110 Mountain Lions of the Black Hills
or even eastern bound aries, and as a consequence, lions from other populations could
either enter the system and establish at any point or in any population, or could move
within the conduit to the north and east or the north and west.
We also estimated effective population size (Ne ) of lions in the Black Hills at 27.9
animals (22.65–38.97; 95% CI) (Thompson 2009); effective population size is an
indication of the number of individuals in the population that are involved with re-
production and thus gene transfer. In species that, like mountain lions, exhibit po-
lygynous mating systems, effective population size can be low, because a few adult
males monopolize females for relatively long periods of time. Our estimate was lower
than expected, but since Ne can be 10% to 20% of the total population, which would
indicate that between 138 and 279 mountain lions inhabited the Black Hills, the esti-
mate of effective population size was in line with our estimates of total population
size of mountain lions, generated from mark- recapture and population modeling.
In 2010, the potential for the use of ge ne tics to improve understanding of this
relatively new mountain lion population came up for discussion. We had been
radio- collaring mountain lions for 10 years, and the South Dakota Department of
Game, Fish and Parks was interested in using ge ne tics with mark- recapture to ascertain
whether this new technique would provide an estimate of population size comparable
to the estimates obtained using the more standard marks, in this case radio- collared
individuals. In addition, the department, through the Game and Fish Commission, had
increased the harvest limit on the population, and there was evidence that the in-
creased harvest had resulted in a reduction in population size. If there was some re-
duced population level that preserved ge ne tic diversity, then the lower population
size might be more manageable, while also preserving the ge ne tic health of the popu-
lation. Given these questions, we began this evaluation of the technique around 2012
(Jua rez 2014).
To complete these analyses, we maintained our relationship with the USDA Forest
Ser vice Ge ne tics Laboratory in Missoula, Montana, because we wanted to eliminate
any potential for laboratory- specific effects (M. Schwartz, USDA Forest Ser vice, Rocky
Mountain Research Station, pers. commun.) that would result in inconsistencies
between results from our first evaluation (Thompson 2009) and those from our new
evaluation (Juarez et al. 2016). We reanalyzed those first results to ensure quality
control of early and late samples using the original 20 microsatellite loci. We also
were able to increase the number of samples obtained from adjacent populations, to
improve our initial evaluation of population structure (how closely related these pop-
ulations were, genet ically, to one another), and generated a new estimate of effective
population size (NB ) (individuals genet ically contributing to the population) (Waples
and Teel 1990; Waples 2005).
Our first question focused on the maintenance of ge ne tic diversity of the lion
population. For this revised analy sis, we were able to include 675 mountain lions sam-
pled from the Black Hills, 113 lions sampled from North Dakota, and 62 lions