Discovery and population genomics of structural variation in a songbird genus

Structural variation (SV) is an important component of genetic mutations providing the raw material for evolution. Here, we uncovered the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining information from short-read (N = 127) and long-read re-sequencing data (N = 31), as well as from optical maps (N = 16) and applying both assembly- and read mapping approaches, we characterized a total of 220,452 insertions, deletions and inversions. We exploited sampling across wide phylogenetic timescales to validate SV genotypes and demonstrate their suitability for standard population genetic analyses. We then assessed the contribution of this hitherto hidden form of genetic variation to evolutionary processes in an avian model of incipient speciation, the Corvus (corone) spp. species complex. Population genetic analysis of SV between two phenotypically diverged populations in Europe revealed an evolutionary young (~530,000 years) cis-acting 2.25-kb retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.