Low effective population size in the genetically bottlenecked Australian sea lion is insufficient to maintain genetic variation

Genetic bottlenecks can reduce effective population sizes (N_e), increase the rate at which genetic variation is lost via drift, increase the frequency of deleterious mutations and thereby accentuate inbreeding risk and lower evolutionary potential. Here, we tested for the presence of a genetic bottleneck in the endangered Australian sea lion (Neophoca cinerea), estimated N_e and predicted future losses of genetic variation under a range of scenarios. We used 2238 genome‐wide neutral single‐nucleotide polymorphisms (SNPs) from 72 individuals sampled from colonies off the southern (SA) and western (WA) coastline of Australia. Coalescent analyses using approximate Bayesian computation (ABC) methods indicated that both the SA and WA populations have experienced a historical genetic bottleneck. Using LD‐based methods, we estimated contemporary N_e to be 160 (CI = 146–178) and 424 (CI = 397–458) for the WA and SA populations respectively. Modelled future population declines suggested that disease epidemics prompted the highest increases in inbreeding relative to fishery‐related mortalities and other modelled threats. Small effective sizes and relatively low genetic variation leave this species vulnerable, and these risks may be compounded if current population declines are not reversed.