Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene

Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20–50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.Author summary: The red junglefowl Gallus gallus from tropical Asia is the ancestral form of the chicken, which is arguably the most important domestic animal on Earth. Here we discovered an increase in genetic exchange between red junglefowl and chickens in recent years, making wild populations increasingly domestic genomically. By using whole genome sequences of chickens and red junglefowl from two time points, we show that domestic introgression has increased across the wild range at varying levels over the course of a century. We also identified genes that might have played a role in the domestication of the species using the samples from a century ago, in which domestic contribution was lower than in modern day samples. We found eight genes under selection which are involved in development, reproduction and vision, and which might be fundamental to the nature of domestic chickens as distinct from their ancestral wild counterparts. Our study brings to light the current and ongoing loss of the wild junglefowl genotype, suggesting that efforts may be needed to safeguard its full genetic diversity.