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Abstract:
Copy number variation represents a major source of genetic divergence, yet the evolutionary dynamics of genic copy number
variation in natural populations during differentiation and adaptation remain unclear. We applied a read depth approach
to genome resequencing data to detect copy number variants (CNVs) ≥1 kb in wild-caught mice belonging to
four populations of Mus musculus domesticus. We complemented the bioinformatics analyses with experimental validation using
droplet digital PCR. The specific focus of our analysis is CNVs that include complete genes, as these CNVs could be
expected to contribute most directly to evolutionary divergence. In total, 1863 transcription units appear to be completely
encompassed within CNVs in at least one individual when compared to the reference assembly. Further, 179 of these CNVs
show population-specific copy number differences, and 325 are subject to complete deletion in multiple individuals. Among
the most copy-number variable genes are three highly conserved genes that encode the splicing factor CWC22, the spindle
protein SFI1, and the Holliday junction recognition protein HJURP. These genes exhibit population-specific expansion patterns
that suggest involvement in local adaptations. We found that genes that overlap with large segmental duplications are
generally more copy-number variable. These genes encode proteins that are relevant for environmental and behavioral interactions,
such as vomeronasal and olfactory receptors, as well as major urinary proteins and several proteins of unknown
function. The overall analysis shows that genic CNVs contribute more to population differentiation in mice than in humans
and may promote and speed up population divergence.
