Genetic variation in a peripheral and declining population of black-tailed prairie dogs (Cynomys ludovicianus) from Mexico

Across North America, anthropogenically induced habitat fragmentation has led to a severe decline in populations of black-tailed prairie dogs (Cynomys ludovicianus). Although the area occupied by black-tailed prairie dogs in Chihuahua, northwestern Mexico, also has recently declined, this site remains comparatively unaffected by human disturbance. Cytochrome-b sequences and 10 nuclear microsatellite loci were analyzed across 13 colonies to test if due to large size, absence of plague, and protected status, the black-tailed prairie dogs from Janos possess relatively high levels of genetic variation and low genetic structure; or if recent population decline and peripheral effects result in relatively low genetic variation and high genetic structure. Analysis suggests moderate mitochondrial genetic variation relative to other sciurids, and not significantly different nuclear genetic variation relative to other populations of prairie dogs. Furthermore, in accordance to black-tailed prairie dog social organization, genetic structure among local populations was significant, and within-colony variation was higher than among-colony variation for both markers. FST was higher for mitochondrial than for nuclear DNA related to female philopatry and male-biased gene flow. Finally, a negative correlation between genetic differentiation as a function of colony area and population size found for nuclear microsatellite loci suggests an increased effect of genetic drift in smaller and less-dense colonies because of recent habitat fragmentation. In conclusion, despite being a peripheral and declining population, Janos black-tailed prairie dogs retained genetic variation that has been maintained by their social structure and dispersal pattern.