Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

Abstract

The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (F_IS and F_ROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.

Keywords: Admixture; Genetic homogenization; Hybridisation; Selective sweeps; Wildlife management.