The Domestication Syndrome Genes Responsible for the Major Changes
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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. -
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. -
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. -
Genes Encoding Plastid Acetyl-Coa Carboxylase and 3-Phosphoglycerate Kinase of the Triticum͞aegilops Complex and the Evolutionary History of Polyploid Wheat
Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum͞Aegilops complex and the evolutionary history of polyploid wheat Shaoxing Huang*†, Anchalee Sirikhachornkit*, Xiujuan Su*, Justin Faris‡§, Bikram Gill‡, Robert Haselkorn*, and Piotr Gornicki*¶ *Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637; and ‡Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 Contributed by Robert Haselkorn, April 12, 2002 The classic wheat evolutionary history is one of adaptive radiation of at the diploid level from a common diploid ancestor and conver- the diploid Triticum͞Aegilops species (A, S, D), genome convergence gence at the polyploid level involving the diverged diploid genomes and divergence of the tetraploid (Triticum turgidum AABB, and (2). Various Aegilops species contributed significantly to the genetic Triticum timopheevii AAGG) and hexaploid (Triticum aestivum, makeup of the polyploid wheats. Extensive classical analyses and AABBDD) species. We analyzed Acc-1 (plastid acetyl-CoA carboxylase) more recent molecular studies have provided information on the and Pgk-1 (plastid 3-phosphoglycerate kinase) genes to determine identity of donors and some of the patterns of genome evolution of phylogenetic relationships among Triticum and Aegilops species of the Triticum͞Aegilops species (3). A review of Triticum and Aegilops the wheat lineage and to establish the timeline of wheat evolution taxonomy and related literature is available from the Wheat based on gene sequence comparisons. Triticum urartu was confirmed Genetic Resource Center at ksu.edu͞wgrc. as the A genome donor of tetraploid and hexaploid wheat. The A The Triticum and Aegilops genera contain 13 diploid and 18 genome of polyploid wheat diverged from T. -
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. -
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. -
Who's Related to Whom?
149 Who’s related to whom? Recent results from molecular systematic studies Elizabeth A Kellogg Similarities among model systems can lead to generalizations systematist’s question-why are there so many different about plants, but understanding the differences requires kinds of organisms? Studies of the evolution of develop- systematic data. Molecular phylogenetic analyses produce ment demand that the investigator go beyond the model results similar to traditional classifications in the grasses system and learn the pattern of variation in its relatives (Poaceae), and relationships among the cereal crops [3*]. This requires a reasonable assessment of the relatives’ are quite clear. Chloroplast-based phylogenies for the identity. Solanaceae show that tomato is best considered as a species of Solarium, closely related to potatoes. Traditional Knowledge of plant relationships has increased rapidly classifications in the Brassicaceae are misleading with in the past decade, reflecting partly the development regard to true phylogenetic relationships and data are only of molecular systematics. It has been known for some now beginning to clarify the situation. Molecular data are time that plant classifications do not reflect phylogeny also being used to revise our view of relationships among accurately, even though both phylogeny and classification flowering plant families. Phylogenetic data are critical for are hierarchical. The hierarchy of classification was interpreting hypotheses of the evolution of development. imposed in the late 18th century, well before ideas of descent with modification (evolution) were prevalent [4]. These pre-evolutionary groups were then re-interpreted in Address an evolutionary context, and were assumed to be products Harvard University Herbaria, 22 Divinity Avenue Cambridge, MA of evolution, rather than man-made artefacts. -
Evolutionary Consequences of Dioecy in Angiosperms: the Effects of Breeding System on Speciation and Extinction Rates
EVOLUTIONARY CONSEQUENCES OF DIOECY IN ANGIOSPERMS: THE EFFECTS OF BREEDING SYSTEM ON SPECIATION AND EXTINCTION RATES by JANA C. HEILBUTH B.Sc, Simon Fraser University, 1996 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Department of Zoology) We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA July 2001 © Jana Heilbuth, 2001 Wednesday, April 25, 2001 UBC Special Collections - Thesis Authorisation Form Page: 1 In presenting this thesis in partial fulfilment of the requirements for an advanced degree at the University of British Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarly purposes may be granted by the head of my department or by his or her representatives. It is understood that copying or publication of this thesis for financial gain shall not be allowed without my written permission. The University of British Columbia Vancouver, Canada http://www.library.ubc.ca/spcoll/thesauth.html ABSTRACT Dioecy, the breeding system with male and female function on separate individuals, may affect the ability of a lineage to avoid extinction or speciate. Dioecy is a rare breeding system among the angiosperms (approximately 6% of all flowering plants) while hermaphroditism (having male and female function present within each flower) is predominant. Dioecious angiosperms may be rare because the transitions to dioecy have been recent or because dioecious angiosperms experience decreased diversification rates (speciation minus extinction) compared to plants with other breeding systems. -
