Adaptive changes in the genomes of wild rabbits after 16 years of viral epidemics

Since its introduction to control overabundant alien rabbits (Oryctolagus cuniculus), the highly virulent Rabbit Haemorrhagic Disease Virus (RHDV) has caused regular annual disease outbreaks in Australian rabbit populations. Although initially reducing rabbit abundance by 60%, continent-wide, experimental evidence has since indicated increased genetic resistance in wild rabbits that have experienced RHDV-driven selection. To identify genetic adaptations, which explain the increased resistance to this biocontrol virus, we investigated genome-wide SNP (single nucleotide polymorphism) allele frequency changes in a South Australian rabbit population that was sampled in 1996 (pre-RHD genomes) and after 16 years of RHDV outbreaks. We identified several SNPs with changed allele frequencies within or in proximity of genes that have roles potentially important for increased RHD resistance. Many of the identified genes are known to be involved in virus infections or immunity, or had previously be...