title: The origin and genetic variation of domestic chickens with special reference to junglefowls Gallus g. gallus and G. varius.
abstract: It is postulated that chickens (Gallus gallus domesticus) became domesticated from wild junglefowls in Southeast Asia nearly 10,000 years ago. Based on 19 individual samples covering various chicken breeds, red junglefowl (G. g. gallus), and green junglefowl (G. varius), we address the origin of domestic chickens, the relative roles of ancestral polymorphisms and introgression, and the effects of artificial selection on the domestic chicken genome. DNA sequences from 30 introns at 25 nuclear loci are determined for both diploid chromosomes from a majority of samples. The phylogenetic analysis shows that the DNA sequences of chickens, red and green junglefowls formed reciprocally monophyletic clusters. The Markov chain Monte Carlo simulation further reveals that domestic chickens diverged from red junglefowl 58,000+/-16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci.
authors.affiliation: Hayama Center for Advanced Studies, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Sawai
authors.forename: Hie Lim
authors.initials: HL
authors.lastname: Kim
authors.forename: Kaori
authors.initials: K
authors.lastname: Kuno
authors.forename: Sayaka
authors.initials: S
authors.lastname: Suzuki
authors.forename: Hideo
authors.initials: H
authors.lastname: Gotoh
authors.forename: Masaru
authors.initials: M
authors.lastname: Takada
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Takahata
authors.forename: Yoko
authors.initials: Y
authors.lastname: Satta
authors.forename: Fumihito
authors.initials: F
authors.lastname: Akishinonomiya
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D002645:Chickens / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D044708:DNA, Concatenated / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D046094:Galliformes / Q000235:genetics*; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics; D007438:Introns / Q000235:genetics; D016013:Likelihood Functions; D008390:Markov Chains; D009010:Monte Carlo Method; D010802:Phylogeny; D011157:Population Dynamics; D013045:Species Specificity
chemical_list: D044708:DNA, Concatenated; D004272:DNA, Mitochondrial