Small populations are characterized by large drift and reduced efficacy of selection effects, which result in fixation of both advantageous and deleterious alleles, accumulation of homozygosity, and often reduction in population fitness. What with plummeting mammal populations across biota, understanding the genomic basis of this dearth in diversity is key to developing informed conservation programs. With this goal in mind, Robinson et al. (2016) sought to estimate levels of genomic diversity in isolated populations of the endangered Island Fox, Urocyon littoralis in six of California’s Channel Islands.
Using newly sequenced genomes from seven representative foxes from the islands and a mainland gray fox from Southern California, they determined that the San Nicolas individuals are nearly identical, with an extreme reduction in genome-wide heterozygosity (3-84 fold), compared to the mainland gray fox. Other island populations exhibited similar reductions in heterozygosity. However, the smallest census population in San Miguel yet comprised foxes harboring greater diversity than the San Nicolas population. To model this, the authors use ABC to simulate data under three scenarios – a population with no demographic changes (sensu mainland foxes), one with an older bottleneck (similar to the San Miguel foxes), and one with a very recent extreme bottleneck (similar to San Nicolas). Estimated effective population sizes under these models were consistent with true estimates, indicating support for the effects of small population sizes (in San Miguel), and recent bottlenecks (in San Nicolas).
Additional characterization of the types of mutations in homozygosity accumulated regions in the islands revealed (a) general increase in loss of function alleles/genotypes, (b) enhancement of olfactory receptor genes in ancestrally heterozygosity rich regions, primarily owing to demographic effects (as confirmed by simulations), and not due to balancing selection. This study puts declining populations in question, which are long thought to be on an evolutionary spiral down to extinction owing to increased genetic load.
The absence of obvious negative effects on population persistence from genetic deterioration may in part reflect a more benign island environment, given the lack of competitors and predators that exist on the mainland…Notably, our results contradict the notion that long-term small effective population size and inbreeding on the islands have enhanced purging and decreased their genetic load.
Robinson, Jacqueline A., et al. “Genomic Flatlining in the Endangered Island Fox.” Current Biology (2016). DOI: 10.1016/j.cub.2016.02.062