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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?

          P Taberlet, A Valentini, H Rezaei … (2008)
          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

            Kevin G. Daly, Pierpaolo Maisano Delser, Victoria E. Mullin … (2018)
            Little is known regarding the location and mode of the early domestication of animals such as goats for husbandry. To investigate the history of the goat, Daly et al. sequenced mitochondrial and nuclear sequences from ancient specimens ranging from hundreds to thousands of years in age. Multiple wild populations contributed to the origin of modern goats during the Neolithic. Over time, one mitochondrial type spread and became dominant worldwide. However, at the whole-genome level, modern goat populations are a mix of goats from different sources and provide evidence for a multilocus process of domestication in the Near East. Furthermore, the patterns described support the idea of multiple dispersal routes out of the Fertile Crescent region by domesticated animals and their human counterparts. Science , this issue p. [Related article:] 85 Ancient goat genomes elucidate a dispersed domestication process across the Near East. Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
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              Deleterious alleles in the context of domestication, inbreeding, and selection

              Mirte Bosse, Hendrik-Jan Megens, Martijn Derks … (2018)
              Abstract Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.
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                Author and article information

                Contributors
                Michael B. Kantar:
                ORCID: http://orcid.org/0000-0001-5542-0975
                mbkantar@hawaii.edu
                Journal
                Journal ID (nlm-ta): Evol Appl
                Journal ID (iso-abbrev): Evol Appl
                Journal ID (doi): 10.1111/(ISSN)1752-4571
                Journal ID (publisher-id): EVA
                Title: Evolutionary Applications
                Publisher: John Wiley and Sons Inc. (Hoboken )
                ISSN (Electronic): 1752-4571
                Publication date (Electronic): 17 September 2018
                Publication date Collection: January 2019
                Volume: 12
                Issue: 1 , Genomics of Domestication ( doiID: 10.1111/eva.2019.12.issue-1 )
                Pages: 3-5
                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

                Author information
                http://orcid.org/0000-0001-5542-0975
                Article
                Publisher ID: EVA12693
                DOI: 10.1111/eva.12693
                PMC ID: 6304677
                PubMed ID: 30622630
                SO-VID: dc34e4b3-c290-41c7-ae6a-a2afafd4a1bb
                Copyright © © 2018 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd
                License:

                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.

                History
                Date received : 22 July 2018
                Date accepted : 05 August 2018
                Page count
                Figures: 0, Tables: 0, Pages: 3, Words: 1866
                Categories
                Subject: Special Issue Perspective
                Subject: Special Issue Perspective
                Custom metadata
                source-schema-version-number 2.0
                component-id eva12693
                cover-date January 2019
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.5.4 mode:remove_FC converted:24.12.2018

                ScienceOpen disciplines: Evolutionary Biology
                Data availability:
                ScienceOpen disciplines: Evolutionary Biology

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