Structural Genomic Variation Underlying Deer Speciation

Speciation is a key driver of biodiversity and understanding its genomic underpinnings is important for predicting and managing biodiversity, especially in the face of environmental changes. Structural variants (SVs) are large-scale (>50 bp) changes in the genome and have been implicated in adaptive divergence and reproductive isolation. We investigated the role of SVs in the speciation and divergence of two deer species ( Odocoileus spp.) across their North American range. Using multiple genome assemblies and a large short-read dataset, our bioinformatics workflow revealed SVs and genome features that were unique to each species. We found no difference in enhancer motifs found in SVs compared to the rest of the genome, while the predominance of species-specific SVs were deletions and insertions suggests that these variants may show higher likelihoods of fixation within populations. Further, while most SVs were intergenic, some genes found to be impacted by species-specific SVs were under positive selection inferred from dN/dS. The SV-affected genes were involved in reproduction, sensory adaptation, and metabolic pathways, which have clear links to fertility and deer biology, supporting their role in reproductive isolation and speciation.