Capture-recapture of white-tailed deer using DNA sampling from fecal pellet-groups

Reliable density estimates of game and keystone species such as white-tailed deer (Odocoileus virginianus) are desirable to set proper management strategies and for evaluating those strategies over time. However, traditional methods for estimating white-tailed deer density have been inhibited by behavior, densely forested areas that can hamper observation (detection), and invalid techniques of estimating effective trapping area. We wanted to evaluate a noninvasive method of mark-recapture estimation using DNA extracted from fecal pellets as the individual marker and for gender determination, coupled with a spatial detection function to estimate density (Spatially Explicit Capture-Recapture, SECR). We collected pellet groups from 11 to 22 January 2010 at randomly selected sites within a 1-km2 area located on Arnold Air Force Base in Coffee and Franklin Counties, Tennessee. We searched 702 plots (10–m radius), collecting 352 pellet-group samples on 197 of the plots. We sent samples to Wildlife Genetics International (Nelson, British Columbia) for genetic analysis. One gender and 6 microsatellite markers with heterozygosity \u3e0.80 were selected for genotyping individuals. Fifteen samples (4%) were not suitable for analysis, 2 (1%) showed evidence of \u3e2 alleles per marker (mixture of DNA), and 114 (32%) failed to provide genotypes during testing. We assigned individual identity and gender to 223 (63%) of the samples which consisted of 39 individuals (18M:21F). We used Program DENSITY (SECR) to fit a model of the detection process to estimate density unbiased by edge effects and incomplete detection. Time of sampling had the largest effect on capture probabilities. Calculated total deer density was 6.2 (SE = 1.39) deer/km2. Buck to doe ratio was 1:1.75 based on density by gender (2.3 (SE = 0.85) bucks; 4.08 (SE = 1.10) does). We also evaluated whether fewer samples could be used to estimate density with similar measures of precision. Standard error increased from 1.39 for total sample analysis to 1.99 when we evaluated 50% of total samples, and 3.09 when we evaluated 20% of samples. We found DNA sampling from pellet groups provided deer density and sex ratio estimates useful for deer management decisions and reduces the risk of overestimating deer density, common in traditional methods