication in Homo sapiens Constantina Theofanopoulou1,2,a, Simone Gastaldon1,a, Thomas O’Rourke1, Bridget D. Samuels3, Angela Messner1, Pedro Tiago Martins1, Francesco Delogu4, Saleh Alamri1, and Cedric Boeckx1,2,5,b 1Section of General Linguistics, Universitat de Barcelona 2Universitat de Barcelona Institute for Complex Systems 3Center for Craniofacial Molecular Biology, University of Southern California 4Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU) 5ICREA aThese authors contributed equally to this work bCorresponding author: [email protected] ABSTRACT This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the “domestication syndrome” in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest. Introduction Recent advances in genomics, coupled with other sources of information, offer new opportunities to test long-standing hypotheses about human evolution. Especially in the domain of cognition, the retrieval of ancient DNA could, with the help of well-articulated linking hypotheses connecting genes, brain and cognition, shed light on the emergence of ‘cognitive modernity’. -
Working with the Public: How an Unusual Museum Enquiry Turned Into Travels Through Time and Space
Freedman, J and Evans, J 2015 Working with the Public: How an Unusual Museum Enquiry Turned into Travels Through Time and Space. Open Quaternary, 1: 8, pp. 1–14, DOI: http://dx.doi.org/10.5334/oq.ah ENGAGEMENT PAPER Working with the Public: How an Unusual Museum Enquiry Turned into Travels Through Time and Space Jan Freedman* and Jane Evans† This article has been corrected here: Museum enquiries offer a unique opportunity to engage on a one-to-one level with members of the pub- lic. This paper covers an unusual enquiry from 2013 of an unknown tooth that was brought into Plym- outh City Museum and Art Gallery for identification. We highlight how museum enquiries can engage with members of the public by involving them directly with original scientific research. The tooth was found in a garden in Plymouth with no associated data of about where it originated. We identified the tooth, and the enquirer researched the history of the house. The tooth gave the appearance of a sub-fossil so with the large number of Quaternary sites in Plymouth, together with the identifica- tion of the previous owner on the site, there were valid reasons to undertake testing of the tooth to determine its origin. Strontium (Sr) isotope analysis of the tooth was carried out to determine if the tooth was British and radiocarbon dating was undertaken to work out the age of the tooth. The 87Sr /86Sr of the leopard tooth gave a value of 0.716131, with Sr concentrations at 568ppm. This is a high concentration of Sr ppm relative to other British data, suggesting a non-British origin. -
Human Origin Sites and the World Heritage Convention in Eurasia
World Heritage papers41 HEADWORLD HERITAGES 4 Human Origin Sites and the World Heritage Convention in Eurasia VOLUME I In support of UNESCO’s 70th Anniversary Celebrations United Nations [ Cultural Organization Human Origin Sites and the World Heritage Convention in Eurasia Nuria Sanz, Editor General Coordinator of HEADS Programme on Human Evolution HEADS 4 VOLUME I Published in 2015 by the United Nations Educational, Scientific and Cultural Organization, 7, place de Fontenoy, 75352 Paris 07 SP, France and the UNESCO Office in Mexico, Presidente Masaryk 526, Polanco, Miguel Hidalgo, 11550 Ciudad de Mexico, D.F., Mexico. © UNESCO 2015 ISBN 978-92-3-100107-9 This publication is available in Open Access under the Attribution-ShareAlike 3.0 IGO (CC-BY-SA 3.0 IGO) license (http://creativecommons.org/licenses/by-sa/3.0/igo/). By using the content of this publication, the users accept to be bound by the terms of use of the UNESCO Open Access Repository (http://www.unesco.org/open-access/terms-use-ccbysa-en). The designations employed and the presentation of material throughout this publication do not imply the expression of any opinion whatsoever on the part of UNESCO concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. The ideas and opinions expressed in this publication are those of the authors; they are not necessarily those of UNESCO and do not commit the Organization. Cover Photos: Top: Hohle Fels excavation. © Harry Vetter bottom (from left to right): Petroglyphs from Sikachi-Alyan rock art site. -
Aurochs Genetics, a Cornerstone of European Biodiversity
Aurochs genetics, a cornerstone of European biodiversity Picture: Manolo Uno (c) Staffan Widstrand Authors: • drs. Ronald Goderie (Taurus Foundation); • dr. Johannes A. Lenstra (Utrecht University, Faculty of Veterinary Medicine); • Maulik Upadhyay (pHD Wageningen University); • dr. Richard Crooijmans (Animal Breeding and Genomics Centre, Wageningen University); • ir. Leo Linnartz (Ark Nature) Summary of: Aurochs Genetics, a cornerstone of biodiversity Preface In 2015 a report is written on Aurochs genetics, made possible by a grant from the Dutch Liberty Wildlife fund. This fund provided the Taurus foundation with a grant of EUR 20.000 to conduct genetic research on aurochs and its relation with nowadays so- called ‘primitive’ breeds. This is the summary of that report. This summary shortly describes the current state of affairs, what we do know early 2015 about the aurochs, about domestic cattle and the relationship of aurochs and the primitive breeds used in the Tauros Programme. Nijmegen, December 2015. page 2 Summary of: Aurochs Genetics, a cornerstone of biodiversity Table of contents Preface 2 Table of contents ......................................................................................................... 3 Summary ..................................................................................................................... 4 1 Introduction .......................................................................................................... 6 2 Aurochs: a short description .................................................................................