Gene study answers where was chicken domesticated, and its ancestor

In a bid to address this issue, researchers analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF).

Gene study answers where was chicken domesticated, and its ancestor

Chickens have played a substantial role in human societies across the world and yet the geographic and temporal origins of their domestication remains a mystery. In a bid to address this issue, researchers analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF).

The study, led by Ming-Shan Wang from the Chinese Academy of Sciences’ Kunming Institute of Zoology, was published on June 24 in Cell Research. It suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar.

Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. A molecular clock analysis suggests that domestic chickens diverged from G. g. spadiceus 9500 ± 3300 years ago, though this node does not necessarily correlate with the beginning of the domestication process, as chickens are archaeologically visible much later.

The domestic village chickens were hybridized with wild G. g. spadiceus in Thailand in the mid-20th century and wild RJF clutches were removed from their nests and hatched by domestic hens.

To establish the primary RJF subspecies from which domestic chickens were derived and to understand the genetic mechanisms underlying chicken domestication, it is necessary to analyze the nuclear genomes of both presumed wild relatives and domestic populations, within and beyond the natural distribution ranges of all RJF subspecies.

The study sequenced 787 whole genomes: 627 domestic chickens, 142 RJFs representing all five subspecies, 12 green jungle fowls, 2 gray jungle fowls and 4 Ceylon jungle fowls. To maximize the likelihood of capturing genetic variability among RJF subspecies, it sampled individuals belonging to each subspecies from at least three geographically distant locations and ensured that at least one individual of each subspecies was sequenced to at least 20× coverage. 

The Principal component analysis (PCA) also highlights a separation among RJF subspecies. It is interesting that some G. g. murghi (distributed across the northern Indian subcontinent) and G. g. jabouillei (confined to South China and North Vietnam) individuals cluster together.

The analyses indicate that all RJF subspecies are genetically differentiated, which generally correspond to their geographic ranges and taxonomic classifications. Of the five RJF subspecies, individuals of G. g. spadiceus are the most closely related to all domestic chicken populations 

By combining the monophyletic nature of all domestic chickens, the results from these analyses collectively suggest that chickens were likely domesticated in the Holocene from the G. g. spadiceus subspecies of RJF.

"Our results contradict previous claims that chickens were domesticated in Neolithic northern China and the Indus Valley Civilization (made on the basis of suspected chicken remains found at the site of Mohenjo-Daro in Pakistan). However, a PCA shows that G. g. murghi samples from westernmost North India showed a deeper divergence from chickens than the remaining birds of G. g. murghi collected from northeastern India," read the paper.