Structural Genomic Variation and Its Potential Role in Deer Speciation

Speciation is a key driver of biodiversity and understanding its genomic underpinnings can be 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 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 were impacted, with 3 species-specific SVs showing signs of selection inferred from dN/dS. We also observed a reduced number of regulatory motifs found in fixed species specific SVs compared to the rest of the genome. The SV-affected genes were often associated with reproduction and sensory adaptation, with such functions being relevant to fertility and deer biology and therefore providing insights into potential mechanisms leading to reproductive divergence.