Scat collection and genotyping
We surveyed approximately 146.8 km of trails between the two study areas
(AEP = 64.0 km and Vinton-Zaleski = 82.8 km) for each survey event. We
collected a total of 813 scats during the three combined survey events
and were able to extract DNA from 789 scats for species identification.
Of those samples, we identified 37.4% (295 scats) as bobcat for density
estimation. The remaining scats were identified as either coyote
(Canis latrans ) 32.3% (255 scats) or were of unknown species
30.3% (239 scats). There were 25 samples identified as both coyote and
bobcat which were included in the first round of amplifications; none of
these samples amplified at any of the four MP1 loci and were removed and
classified as unknown species. Of the initial 295 bobcat samples
amplified at Multiplex 1, 164 reached the criteria to move onto
amplification with Multiplex 2. We achieved consensus genotypes at a
minimum of 5 loci for 102 samples (34.6% genotype success rate) of
which 48 samples reached consensus at all 8 loci. Overall PCR
amplification success across all samples was typical for scat studies at
50.9% and ranged from 27.2%-75.9% per locus (Table 2. The
probabilities that two individual genotypes (PID) and
two sibling genotypes (PIDsibs) are identified as the
same individual for the 8-locus dataset was low at 8e-8 and 1.5e-3,
respectively, illustrating the high power of the locus set to
distinguish individuals.
We identified a total of 55 individual bobcats from 102 unique captures
(genotyped scats); the AEP study area had a higher number of individuals
(n = 33) compared to the Vinton-Zaleski study area (n = 22). Overall, we
identified more female bobcats than male bobcats (female = 28, male =
19, unknown = 8). We also identified more female bobcats in AEP (female
= 20, male = 8, unknown = 5), while Vinton-Zaleski had a more even
distribution of sexes (female = 8, male = 11, unknown = 3). Recapture
rates (those with multiple scats) were similar between sites (average of
1.97 ± 0.17 SE detections per individual in AEP and 2.31 ± 0.34 SE
detections per individual in Vinton-Zaleski), and sexes (average of 2.42
± 0.35 SE detection per individual for males and 2.04 ± 0.18 SE
detections per individual for females). The maximum number of detections
for any individual was 9 (male in Vinton-Zaleski), and 47 bobcats were
recaptured at least once. Of the 47 bobcats that were recaptured, the
average distance between successive recaptures was 1.68 km ± 0.25 SE.
The minimum distance between successive recaptures was 0 km (bobcats
recaptured within the same grid cell), and the maximum distance between
successive recaptures was 9.06 km (a male bobcat in AEP; Figure 3).