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. 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 long-read and a short-read datasets, our bioinformatics workflow revealed SVs and genomic features that were unique to each species. The majority of species-specific SVs were deletions and insertions suggesting 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. We also observed an increased number of enhancer motifs found in SVs compared to the rest of the genome. The SV-affected genes were associated with reproduction, sensory adaptation, and several metabolic pathways. Many of these functions are relevant to fertility and deer biology and therefore may provide insights into potential mechanisms leading to reproductive divergence.