Genetic applications to inform invasive species management on islands: Sitka black-tailed deer in Haida Gwaii

Background/Question/Methods

: Invasive species are a primary driver of biodiversity decline, especially on islands, which face elevated extinction rates. Across Haida Gwaii (Canada), islands with invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) exhibit significantly lower species richness and population decline of many ecologically and culturally important species. To date, deer management has been challenging due to knowledge gaps of key population information. Here we used genetic and genomic data to understand patterns of deer movement across the archipelago and develop tools to inform active management. (1) We employed restriction-site associated DNA sequencing to genotype 181 deer across 15 islands at ~13,000 single nucleotide polymorphisms (SNPs) to estimate gene flow across the archipelago. (2) We then developed a Genotyping-in-Thousands by sequencing (GT-seq) panel to evaluate and support management of deer by providing accurate individual and sex identification, and pairwise kinship estimations. Using paired high-quality tissue and non-invasive feces and hair, we optimized the panel for poor-quality samples. (3) Finally, we used GT-seq to investigate the unbiased patterns of genetic isolation on islands that had been previously culled and determine the genetic consequences of culling. At 236 SNPs, we genotyped pre- and post-cull deer on managed islands to examine the viability of sustainable eradications.

Results/Conclusions

: (1) We detected little population structure across 14 islands and provided evidence of contemporary inter-island deer movement. The culturally significant island of SGang Gwaay exhibited genetic isolation, constituting a possible eradication target; however, deer here have been culled previously, suggesting the observed patterns may be due a genetic bottleneck rather than isolation. Overall, the high connectivity indicates sustainable eradications are likely not possible in most cases, and alternative management interventions may be required. (2) Our GT-seq panel demonstrated high levels of genotyping success (90.3%) and sample retention (97.6%) at 244 SNPs, as well as low levels of genotyping discordance between paired tissue and non-invasive samples (0.51%), providing researchers with guidelines for efficient high-density genotyping of poor-quality samples that are typical of elusive or at-risk species. (3) Pre-cull deer on SGang Gwaay exhibited patterns of genetic isolation and lower levels of genetic diversity compared to unmanaged islands, suggesting a possible founder effect and infrequent immigration, which is promising for future management goals. This research will directly inform deer management to help restore ecological integrity in Haida Gwaii. More broadly, we demonstrate the utility of population genetics and genomics for improving invasive species management on islands.