The recent development of fecal-genetic capture-mark-recapture (CMR) methods has increased the feasibility of estimating abundance of forest-dwelling ungulates that are difficult to survey using visual methods. Unless genetic markers differentiating sex are incorporated into such studies, however, genetic CMR approaches risk missing sex-specific differences in population trends. We developed a singlereaction genetic assay for sex and individual identification, including 10 microsatellites and an SRY marker, and applied it in the context of a post-fawning CMR study of Columbian black-tailed deer (Odocoileus hemionus columbianus) in forested habitat of coastal California during 2011 and 2012. We measured sexspecific abundance and sex ratios in high-quality summer habitats encompassing 4 distinct fawning areas. We detected a significant interaction between sex and year, indicating different trends in the abundance of males and females. We also detected a significant decline in abundance of females between years (P ¼ 0.045), which agreed with independent telemetry-based estimates, and significant differences in female abundance among fawning areas (P ¼ 0.020) but no significant differences in the abundance of males for either variable (F 1-3,20 < 0.710, P > 0.410). When sex was not considered in the analysis, we found no significant differences in abundance between the 2 years, suggesting that differing trends between the 2 sexes obscured the femalespecific patterns. We estimated average local (i.e., on the high-quality summer ranges) density (D) for females at 41.0 (AE 5.9) deer/km 2 in 2011 and 29.1 (AE 6.8) deer/km 2 in 2012, and local density of males at 15.7 (AE 3.0) deer/km 2 across the 2 study years. Accordingly, sex ratios differed between years (95% CI ¼ 3.0-4.2 F:M ratio in 2011, 2.0-2.3 F:M ratio in 2012). Incorporating sex and individual markers into a single assay provided a cost-effective means of applying CMR estimation based on fecal DNA to a high-density ungulate population in a forested ecosystem and emphasized the importance of explicitly modeling sex in abundance estimation. Ó

Informed management of wildlife populations requires the accurate estimation of abundance, sex ratio, and other population parameters. For deer (Odocoileus spp.), the use of closed‐population, capture‐recapture (CR) methods, in conjunction with noninvasive DNA sampling, has become increasingly practical, but, up to now, these methods have been used in a non‐spatial modeling framework, which has limited their utility for population‐level inferences. In particular, extrapolation of plot‐level CR abundance estimates to the population required the use of multipliers of unknown reliability and potential bias. Spatially explicit capture‐recapture (SCR) models provide an integrated framework for directly estimating density as a function of spatial and habitat variables at landscape scales. We used fecal DNA samples in conjunction with SCR to estimate density, sex ratio, and habitat correlates to density for a mule deer (O. hemionus) population across a large (∼500 km2) area in the central Sierra Nevada Range, California, USA during 2013 and 2014. We surveyed 24 random transects within 4 30‐km2 sites representative of the study area. Based on 411 samples genotyped at a sex marker and 8–10 microsatellite loci, the sex‐ratio for the study area was 62 (95% CI = 41–93) males/100 females in 2013 and 65 (95% CI = 45–94) males/100 females in 2014. Using SCR, we estimated density at 5.0 (95% CI = 2.3–7.8) deer/km2 in 2013 and 5.1 (95% CI = 3.1–7.2) deer/km2 in 2014. In comparison, non‐spatial CR analysis produced density estimates on average 60% higher, likely reflecting bias resulting from use of the commonly employed mean maximum recapture distance (MMRD) to estimate effective sampling area. The SCR models indicated that density was effectively homogeneous throughout the study area, with no strong relationship to habitat correlates. Altogether, these results demonstrate the utility of noninvasive fecal DNA methods in a SCR framework for estimation of abundance and density in deer populations at landscape scales. © 2017 The Wildlife Society

