Paleogenomics of Animal Domestication
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Maladaptation in Feral and Domesticated Animals
Nova Southeastern University NSUWorks Biology Faculty Articles Department of Biological Sciences 8-2019 Maladaptation in Feral and Domesticated Animals Eben Gering Michigan State University, [email protected] Darren Incorvaia Michigan State University R. Henriksen Linkoping University- Sweden Dominic Wright Linkoping University- Sweden Follow this and additional works at: https://nsuworks.nova.edu/cnso_bio_facarticles Part of the Biology Commons NSUWorks Citation Gering, Eben; Darren Incorvaia; R. Henriksen; and Dominic Wright. 2019. "Maladaptation in Feral and Domesticated Animals." Evolutionary Applications 12, (7): 1274-1286. doi:10.1111/eva.12784. This Article is brought to you for free and open access by the Department of Biological Sciences at NSUWorks. It has been accepted for inclusion in Biology Faculty Articles by an authorized administrator of NSUWorks. For more information, please contact [email protected]. Received: 17 October 2018 | Revised: 10 January 2019 | Accepted: 7 February 2019 DOI: 10.1111/eva.12784 SPECIAL ISSUE REVIEW AND SYNTHESES Maladaptation in feral and domesticated animals Eben Gering1 | Darren Incorvaia1 | Rie Henriksen2 | Dominic Wright2 | Thomas Getty1 1Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Abstract Program, Michigan State University, East Selection regimes and population structures can be powerfully changed by domesti‐ Lansing, Michigan cation and feralization, and these changes can modulate animal fitness in both cap‐ 2IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping tive and natural environments. In this review, we synthesize recent studies of these University, Sweden two processes and consider their impacts on organismal and population fitness. Correspondence Domestication and feralization offer multiple windows into the forms and mecha‐ Eben Gering, Department of Integrative nisms of maladaptation. -
The Evolution of Animal Domestication
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/266740619 The Evolution of Animal Domestication Article in Annual Review of Ecology Evolution and Systematics · October 2014 DOI: 10.1146/annurev-ecolsys-120213-091620 CITATIONS READS 179 3,162 2 authors: Greger Larson Dorian Q Fuller University of Oxford University College London 196 PUBLICATIONS 6,523 CITATIONS 322 PUBLICATIONS 12,021 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Dog Domestication View project Rwandan Archaeology View project All content following this page was uploaded by Dorian Q Fuller on 12 October 2014. The user has requested enhancement of the downloaded file. ES45CH06-Larson ARI 16 September 2014 11:18 V I E E W R S I E N C N A D V A The Evolution of Animal Domestication Greger Larson1 and Dorian Q. Fuller2 1Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham, DH1 3LE, United Kingdom; email: [email protected] 2Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom Annu. Rev. Ecol. Evol. Syst. 2014. 66:115–36 Keywords The Annual Review of Ecology, Evolution, and archaeology, genetics, livestock, introgression, selection, agriculture Systematics is online at ecolsys.annualreviews.org This article’s doi: Abstract 10.1146/annurev-ecolsys-120213-091620 The domestication of plants and animals over the past 11,500 years has Copyright c 2014 by Annual Reviews. had a significant effect not just on the domesticated taxa but also on human All rights reserved evolution and on the biosphere as a whole. -
Archaeological Central American Maize Genomes Suggest Ancient Gene Flow from South America
Archaeological Central American maize genomes suggest ancient gene flow from South America Logan Kistlera,1, Heather B. Thakarb, Amber M. VanDerwarkerc, Alejandra Domicd,e, Anders Bergströmf, Richard J. Georgec, Thomas K. Harperd, Robin G. Allabyg, Kenneth Hirthd, and Douglas J. Kennettc,1 aDepartment of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560; bDepartment of Anthropology, Texas A&M University, College Station, TX 77843; cDepartment of Anthropology, University of California, Santa Barbara, CA 93106; dDepartment of Anthropology, The Pennsylvania State University, University Park, PA 16802; eDepartment of Geosciences, The Pennsylvania State University, University Park, PA 16802; fAncient Genomics Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; and gSchool of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom Edited by David L. Lentz, University of Cincinnati, Cincinnati, OH, and accepted by Editorial Board Member Elsa M. Redmond November 3, 2020 (received for review July 24, 2020) Maize (Zea mays ssp. mays) domestication began in southwestern 16). However, precolonial backflow of divergent maize varieties Mexico ∼9,000 calendar years before present (cal. BP) and humans into Central and Mesoamerica during the last 9,000 y remains dispersed this important grain to South America by at least 7,000 understudied, and could have ramifications for the history of cal. BP as a partial domesticate. South America served as a second- maize as a staple in the region. ary improvement center where the domestication syndrome be- Morphological evidence from ancient maize found in ar- came fixed and new lineages emerged in parallel with similar chaeological sites combined with DNA data confirms a complex processes in Mesoamerica. -
"Paleogenomics" In
Rev. Cell Biol. Mol. Medicine Paleogenomics 243 Paleogenomics Peter D. Heintzman*, André E. R. Soares*, Dan Chang, and Beth Shapiro Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA 1 Reconstructing Paleogenomes 245 1.1 Ancient DNA 245 1.1.1 The Nature of Ancient DNA 245 1.1.2 The Common Effects of DNA Damage 246 1.2 The Recovery and Sequencing of Ancient DNA 246 1.2.1 Ancient DNA Extraction 246 1.2.2 DNA Library Preparation 247 1.2.3 Capture-Based Target Enrichment 248 1.2.4 Quantification of aDNA and Sequencing 249 1.3 Assembly and Analysis of a Paleogenome 250 1.3.1 Initial Data Processing 251 1.3.2 Mapping and Quality Control 252 1.3.3 Paleogenomic Analysis 253 2 Case Studies 253 2.1 Hominin Paleogenomics 253 2.1.1 The Origin of Hominin Paleogenetics 253 2.1.2 Entering the Paleogenomics Era 254 2.1.3 The First Complete Human Paleogenome 255 2.1.4 Human and Neandertal Paleogenomics 255 2.2 The Black Death and Insights into Ancient Plagues 257 2.3 Reconstruction and Selection of Ancient Phenotypes 258 2.4 Epigenetics of Ancient Species 260 3 Conclusions 261 Acknowledgments 261 References 261 ∗These authors contributed equally to this study. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA Vol 1 | No 3 | 2015 244 Paleogenomics Rev. Cell Biol. Mol. Medicine Keywords Paleogenomics The science of reconstructing and analyzing the genomes of organisms that are not alive in the present day. Ancient DNA (aDNA) Ancient DNA is DNA that is extracted and characterized from degraded biological spec- imens, including preserved bones, teeth, hair, seeds, or other tissues. -
Inference of Natural Selection from Ancient DNA
COMMENT AND OPINION doi:10.1002/evl3.165 Inference of natural selection from ancient DNA Marianne Dehasque,1,2,3,4 Marıa´ C. Avila-Arcos,´ 5 David Dıez-del-Molino,´ 1,3 Matteo Fumagalli,6 Katerina Guschanski,7 Eline D. Lorenzen,8 Anna-Sapfo Malaspinas,9,10 Tomas Marques-Bonet,11,12,13,14 Michael D. Martin,15 Gemma G. R. Murray,16 Alexander S. T. Papadopulos,17 Nina Overgaard Therkildsen,18 Daniel Wegmann,19,20 Love Dalen,´ 1,2 and Andrew D. Foote17,21 1Centre for Palaeogenetics 10691, Stockholm, Sweden 2Department of Bioinformatics and Genetics, Swedish Museum of Natural History 10405 Stockholm, Sweden 3Department of Zoology, Stockholm University 10691 Stockholm, Sweden 4E-mail: [email protected] 5International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro 76230, Mexico 6Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot SL5 7PY, United Kingdom 7Animal Ecology, Department of Ecology and Genetics, Science for Life Laboratory, Uppsala University 75236, Uppsala, Sweden 8Globe Institute, University of Copenhagen DK-1350, Copenhagen, Denmark 9Department of Computational Biology, University of Lausanne 1015, Lausanne, Switzerland 10SIB Swiss Institute of Bioinformatics 1015, Lausanne, Switzerland 11Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomedica` de Barcelona, Barcelona, Spain 12National Centre for Genomic Analysis—Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028, Barcelona, Spain 13Institucio Catalana -
The History of Farm Foxes Undermines the Animal Domestication Syndrome, Trends in Ecology & Evolution (2019)
