TreeBASE Search-Matrices for study 18595

@ARTICLE{TreeBASE2Ref25372, author = {Licia Colli and Hovirag Lancioni and Irene Cardinali and Anna Olivieri and Marco Rosario Capodiferro and Marco Pellecchia and Marcin Rzepus and Wahid Zamani and Saeid Naderi and Francesca Gandini and Seyed Mohammad Farhad Vahidi and Saif Agha and Ettore Randi and Vincenza Battaglia and Maria Teresa Sardina and Baldassare Portolano and Hamid Reza Rezaei and Petros Lymberakis and Frédéric Boyer and Eric Coissac and François Pompanon and Pierre Taberlet and Paolo Ajmone Marsan and Alessandro Achilli}, title = {Whole Mitochondrial Genomes Unveil the Impact of Domestication on Goat Matrilineal Variability}, year = {2015}, keywords = {Goat mitochondrial genome; mtDNA haplogroups; domestication; origin of Capra hircus; Capra aegagrus.}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Genomics}, volume = {}, number = {}, pages = {}, 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 thousand 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. } }