1 the Limits of Selection Under Plant Domestication Robin G Allaby1
The limits of selection under plant domestication Robin G Allaby1* ,Dorian Q Fuller2, James L Kitchen1, 3 1. School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL 2. Institute of Archaeology, University College London, 31-34 Gordon Square, London WC1H 0PY 3. Computational and Systems Biology, Rothamsted, Harpenden, Herts. * corresponding author email: [email protected] 1 Abstract Plant domestication involved a process of selection through human agency of a series of traits collectively termed the domestication syndrome. Current debate concerns the pace at which domesticated plants emerged from cultivated wild populations and how many genes were involved. Here we present simulations that test how many genes could have been involved by considering the cost of selection. We demonstrate the selection load that can be endured by populations increases with decreasing selection coefficients and greater numbers of loci down to values of about s = 0.005, causing a driving force that increases the number of loci under selection. As the number of loci under selection increases, an effect of co-selection increases resulting in individual unlinked loci being fixed more rapidly in out-crossing populations, representing a second driving force to increase the number of loci under selection. In inbreeding systems co-selection results in interference and reduced rates of fixation but does not reduce the size of the selection load that can be endured. These driving forces result in an optimum pace of genome evolution in which 50-100 loci are the most that could be under selection in a cultivation regime. Furthermore, the simulations do not preclude the existence of selective sweeps but demonstrate that they come at a cost of the selection load that can be endured and consequently a reduction of the capacity of plants to adapt to new environments, which may contribute to the explanation of why selective sweeps have been so rarely detected in genome studies. -
Large Trees, Supertrees and the Grass Phylogeny
LARGE TREES, SUPERTREES AND THE GRASS PHYLOGENY Thesis submitted to the University of Dublin, Trinity College for the Degree of Doctor of Philosophy (Ph.D.) by Nicolas Salamin Department of Botany University of Dublin, Trinity College 2002 Research conducted under the supervision of Dr. Trevor R. Hodkinson Department of Botany, University of Dublin, Trinity College Dr. Vincent Savolainen Jodrell Laboratory, Molecular Systematics Section, Royal Botanic Gardens, Kew, London DECLARATION I thereby certify that this thesis has not been submitted as an exercise for a degree at any other University. This thesis contains research based on my own work, except where otherwise stated. I grant full permission to the Library of Trinity College to lend or copy this thesis upon request. SIGNED: ACKNOWLEDGMENTS I wish to thank Trevor Hodkinson and Vincent Savolainen for all the encouragement they gave me during the last three years. They provided very useful advice on scientific papers, presentation lectures and all aspects of the supervision of this thesis. It has been a great experience to work in Ireland, and I am especially grateful to Trevor for the warm welcome and all the help he gave me, at work or outside work, since the beginning of this Ph.D. in the Botany Department. I will always remember his patience and kindness to me at this time. I am also grateful to Vincent for his help and warm welcome during the different periods of time I stayed in London, but especially for all he did for me since my B.Sc. at the University of Lausanne. I wish also to thank Prof. -
Phylogeny of Elymus Ststhh Allotetraploids Based on Three Nuclear Genes
Reticulate Evolutionary History of a Complex Group of Grasses: Phylogeny of Elymus StStHH Allotetraploids Based on Three Nuclear Genes Roberta J. Mason-Gamer*, Melissa M. Burns¤a, Marianna Naum¤b Department of Biological Sciences, The University of Illinois at Chicago, Chicago, Illinois, United States of America Abstract Background: Elymus (Poaceae) is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of Elymus species with a tetraploid genome complement derived from Pseudoroegneria (genome St) and Hordeum (H). We confirm the species’ allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting. Methodology/Principal Findings: We sequenced portions of three unlinked nuclear genes—phosphoenolpyruvate carboxylase, b-amylase, and granule-bound starch synthase I—from 27 individuals, representing 14 Eurasian and North American StStHH Elymus species. Elymus sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the StStHH genome configuration of the Elymus species. They suggest that the StStHH group originated in North America, and do not support separate North American and European origins. Our results point to North American Pseudoroegneria and Hordeum species as potential genome donors to Elymus. Diploid P. spicata is a prospective St-genome donor, though conflict among trees involving P. spicata and the Eurasian P.