The origin and genetic variation of domestic chickens with special reference to junglefowls Gallus g. gallus and G. varius.

Hiromi Sawai,Hie Lim Kim,Fumihito Akishinonomiya,Sayaka Suzuki,Naoyuki Takahata,Kaori Kuno,Hideo Gotoh,Yoko Satta,Masaru Takada,Laszlo Orban

doi:10.1371/journal.pone.0010639

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.

Highlights

When and how domestication proceeded during the history of modern humans are intriguing questions that have attracted much attention from researchers in natural and cultural sciences
It has been a great challenge to identify genetic changes that resulted from artificial selection during the domestication process
In conclusion, domestic chickens are closely related to red junglefowl, genetic contribution from other junglefowls remains to be answered

Summary

Introduction

When and how domestication proceeded during the history of modern humans are intriguing questions that have attracted much attention from researchers in natural and cultural sciences. Given the progress in genomic sequencing of various animals, the search for target genes of artificial selection during the domestication process has been a focus of recent studies. Because of the relatively short divergence times of domestic animals from their wild ancestors, genomic differences are likely to be subtle. It has been a great challenge to identify genetic changes that resulted from artificial selection during the domestication process. The discovery of genetic differences among domestic breeds should, provide some clues. Some recent studies reveal genetic determinants of changes in body size and coat color in dogs [1,2]. Molecular searches for the origins of domestic animals are conducted on other animals such as pigs, sheep, cows, and chickens [3,4,5,6,7,8]

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Conclusion