title: Chicken domestication: an updated perspective based on mitochondrial genomes.
abstract: Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A-I and W-Z. Common haplogroups A-G were shared by domestic chickens and red junglefowl. Rare haplogroups H-I and W-Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.
authors.affiliation: Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China.
authors.forename: Y-W
authors.initials: YW
authors.lastname: Miao
authors.forename: M-S
authors.initials: MS
authors.lastname: Peng
authors.forename: G-S
authors.initials: GS
authors.lastname: Wu
authors.forename: Y-N
authors.initials: YN
authors.lastname: Ouyang
authors.forename: Z-Y
authors.initials: ZY
authors.lastname: Yang
authors.forename: N
authors.initials: N
authors.lastname: Yu
authors.forename: J-P
authors.initials: JP
authors.lastname: Liang
authors.forename: G
authors.initials: G
authors.lastname: Pianchou
authors.forename: A
authors.initials: A
authors.lastname: Beja-Pereira
authors.forename: B
authors.initials: B
authors.lastname: Mitra
authors.forename: M G
authors.initials: MG
authors.lastname: Palanichamy
authors.forename: M
authors.initials: M
authors.lastname: Baig
authors.forename: T K
authors.initials: TK
authors.lastname: Chaudhuri
authors.forename: Y-Y
authors.initials: YY
authors.lastname: Shen
authors.forename: Q-P
authors.initials: QP
authors.lastname: Kong
authors.forename: R W
authors.initials: RW
authors.lastname: Murphy
authors.forename: Y-G
authors.initials: YG
authors.lastname: Yao
authors.forename: Y-P
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001210:Asia, Southeastern; D001483:Base Sequence; D001947:Breeding; D002645:Chickens / Q000145:classification / Q000235:genetics*; D002875:Chromosomes; D004272:DNA, Mitochondrial / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D006239:Haplotypes; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial