Structural genomic variation and migratory behavior in wild songbirds

Abstract

Structural variants (SVs) are a major source of genetic variation, but accurate descriptions in natural populations and connections with phenotypic traits remain scarce. We integrated advances in genomic sequencing and animal tracking to begin filling this knowledge gap in the Eurasian blackcap. Specifically, we (i) characterized the genome-wide distribution, frequency and overall fitness effects of SVs using haplotype-resolved assemblies for 79 birds, and (ii) used these SVs to study the genetics of seasonal migration. We detected >15K SVs. Many SVs overlapped repetitive regions and exhibited evidence of purifying selection suggesting they have overall deleterious effects on fitness. We used estimates of genomic differentiation to identify SVs exhibiting evidence of selection in blackcaps with different migratory strategies. Insertions and deletions dominated these SVs and were associated with genes that are either directly (e.g., regulatory motifs that maintain circadian rhythms) or indirectly (e.g., through immune response) related to migration. We also broke migration down into individual traits (direction, distance and timing) using existing tracking data and tested if genetic variation at the SVs we identified could account for phenotypic variation at these traits. This was only the case for one trait – direction – and one specific SV (a deletion on chromosome 27) accounted for much of this variation. Our results highlight the evolutionary importance of SVs in natural populations and provide insight into the genetic basis of seasonal migration.

Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure

“…We used an independent set of blackcap individuals (hereafter “10x individuals”) whose genomes were sequenced with the 10x linked-read technology (Delmore et al, 2023, NCBI BioProject PRJEB65115). We genotyped the 10x individuals at the two putative inversion loci (i.e.…”