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The genomics of domestication special issue editorial

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      Abstract

      Domestication has been of major interest to biologists for centuries, whether for creating new plants and animal types or more formally exploring the principles of evolution. Such studies have long used combinations of phenotypic and genetic evidence. Recently, the advent of a large number of genomes and genomic tools across a wide array of domesticated plant and animal species has reinvigorated the study of domestication. These genomic data, which can be easily generated for nearly any species, often provide great insight with or without a reference genome. The comparison of genome wide data from domestic and wild species has ignited a wave of insight into human, plant, and animal history with a new range of questions becoming accessible. With this in mind, this issue of Evolutionary Applications includes eleven papers covering a wide range of perspectives and methodologies relevant to understanding genomic variation under domestication.

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      Are cattle, sheep, and goats endangered species?

      For about 10 000 years, farmers have been managing cattle, sheep, and goats in a sustainable way, leading to animals that are well adapted to the local conditions. About 200 years ago, the situation started to change dramatically, with the rise of the concept of breed. All animals from the same breed began to be selected for the same phenotypic characteristics, and reproduction among breeds was seriously reduced. This corresponded to a strong fragmentation of the initial populations. A few decades ago, the selection pressures were increased again in order to further improve productivity, without enough emphasis on the preservation of the overall genetic diversity. The efficiency of modern selection methods successfully increased the production, but with a dramatic loss of genetic variability. Many industrial breeds now suffer from inbreeding, with effective population sizes falling below 50. With the development of these industrial breeds came economic pressure on farmers to abandon their traditional breeds, and many of these have recently become extinct as a result. This means that genetic resources in cattle, sheep, and goats are highly endangered, particularly in developed countries. It is therefore important to take measures that promote a sustainable management of these genetic resources; first, by in situ preservation of endangered breeds; second, by using selection programmes to restore the genetic diversity of industrial breeds; and finally, by protecting the wild relatives that might provide useful genetic resources.
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        Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

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          Domestication of cattle: Two or three events?

          Abstract Cattle have been invaluable for the transition of human society from nomadic hunter‐gatherers to sedentary farming communities throughout much of Europe, Asia and Africa since the earliest domestication of cattle more than 10,000 years ago. Although current understanding of relationships among ancestral populations remains limited, domestication of cattle is thought to have occurred on two or three occasions, giving rise to the taurine (Bos taurus) and indicine (Bos indicus) species that share the aurochs (Bos primigenius) as common ancestor ~250,000 years ago. Indicine and taurine cattle were domesticated in the Indus Valley and Fertile Crescent, respectively; however, an additional domestication event for taurine in the Western Desert of Egypt has also been proposed. We analysed medium density Illumina Bovine SNP array (~54,000 loci) data across 3,196 individuals, representing 180 taurine and indicine populations to investigate population structure within and between populations, and domestication and demographic dynamics using approximate Bayesian computation (ABC). Comparative analyses between scenarios modelling two and three domestication events consistently favour a model with only two episodes and suggest that the additional genetic variation component usually detected in African taurine cattle may be explained by hybridization with local aurochs in Africa after the domestication of taurine cattle in the Fertile Crescent. African indicine cattle exhibit high levels of shared genetic variation with Asian indicine cattle due to their recent divergence and with African taurine cattle through relatively recent gene flow. Scenarios with unidirectional or bidirectional migratory events between European taurine and Asian indicine cattle are also plausible, although further studies are needed to disentangle the complex human‐mediated dispersion patterns of domestic cattle. This study therefore helps to clarify the effect of past demographic history on the genetic variation of modern cattle, providing a basis for further analyses exploring alternative migratory routes for early domestic populations.
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            Author and article information

            Affiliations
            [ 1 ] Department of Tropical Plant and Soil Sciences University of Hawai'i Honolulu Hawaii
            [ 2 ] School of Biosciences Cardiff University Cardiff UK
            [ 3 ] Sustainable Places Research Institute Cardiff University Cardiff UK
            [ 4 ] Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver British Columbia Canada
            Author notes
            [* ] Correspondence

            Michael B. Kantar, Department of Tropical Plant and Soil Sciences, University of Hawai'i, Manoa, Maile Way, Honolulu, HI.

            Email: mbkantar@ 123456hawaii.edu

            Contributors
            ORCID: http://orcid.org/0000-0001-5542-0975, mbkantar@hawaii.edu
            Journal
            Evol Appl
            Evol Appl
            10.1111/(ISSN)1752-4571
            EVA
            Evolutionary Applications
            John Wiley and Sons Inc. (Hoboken )
            1752-4571
            17 September 2018
            January 2019
            : 12
            : 1 , Genomics of Domestication ( doiID: 10.1111/eva.2019.12.issue-1 )
            : 3-5
            6304677 10.1111/eva.12693 EVA12693
            © 2018 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd

            This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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            Figures: 0, Tables: 0, Pages: 3, Words: 1866
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            Special Issue Perspective
            Custom metadata
            2.0
            eva12693
            January 2019
            Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.5.4 mode:remove_FC converted:24.12.2018

            Evolutionary Biology

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