Please cite this article in press as: Lord et al., The History of Farm Foxes Undermines the Animal Domestication Syndrome, Trends in Ecology & Evolution (2019), https://doi.org/10.1016/j.tree.2019.10.011 Trends in Ecology & Evolution Opinion The History of Farm Foxes Undermines the Animal Domestication Syndrome Kathryn A. Lord,1,2 Greger Larson,3,@ Raymond P. Coppinger,4,6 and Elinor K. Karlsson1,2,5,@,* The Russian Farm-Fox Experiment is the best known experimental study in animal domestication. Highlights By subjecting a population of foxes to selection for tameness alone, Dimitry Belyaev generated The ‘domestication syndrome’ has foxes that possessed a suite of characteristics that mimicked those found across domesticated been a central focus of research species. This ‘domestication syndrome’ has been a central focus of research into the biological into the biological processes un- pathways modified during domestication. Here, we chart the origins of Belyaev’s foxes in derlying domestication. The eastern Canada and critically assess the appearance of domestication syndrome traits across an- Russian Farm-Fox Experiment was imal domesticates. Our results suggest that both the conclusions of the Farm-Fox Experiment the first to test whether there is a and the ubiquity of domestication syndrome have been overstated. To understand the process causal relationship between selec- tion for tameness and the domes- of domestication requires a more comprehensive approach focused on essential adaptations to tication syndrome. human-modified environments. Historical records and genetic The Origins of Domestication Syndrome analysis show that the foxes used in The domestication syndrome describes a suite of behavioral and morphological characteristics the Farm-Fox Experiment origi- consistently observed in domesticated populations. -
Vulpes Vulpes) Evolved Throughout History?
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Environmental Studies Undergraduate Student Theses Environmental Studies Program 2020 TO WHAT EXTENT HAS THE RELATIONSHIP BETWEEN HUMANS AND RED FOXES (VULPES VULPES) EVOLVED THROUGHOUT HISTORY? Abigail Misfeldt University of Nebraska-Lincoln Follow this and additional works at: https://digitalcommons.unl.edu/envstudtheses Part of the Environmental Education Commons, Natural Resources and Conservation Commons, and the Sustainability Commons Disclaimer: The following thesis was produced in the Environmental Studies Program as a student senior capstone project. Misfeldt, Abigail, "TO WHAT EXTENT HAS THE RELATIONSHIP BETWEEN HUMANS AND RED FOXES (VULPES VULPES) EVOLVED THROUGHOUT HISTORY?" (2020). Environmental Studies Undergraduate Student Theses. 283. https://digitalcommons.unl.edu/envstudtheses/283 This Article is brought to you for free and open access by the Environmental Studies Program at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Environmental Studies Undergraduate Student Theses by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. TO WHAT EXTENT HAS THE RELATIONSHIP BETWEEN HUMANS AND RED FOXES (VULPES VULPES) EVOLVED THROUGHOUT HISTORY? By Abigail Misfeldt A THESIS Presented to the Faculty of The University of Nebraska-Lincoln In Partial Fulfillment of Requirements For the Degree of Bachelor of Science Major: Environmental Studies Under the Supervision of Dr. David Gosselin Lincoln, Nebraska November 2020 Abstract Red foxes are one of the few creatures able to adapt to living alongside humans as we have evolved. All humans and wildlife have some id of relationship, be it a friendly one or one of mutual hatred, or simply a neutral one. Through a systematic research review of legends, books, and journal articles, I mapped how humans and foxes have evolved together. -
Hered 445 Master..Hered 445 .. Page648
Heredity 81 (1998) 648–658 Received 19 March 1998, accepted 15 June 1998 Genetic analysis of the domestication syndrome in pearl millet (Pennisetum glaucum L., Poaceae): inheritance of the major characters V. PONCET*%, F. LAMY%, J. ENJALBERT^, H. JOLY§, A. SARR% & T. ROBERT% %Laboratoire d’Evolution et Syst´ematique, Universit´e Paris XI, Bˆat. 362, F-91405 Orsay Cedex, France, ^Station de G´en´etique V´eg´etale, Ferme du Moulon, F-91190 Gif sur Yvette, France and §CIRAD-Forˆet, campus international de Baillarguet, BP 5035, F-34032 Montpellier Cedex 1, France The inheritance of domestication traits distinguishing pearl millet (Pennisetum glaucum) from its wild relatives (P. mollissimum) was assessed in F2 progenies derived from a cross between a typical