Testing a single-visit sampling approach for fecal DNA abundance estimation of tule elk in the Lake Pillsbury Basin

Robustness of fecal DNA spatial capture‐recapture to clustered space‐use by tule elk

“…In We observed little evidence of spatial dependence among activity centers of males but relatively strong clustering among females in the telemetry data and genotyped fecal samples. As expected based on previous aerial and ground surveys (Bush et al 2020) and confirmed after the present study (Sacks et al 2022), the most extreme case was in the LPB population, where females were clustered in a small location, effectively sharing a single activity center. Within the CC range, we observed ≥4 distinct female groups, each of which had highly correlated activity centers.…”

“…We chose to sample during this period to ensure population closure (i.e., avoiding calving), to avoid rainfall, which can reduce DNA recovery, and because group sizes tended to be smaller and social interactions more fluid than during rut (McCullough 1969). A separate sampling of the LPB population conducted later in the year (2019) confirmed that group size and the degree of clustering increased in fall (Sacks et al 2022), supporting our decision to avoid the rut for the SCR study. In other regions where climatic conditions differ, such as northern latitudes where freezing temperatures help to preserve DNA, it might be equally or more effective to conduct pre‐calving sampling in late winter, after rut but before calving (McFarlane et al 2020).…”

“…In the auxiliary study, pellets were sampled in the rut during a 1‐day intensive search focused where the female group was centered, and abundance was estimated using Capwire (Miller et al 2005), which does not consider spatial distribution. The auxiliary study produced an estimate of female abundance (159, 95% CI = 106‒189) that was similar to that of our combined‐sex SCR model (136 females, 95% CI = 100‒172) but considerably lower than our biased female‐only SCR model (283, 95% CI = 189‒397; Sacks et al 2022). Thus, we found evidence of significant bias in SCR only when employing single‐sex models for females under the most extreme level of spatial clustering.…”

“…Our independent sampling of elk using traditional capture methods in combination with fDNA recaptures yielded non‐spatial estimates of abundance that were statistically indistinguishable from those of our combined‐sex SCR models. Additionally, our combined‐sex SCR estimate in the LPB population was validated by an auxiliary study conducted in October 2019 (soon after the present study of the same year) to estimate abundance using an alternative sampling and analysis approach (Sacks et al 2022). In the auxiliary study, pellets were sampled in the rut during a 1‐day intensive search focused where the female group was centered, and abundance was estimated using Capwire (Miller et al 2005), which does not consider spatial distribution.…”

Genetic structure of California's elk: a legacy of extirpations, reintroductions, population expansions, and admixture

“…Tissue and blood samples consisted of muscle or skin and were stored in desiccant after collection during 1995-2022. Genotypes for fecal samples had been analyzed as part of prior research projects conducted during 2017-2019, allowing us to select only a single genotype per individual for this study (Batter et al 2021(Batter et al , 2022Sacks et al 2022), which was described in detail for the same 427 fecal samples by Batter et al (2021). Specifically, only fecal DNA genotypes with ≥18 of the 20 loci were retained (Batter et al 2021) and genotype error rates for those genotypes were estimated at 0.011 allelic dropout and <0.001 false alleles (Batter et al 2022).…”