1. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability
- Author
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Francesca Gandini, Alessandro Achilli, Licia Colli, Frédéric Boyer, Baldassare Portolano, Saif Agha, Irene Cardinali, Petros Lymberakis, Marcin Rzepus, S.M.F. Vahidi, Wahid Zamani, Marco Pellecchia, Hamid Reza Rezaei, Paolo Ajmone Marsan, Anna Olivieri, Hovirag Lancioni, Marco Rosario Capodiferro, Ettore Randi, François Pompanon, Maria Teresa Sardina, Vincenza Battaglia, Saeid Naderi, Pierre Taberlet, Eric Coissac, Institute of Zootechnics [Piacenza], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Research Center on Biodiversity and Ancient DNA – BioDNA, Dipartimento di Chimica [Perugia], Università degli Studi di Perugia (UNIPG), Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Institute of Food Science and Nutrition [Piacenza] (ISAN), Department of Environmental Sciences [Tarbiat], Faculty of Natural Resources and Marine Sciences [Tarbiat], Tarbiat Modaras University-Tarbiat Modaras University, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Natural Ressource Faculty [Guilan], University of Guilan, School of Applied Sciences [Huddersfield], University of Huddersfield, Agricultural Biotechnology Research Institute of Iran, Department of Animal Production, Université Ain Shams, Laboratorio di Genetica [Bologna], Italian National Institute of Environmental Protection and Research (ISPRA), Dipartimento Scienze Agrarie e Forestali [Palermo], Università degli studi di Palermo - University of Palermo, Environmental Sciences Department [Gorgan], Gorgan University of Agricultural Sciences and Natural Resources, Natural History Museum of Crete, Colli, L., Lancioni, H., Cardinali, I., Olivieri, A., Capodiferro, M., Pellecchia, M., Rzepus, M., Zamani, W., Naderi, S., Gandini, F., Vahidi, S., Agha, S., Randi, E., Battaglia, V., Sardina, M., Portolano, B., Rezaei, H., Lymberakis, P., Boyer, F., Coissac, E., Pompanon, F., Taberlet, P., Ajmone Marsan, P., and Achilli, A.
- Subjects
Most recent common ancestor ,[SDV]Life Sciences [q-bio] ,Population ,Molecular Sequence Data ,MtDNA haplogroups ,Capra aegagrus ,Biology ,DNA, Mitochondrial ,Haplogroup ,Domestication ,QH301 ,Settore AGR/17 - Zootecnica Generale E Miglioramento Genetico ,Capra hircus ,Genetics ,Animals ,Capra aegagru ,education ,QH426 ,Phylogeny ,2. Zero hunger ,education.field_of_study ,Origin of Capra hircus ,Genome ,MtDNA haplogroup ,Phylogenetic tree ,Goats ,Haplotype ,Genetic Variation ,DNA ,Origin of Capra hircu ,Mitochondrial ,Goat mitochondrial genome ,Biotechnology ,Haplotypes ,Evolutionary biology ,Genome, Mitochondrial ,Female ,mtDNA haplogroups ,Research Article ,Human mitochondrial DNA haplogroup - Abstract
Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Conclusions Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.
- Published
- 2015