Disentangling Genetic Exchanges Between Gallus gallus and Gallus sonneratii in Order to Better Understand the Domestication of Chickens

The red junglefowl (Gallus gallus) is considered as the main ancestor of the domestic chicken, but the genus Gallus includes three other species: Gallus sonneratii, Gallus lafayetii and Gallus varius . Deep genome sequencing (25-30X paired-end) was undertaken for the 4 species (18 individuals in total) in order to analyze the genetic diversity within the genus Gallus and to better understand the genetic make-up of domestic chickens. G. gallus samples were obtained in the wild and in zoological gardens, whereas birds from the 3 other species were sampled in zoological gardens only. A set of 18 domestic chickens with a wide geographic origin (Europe, Africa, Asia, South America) was also sequenced. Phylogenetic trees were established on the basis of three types of genomic data: autosomal chromosomes (Tree-a), W chromosome (Tree-w), mitochondrial DNA (Tree-mt). Surprisingly, the position of G. sonneratii differed markedly between trees: it was clearly separated from G. gallus, either wild or domestic, in Tree-a, whereas it was intermingled with G. gallus in Tree-w and Tree-mt. The same situation occurred for other G. sonneratii in literature data, except for one from the zoological garden of New Delhi. In addition, 9.6% of autosomes of G. sonneratii exhibited introgression of rather large regions from G. gallus. The likely explanation of this result is an introgression from one or a few G. gallus female(s) into G. sonneratii flocks maintained in zoological gardens, around the 1700s. This event should be taken into account in further studies of the genetic make-up of domestic chickens.