Leveraging Next-Generation Tools for Genetic Assessment and Demographic Monitoring in Threatened and Elusive Humboldt...

Conservation assessments of imperiled species require information on population structure, abundance, and connectivity which benefit from integrated demographic and genetic data. Humboldt martens (Martes caurina humboldtensis) are a federally threatened subspecies of Pacific marten (Martes caurina) whose conservation has been hindered by knowledge gaps and data deficiencies due to rarity and elusiveness. Here, we assessed population structure and genetic viability of Humboldt martens by exploring synergies between reduced representation sequencing and noninvasive genetic approaches. We used ddRADseq to discover 14,652 SNPs from 63 Pacific martens, then used these data to develop and validate a 94-amplicon SNP panel for accurate individual and sex identification and broadscale genetic structure inference from Humboldt marten scats. Applying this SNP panel to 209 scats, two hair samples, and 24 low-quality tissue samples, we identified 93 additional individuals and spatially expanded genetic structure inference relative to ddRADseq, including discovery of a previously undescribed population. We found genetic diversity was ~20% lower and inbreeding ~3 times higher on average in Humboldt martens relative to other Pacific marten populations, and Humboldt martens showed lower mitogenome nucleotide diversity than other genetically depauperate carnivore species and populations. Our combined analyses support genetic distinctness of Humboldt martens with limited evidence for hybridization with Oregon Cascades martens. Our data suggest geographic structuring of genetic viability within Humboldt martens, with strong signatures of isolation and small population size in the northernmost populations. Our approach demonstrates advantages and limitations of combining small genomic datasets and targeted SNP panels for conservation assessment and monitoring in fragmented and genetically depauperate species, and we call for expanded genetic viability assessment and monitoring in Humboldt martens.