title: Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability.
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.
authors.affiliation: Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. licia.colli@unicatt.it.|Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. licia.colli@unicatt.it.
authors.forename: Licia
authors.initials: L
authors.lastname: Colli
authors.affiliation: Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. hovirag.lancioni@unipg.it.
authors.forename: Hovirag
authors.initials: H
authors.lastname: Lancioni
authors.affiliation: Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. cardinali_irene@libero.it.
authors.forename: Irene
authors.initials: I
authors.lastname: Cardinali
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. anna.olivieri@unipv.it.
authors.forename: Anna
authors.initials: A
authors.lastname: Olivieri
authors.affiliation: Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. marcocapo87@yahoo.it.|Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. marcocapo87@yahoo.it.
authors.forename: Marco Rosario
authors.initials: MR
authors.lastname: Capodiferro
authors.affiliation: Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. marcopellecchia@koineambiente.com.
authors.forename: Marco
authors.initials: M
authors.lastname: Pellecchia
authors.affiliation: Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. Marcin.Rzepus@unicatt.it.|Institute of Food Science and Nutrition - ISAN, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. Marcin.Rzepus@unicatt.it.
authors.forename: Marcin
authors.initials: M
authors.lastname: Rzepus
authors.affiliation: Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. zamani_wahid@yahoo.com.|Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, 46414-356, Iran. zamani_wahid@yahoo.com.
authors.forename: Wahid
authors.initials: W
authors.lastname: Zamani
authors.affiliation: Natural Resources Faculty, University of Guilan, Guilan, 41335-1914, Iran. naderi@guilan.ac.ir.
authors.forename: Saeid
authors.initials: S
authors.lastname: Naderi
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. francesca.gandini01@universitadipavia.it.|School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK. francesca.gandini01@universitadipavia.it.
authors.forename: Francesca
authors.initials: F
authors.lastname: Gandini
authors.affiliation: Agricultural Biotechnology Research Institute of Iran (ABRII), North Branch, Rasht, 41635-4115, Iran. smf.vahidi@gmail.com.
authors.forename: Seyed Mohammad Farhad
authors.initials: SM
authors.lastname: Vahidi
authors.affiliation: Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt. safsoof23@hotmail.com.
authors.forename: Saif
authors.initials: S
authors.lastname: Agha
authors.affiliation: Laboratorio di Genetica, Istituto per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, 40064, Italy. ettore.randi@isprambiente.it.|Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, DK-9000, Denmark. ettore.randi@isprambiente.it.
authors.forename: Ettore
authors.initials: E
authors.lastname: Randi
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. vincenza.battaglia@unipv.it.
authors.forename: Vincenza
authors.initials: V
authors.lastname: Battaglia
authors.affiliation: Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy. mariateresa.sardina@unipa.it.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Sardina
authors.affiliation: Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy. baldassare.portolano@unipa.it.
authors.forename: Baldassare
authors.initials: B
authors.lastname: Portolano
authors.affiliation: Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, 49138-15739, Iran. hamid.r.rezaei@gmail.com.
authors.forename: Hamid Reza
authors.initials: HR
authors.lastname: Rezaei
authors.affiliation: Natural History Museum of Crete, University of Crete, Iraklio, Crete, 71409, Greece. lyberis@nhmc.uoc.gr.
authors.forename: Petros
authors.initials: P
authors.lastname: Lymberakis
authors.affiliation: Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. frederic.boyer@ujf-grenoble.fr.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Boyer
authors.affiliation: Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. eric.coissac@inria.fr.
authors.forename: Eric
authors.initials: E
authors.lastname: Coissac
authors.affiliation: Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. francois.pompanon@ujf-grenoble.fr.
authors.forename: François
authors.initials: F
authors.lastname: Pompanon
authors.affiliation: Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. pierre.taberlet@ujf-grenoble.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.affiliation: Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. paolo.ajmone@unicatt.it.|Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. paolo.ajmone@unicatt.it.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ajmone Marsan
authors.affiliation: Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. alessandro.achilli@unipv.it.|Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. alessandro.achilli@unipv.it.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Achilli
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D014644:Genetic Variation / Q000235:genetics; D054629:Genome, Mitochondrial / Q000235:genetics*; D006041:Goats / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial