Dog-assisted scat sampling reveals genetic diversity, structure, and relatedness in black-footed cats (Felis nigripes)

Advances in molecular techniques for non-invasive genetic sampling have strengthened wildlife genetics, enabling researchers to study elusive and difficult-to-study species with minimal disturbance, and conservation detection dogs can greatly increase sample numbers and the area covered. However, this combination is rarely used in Africa and has perhaps never been applied to a small carnivore on the continent. Here we use dog-assisted scat surveys to carry out the first fine-scale population genetic study of the black-footed cat (Felis nigripes), Africa's smallest and most range-restricted endemic felid, and a threatened species for which conventional survey methods are largely ineffective. Using 130 successfully genotyped scat samples (nine microsatellite loci) from two populations about 650 km apart, we identified 65 individuals and assessed genetic diversity and fine-scale relatedness to explore aspects of dispersal and reproductive ecology. Both populations exhibited similar observed heterozygosity (Ho = 0.67-0.69) and allelic richness, with no heterozygote deficit (FIS = -0.02 to -0.08). Differentiation between the southern Namibia and central South Africa sites was low but detectable (FST = 0.03-0.05). We used pairwise relatedness and candidate pedigree results to explore hypotheses about sex-specific relatedness patterns. Female-female dyads were more related than male-male dyads at the shortest distance class (0-2 km), a pattern compatible with female philopatry. There were more half-sibling than full-sibling assignments and uneven representation of candidate fathers, which may indicate polygamy and reproductive skew. These results provide baseline genetic data for a Vulnerable species and show that this approach is feasible for Africa's small, elusive carnivores, whose dispersal, mating systems and population structure remain largely unknown. Broader spatial and temporal sampling could help assess population connectivity and reveal how threats and changing land use impact genetic diversity and structure.