Ecological Archives C006-084-A1
K. M. Proffitt, J. F. Goldberg, M. Hebblewhite, R. Russell, B. S. Jimenez, H. S. Robinson, K. Pilgrim, and M. K. Schwartz. 2015. Integrating resource selection into spatial capture-recapture models for large carnivores. Ecosphere 6:239. http://dx.doi.org/10.1890/es15-00001.1
Appendix A. Protocol of genetic analysis of individual mountain lion identity.
We genotyped tissue samples using 20 variable microsatellite loci used previously in mountain lions: Fca08, Fca30, Fca35, Fca43, Fca57, Fca77, Fca82, Fca90, Fca96, Fca132, Fca149, Fca176, Fca391, Fca559, LC109 (Biek et al. 2006, Culver et al. 2000, Menotti-Raymond et al. 2003), PcoA208w, PcoB010w, PcoB210w, PcoC108w, and PcoC112w (Kurushima at al. 2006). We amplified all scat and hair samples 3 times using protocols outlined in Biek et al. (2006) to eliminate most genotyping errors associated with identifying unique individuals. When we detected inconsistencies between amplifications, we ran samples an additional 3 times. We used 2 computer algorithms in program DROPOUT (Mckelvey and Schwartz 2004, 2005) as implemented in Schwartz et al. (2006) to ensure that the genotypes produced did not inflate the estimate of mountain lions in this study. We also checked for genotyping errors by running samples through program MICROCHECKER (van Oosterhout et al. 2004). The power to detect unique individuals using this marker panel was high; probability of identity was 3.60E-14, and probability of identity given siblings was 1.30E-06. Several of the non-invasive genetic samples did not amplify at all loci although 74.4% of all samples had no missing data. Missing data can be problematic if two samples had missing data at opposite loci. We examined the worst case where two samples each had missing data, some at opposite loci. The probability of identity given the loci that amplified in both of these samples was 8.01E-05, suggesting we had adequate power to discern individuals even in the worst case scenarios.
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