Genomics of avian migratory phenotypes

Partial migration is a phenomenon where migratory and resident individuals of the same species co-exist within a population, and has been linked to both intrinsic (e.g., genetic) as well as environmental factors. Here we investigated the genomic architecture of partial migration in the European blackbird, a common songbird that shows partial migratory behavior across its distribution range. We generated whole-genome sequencing data for 60 individuals across the species' distribution range, including resident populations (Spain and France), obligate migrants (Russia), and a partial migratory population with equal numbers of migratory and resident individuals in Germany. We estimated average genetic differentiation (FST) between all possible population and migratory phenotype combinations of SNVs in 2.5 kb windows, and focussed our characterization on birds from the partially migratory population in Germany that have been individually phenotype with radio-telemetry tracking. Despite overall low differentiation within the partial migratory German population we identified several outlier regions with elevated differentiation on four distinct chromosomes. The region with the highest relative and absolute differentiation was located on chromosome 9, overlapping PER2, which has previously been shown to be involved in the control of the circadian rhythm across vertebrates. While this region showed high levels of differentiation, no fixed variant could be identified, supporting the notion that a complex phenotype such as migratory behavior is likely controlled by a large number of genetic loci.