Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken

<p>Abstract</p> <p>Background</p> <p>Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. However, non-inclusion of Indian red jungle fowl (RJF), <it>Gallus gallus murghi </it>in previous studies has left a big gap in understanding the relationship of this major group of birds. In the present study, we addressed this issue by analyzing 76 Indian birds that included 56 <it>G. g. murghi </it>(RJF), 16 <it>G. g. domesticus </it>(domestic chicken) and 4 <it>G. sonneratii </it>(Grey JF) using both microsatellite markers and mitochondrial D-loop sequences. We also compared the D-loop sequences of Indian birds with those of 779 birds obtained from GenBank.</p> <p>Results</p> <p>Microsatellite marker analyses of Indian birds indicated an average F_STof 0.126 within <it>G. g. murghi</it>, and 0.154 within <it>G. g. domesticus </it>while it was more than 0.2 between the two groups. The microsatellite-based phylogenetic trees showed a clear separation of <it>G. g. domesticus </it>from <it>G. g. murghi</it>, and <it>G. sonneratii</it>. Mitochondrial DNA based mismatch distribution analyses showed a lower Harpending's raggedness index in both <it>G. g. murghi </it>(0.001515) and in Indian <it>G. g. domesticus </it>(0.0149) birds indicating population expansion. When meta analysis of global populations of 855 birds was carried out using median joining haplotype network, 43 Indian birds of <it>G. g. domesticus </it>(19 haplotypes) were distributed throughout the network sharing haplotypes with the RJFs of different origins.</p> <p>Conclusion</p> <p>Our results suggest that the domestication of chicken has occurred independently in different locations of Asia including India. We found evidence for domestication of Indian birds from <it>G. g. spadiceus </it>and <it>G. g. gallus </it>as well as from <it>G. g. murghi</it>, corroborating multiple domestication of Indian and other domestic chicken. In contrast to the commonly held view that RJF and domestic birds hybridize in nature, the present study shows that <it>G. g. murghi </it>is relatively pure. Further, the study also suggested that the chicken populations have undergone population expansion, especially in the Indus valley.</p