Structural genomic variation and migratory behavior in a wild songbird

Kira E Delmore* (Corresponding author), Benjamin M Van Doren, Kristian Ullrich, Teja Curk, Henk P van der Jeugd, Miriam Liedvogel* (Corresponding author)

*Corresponding author for this work

Research output: Contribution to journal/periodicalArticleScientificpeer-review

3 Citations (Scopus)


Structural variants (SVs) are a major source of genetic variation; and descriptions in natural populations and connections with phenotypic traits are beginning to accumulate in the literature. We integrated advances in genomic sequencing and animal tracking to begin filling this knowledge gap in the Eurasian blackcap. Specifically, we (a) characterized the genome-wide distribution, frequency, and overall fitness effects of SVs using haplotype-resolved assemblies for 79 birds, and (b) used these SVs to study the genetics of seasonal migration. We detected >15 K 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 the SVs we identified 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 1 trait—direction—and 1 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.
Original languageEnglish
Pages (from-to)401-412
Number of pages12
JournalEvolution Letters
Issue number6
Early online date07 Oct 2023
Publication statusPublished - Dec 2023


  • bird
  • haplotype-resolved de novo assembly
  • migration genetics
  • purifying selection
  • structural variants


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