Identifying the Ancestor of a Domesticated Animal Using Whole-Genome Sequencing

What animal can be found around the globe that outnumbers humans three to one? Gallus gallus domesticus, the humble chicken. The human appetite for eggs and lean meat drive demand for this feathered bird, resulting in a poultry population of over 20 billion.

Controversy over the origin of the domestic chicken (when, where and which species) have lead some researchers to look for that information in the genomes of contemporary chicken breeds and wild jungle fowl, the candidates from which chickens were derived. By sequencing over 600 genomes from Asian domestic poultry as well as 160 genomes from all four wild jungle fowl species and the five red jungle fowl subspecies, Wang et al. wanted to understand and identify the relationships and relatedness among these species and derive where domesticated chickens first arose.

Red jungle fowl, which are found in Asia, have long been the likely wild candidate for the domesticated chicken. However, researchers first used the data they acquired on the wild jungle fowl to understand the relationship among these birds. They found that all jungle fowl species and red jungle fowl subspecies were genetically different. Each of the wild bird species was located in geographically distinct areas of Asia (e.g., G. g. murghi is found in northern India while G. g. bankiva is in eastern Java). The researchers concluded that G. g. bankiva showed the greatest diversity, making it ancestral to the other red jungle fowl in a phylogenetic tree.

Who is the Ancestor to the Domestic Chicken?

Phylogenetic analysis was also used to determine which red jungle fowl subspecies might be the origin for domestic chickens. Based on the 149 red jungle fowl genomes and the 696 domestic chicken genomes, including sequences available prior to this study, all but two domestic chickens formed a single clade with ten of the wild G. g. spadiceus individuals, suggesting that these birds shared a common ancestor. Additional analyses indicated that domestic chicken genomes clustered closer to G. g. spadiceus, currently found in southwestern China, Thailand and Myanmar, than any of the other four red jungle fowl subspecies. Using an algorithm to estimate when G. g. spadiceus and domestic chickens separated from each other, Wang et al. calculated the split took place approximately 9,500 years ago, contradicting other archeological research that suggested chickens were domesticated during the Neolithic in northern China and the Indus Valley.

Gallus gallus spadiceus, a red jungle fowl subspecies. Image copyright: Garry Bakker hosted on PBase.

While this genomic study indicates a specific red jungle fowl subspecies was the likely ancestor of the domestic chicken, there is still some gene flow among domestic chickens and red jungle fowl. While some of this genetic exchange is due to geography, Wang et al. found that the commercial egg-laying breed White Leghorn, regardless if the genome sample was from Iran, China, Italy or the US, had about 25% of its ancestry from G. g. murghi, a red fowl subspecies local to northern India. This interbreeding event likely happened after chicken domestication based on the length of the haplotype blocks shared between White Leghorns and G. g. murghi compared to the shorter ones shared between White Leghorns and G. g. spadiceus.

Gene Selection in Domestic Chickens

With all this genomic data, could researchers draw any conclusions about which genes were selected for in domesticated chickens compared with their wild red jungle fowl relatives? Domestic chickens mature faster and produce more eggs compared to jungle fowl. Not surprisingly, genes that are involved in regulating sexual maturity and reproduction, metabolism, muscle and bone development showed changes. And a nonsense mutation that is a suspected locus for domestication is fixed in domestic chickens and absent in red jungle fowl. Wang et al. noted that this mutation is found at high frequency in G. g. spadiceus, the ancestor to the domestic chicken identified by this study, but at low frequency other red jungle fowl subspecies.

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By gathering DNA samples from hundreds of chickens and wild jungle fowl in Asia, researchers examined the relatedness among these birds, created a family tree for the domestic chicken and determined which wild jungle fowl was the likely ancestor to chickens. Unlike previous research, this study identified a specific red jungle fowl subspecies as the likely ancestor and placed the domestication event based on the current geographical location of G. g. spadiceus. One caveat of these conclusions is the genomes examined are all from modern species, both chickens and jungle fowl. While Wang et al. believed the number of genomes sequenced could differentiate between crossbreeding among jungle fowl and chickens and identifying the domestic chicken ancestor, sequencing ancient chicken remains would help bolster the assertions made in this Cell Research article.

Reference:
Wang, M. et al. (2020) 863 genomes reveal the origin and domestication of chicken. Cell Res. 30, 693–701. https://doi.org/10.1038/s41422-020-0349-y

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Sara Klink

Technical Writer at Promega Corporation
Sara is a native Wisconsinite who grew up on a fifth-generation dairy farm and decided she wanted to be a scientist at age 12. She was educated at the University of Wisconsin—Parkside, where she earned a B.S. in Biology and a Master’s degree in Molecular Biology before earning her second Master’s degree in Oncology at the University of Wisconsin—Madison. She has worked for Promega Corporation for more than 15 years, first as a Technical Services Scientist, currently as a Technical Writer. Sara enjoys talking about her flock of entertaining chickens and tries not to be too ambitious when planning her spring garden.

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