Convergent genomic signatures of domestication in sheep and goats

Abstract

The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species.

Fig. 1

Sampling with regard to the domestication center and main colonizations routes. a Sampling locations represented by the animal’s silhouettes. The domestication center and the main colonization routes (Northern and Southern Mediterranean routes and Danubian route) are presented. Proportion of genomes assigned to K genetic clusters for Ovis (K = 2 and K = 3) (b) and Capra (K = 2 and K = 6) (c) individuals. The number of sampled individuals (n) is given

Fig. 2

Specific and shared chromosomal regions selected during domestication. a Circular representation of the sheep (left) and goat (right) genomes. Dots represent regions under selection, lines indicate shared selected regions. Chromosomes sizes are in Megabases. b Convergence in the signals of selection between Capra and Ovis. In homologous genomic regions, the proportion of significant SNPs found under selection in Ovis, respectively Capra (y-axis), increases with the stringency for detecting selection in Capra, respectively Ovis (x-axis)

Fig. 3

Chromosomal regions under selection overlapping the KITLG gene. Each genus bears two signatures of selection from which one comprises a part strictly homologous between genera. Both regions exhibit a lower diversity in domestics for Ovis and a higher diversity in domestics for Capra