landrace of pearl millet and a wild ecotype. Despite a high level of recombination between the two genomes, the existence of preferential associations between some characters was demonstrated, leading, in particular, to cultivated-like phenotypes. Traits determining spikelet structure showed simple Mendelian inheritance. Moreover, the genes encoding these traits mapped in a linkage group where quantitative trait loci for spike size and tillering habit were found. This linkage group could correspond to one of the two chromosome segments that have already been shown to be involved in the variation for spikelet structure in progenies from several cultivatedÅwild crosses. A synthetic map of these two regions is given. The evolutionary significance of this genomic organization in relation to the domestication process is discussed, as well as its potential use for pearl millet genetic resources enhancement. Keywords: domestication, genetic map, pearl millet, Pennisetum glaucum. -
UNIVERSITY of CALIFORNIA Los Angeles the Evolution of Animals Through Domestication and Other Human Relationships
UNIVERSITY OF CALIFORNIA Los Angeles The Evolution of Animals through Domestication and other Human Relationships: An Animal-Centered Approach A thesis submitted in partial satisfaction of the requirements for the degree Master of Arts in Anthropology by Steven Michael Ammerman 2017 ©Copyright by Steven Michael Ammerman 2017 ABSTRACT OF THE THESIS The Evolution of Animals through Domestication and other Human Relationships: An Animal-Centered Approach by Steven Michael Ammerman Master of Arts in Anthropology University of California, Los Angeles, 2017 Professor Monica L. Smith, Chair As a component of the environment themselves, humans maintain a mutualistic modifying process with that environment. The interaction between humans and animals has led to different categories of relationships—commensal animals, tame animals, domesticated animals, and feral animals. In the study of human-animal interactions, the foremost consideration is how the niche construction of humans affects the evolutionary trajectory of other animals, but other animals also construct niches within this human-impacted environment to enhance their survival. The concept of niche construction provides a useful way of thinking about how humans and animals interact in the environment because this concept considers physical changes, behavioral changes, and cultural changes. In an animal-centered approach, consideration of how the traits and actions of animals play an active role in allowing and encouraging their ongoing relationships with humans is just as important as the consideration of actions of humans. ii The thesis of Steven Michael Ammerman is approved. Nancy E. Levine P. Jeffrey Brantingham Monica L. Smith, Committee Chair University of California, Los Angeles 2017 iii Table of Contents 1. -
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. -
Awn Reduction and the Domestication of Asian Rice: a Syndrome Or Crop Improvement Trait? Serge Svizzero, Avik Ray, Debarati Chakraborty
Awn Reduction and the Domestication of Asian Rice: A Syndrome or Crop Improvement Trait? Serge Svizzero, Avik Ray, Debarati Chakraborty To cite this version: Serge Svizzero, Avik Ray, Debarati Chakraborty. Awn Reduction and the Domestication of Asian Rice: A Syndrome or Crop Improvement Trait?. Economic Botany, Springer Verlag, 2019, pp.1-12. 10.1007/s12231-019-09465-0. hal-02275855 HAL Id: hal-02275855 https://hal.univ-reunion.fr/hal-02275855 Submitted on 2 Sep 2019 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. 1 Awn Reduction and the Domestication of Asian Rice: A Syndrome or Crop Improvement Trait? Serge Svizzero1, Avik Ray2,*, Debarati Chakraborty2,3 1- Faculté de Droit et d’Economie, Université de La Réunion, 15 Avenue René Cassin. CS 92003, 97744 Saint Denis Cedex 9, France, Tel: +262 262 13 82 58; ORCID: 0000-0003- 3895-7273 2 - Center for studies in Ethnobiology, Biodiversity, and sustainability (CEiBa), B.G. Road, Mokdumpur, Malda – 732103, West Bengal, India; ORCID: 0000-0003-1662-7679 3 - Department of Molecular Biology and Biotechnology, University of Kalyani, Kalyani, India; ORCID: 0000-0002-1939-9889 * [email protected] Running title: SVIZZERO, RAY AND CHAKRABORTY: RICE AWN REDUCTION Words account: 7596; Abstract: 180. -
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,