Invasive mammalian carnivores contribute disproportionately to declines in global biodiversity. In California, nonnative red foxes (Vulpes vulpes) have significantly impacted endangered ground‐nesting birds and native canids. These foxes derive primarily from captive‐reared animals associated with the fur‐farming industry. Over the past five decades, the cumulative area occupied by nonnative red fox increased to cover much of central and southern California. We used a landscape‐genetic approach involving mitochondrial DNA (mtDNA) sequences and 13 microsatellites of 402 nonnative red foxes removed in predator control programs to investigate source populations, contemporary connectivity, and metapopulation dynamics. Both markers indicated high population structuring consistent with origins from multiple introductions and low subsequent gene flow. Landscape‐genetic modeling indicated that population connectivity was especially low among coastal sampling sites surrounded by mountainous wildlands but somewhat higher through topographically flat, urban and agricultural landscapes. The genetic composition of populations tended to be stable for multiple generations, indicating a degree of demographic resilience to predator removal programs. However, in two sites where intensive predator control reduced fox abundance, we observed increases in immigration, suggesting potential for recolonization to counter eradication attempts. These findings, along with continued genetic monitoring, can help guide localized management of foxes by identifying points of introductions and routes of spread and evaluating the relative importance of reproduction and immigration in maintaining populations. More generally, the study illustrates the utility of a landscape‐genetic approach for understanding invasion dynamics and metapopulation structure of one of the world's most destructive invasive mammals, the red fox.

Site fidelity and philopatry are behavioral adaptations found in many species and their fitness benefits are well documented. The combined population level consequences of site fidelity and philopatry, however, have received little attention despite their importance for understanding spatial patterns in connectivity and population dynamics. We used an integrative approach to explore consequences of fidelity and philopatry on the fine-scale genetic structure of black-tailed deer (Odocoileus hemionus columbianus). We assessed fidelity to seasonal home ranges based on location data from 64 female deer fitted with global positioning system (GPS) collars between 2004 and 2013. We assessed philopatry from mitochondrial DNA (mtDNA) haplotypes using DNA extracted from 48 deer. Results based on location data revealed very small movements and seasonal home ranges together with high site fidelity. Fidelity improved survival; every 1 km increase in mean interlocation distances between consecutive summers increased the risk of mortality by 56.5%. Results from mtDNA sequencing revealed high genetic differentiation (F ST > 0.30) and low haplotype sharing among geographic areas separated by as little as 4-10 km. The high genetic differentiation indicated multigenerational periods of philopatric behavior in the matrilineage of black-tailed deer. Combined these results suggest that site fidelity together with strong sex-biased philopatry can create marked short-and long-term demographic isolation and trap matriarchal units as a subset of the larger population with locally determined vital rates. Where such fine-scale population structuring as a consequence of fidelity and philopatry occurs, matrilineal groups might in some cases best serve as the basic units of conservation and management.

Non-invasive genetic sampling and spatially explicit capture-recapture (SCR) models are used increasingly to estimate abundance of wildlife populations, but have not been adequately tested on gregarious animals such as elk (Cervus canadensis), for which correlated space use and movements violate model assumptions of independence. To evaluate the robustness and accuracy of SCR, and to assess the utility of an alternative non-invasive method for estimating density of gregarious ungulates, we utilized a tule elk (Cervus canadensis nannodes) population of known size within a fenced enclosure on the San Luis National Wildlife Refuge in central California. We evaluated fecal genetic SCR to camera trap-based random encounter model (REM) approaches to density estimation based on comparison to the true abundance. We also subsampled the dataset to explore the effects of varying search effort and elk density on the precision and accuracy of results. We found that SCR outperformed REM methods in the full datasets, and reliably provided accurate (relative bias <10%) and reasonably precise (relative standard error ≤20%) estimates of density at moderately low to high densities (6-17 elk/km2), when the subsampling scenarios yielded a minimum average of 20 recaptures. We also found that the number of samples used to construct detection histories was a reliable predictor of precision, and could be used to establish minimum sampling requirements in future population surveys of elk. Although field-testing in free-ranging populations is needed, our results suggest that non-invasive genetic SCR is a promising tool for future population studies and monitoring of elk and potentially other gregarious ungulates. In contrast, the REM estimate of density was highly inaccurate, imprecise, and highly sensitive to camera parameters.