Evalutaing Methods to Estimate Population Size and Assessing Temporal Genetic Variation of Cougars in the Black Hills

The re-colonization of cougars (Puma concolor) to the Black Hills provides a unique opportunity to document the influence of harvest on this semi-isolated population. Increasing harvest quotas may have adverse effects on the viability of populations; therefore, our objectives were to 1) compare methods of population estimates of cougars ≥2 years of age (i.e., independent of females) using mark–recapture of radio-marked and DNA-marked individuals, 2a) assess genetic viability of cougars in South Dakota pre- (2003–2006), moderate (2007–2010), and heavy-harvest (2011–2013), 2b) measure effective population size (Ne) of cougars in South Dakota, and 2c) compare genetic structure of the South Dakota cougar population with cougar populations in Wyoming and North Dakota. Cougars were captured and fitted with radio-collars for radio mark–recapture analysis. Blood samples were taken from all captured animals, tissue samples were taken from all harvested animals, as well as non-harvest related mortalities, for DNA mark–recapture and genetic analysis using 20 microsatellite loci. DNA samples from Wyoming and North Dakota cougar populations also were used in genetic analyses. Population estimates of cougars for 2012 were: 165 (SE=32) using radio-marked methods; and 253–266 (SE=68–72) using DNA-marked methods. Estimates for 2013 were: 188 (SE=44) using radio-marked methods; and 151–162 (SE=35–39) using DNA-marked methods. Expected (HE) and observed (HO) heterozygosities were 0.56 (SE=0.04), and allelic richness (Ar) was 4.29 (SE=0.32). Effective population size (Ne) of cougars in the Black Hills was 28 (23 – 37; 95% CL) using a single sample method and 66 (49–99; 95% CL) using the temporal method. We determined that Wyoming cougars had expected (HE) and observed (HO) heterozygosities of 0.55 (SE=0.04). In contrast, North Dakota cougars had expected (HE) and observed (HO) heterozygosities of 0.50 (SE=0.04) and 0.51 (SE=0.04), respectively. Our results indicate that the Black Hills cougar population has maintained genetic diversity despite increasing harvest. Furthermore, genetic similarity with Wyoming cougars suggests that these two populations are acting as a large panmictic population, likely preserving the population’s viability as a result of immigration. Reassessment of population estimate methods and continued genetic monitoring of this population is recommended