High genetic diversity and distinct ancient lineage of Asiatic black bears revealed by non-invasive surveys in the Annapurna Conservation Area, Nepal

Abstract

Asiatic black bears (Ursus thibetanus) have a widespread distribution in mountain landscapes, and are considered vulnerable globally, but are low-priority species for conservation in Nepal. Habitat fragmentation, illegal hunting, and human-bear conflict are the major threats to Asiatic black bears across their global range. Having an adequate level of genetic variation in a population helps with adapting to rapidly changing environments, and thus is important for the long-term health of bear populations. Accordingly, we conducted non-invasive surveys of bear populations in the Annapurna Conservation Area (ACA) to elucidate genetic diversity, genetic structure, and the phylogenetic relationship of Asiatic black bears from this region of Nepal to other subspecies. To assess levels of genetic diversity and population genetic structure, we genotyped eight microsatellite loci using 147 samples, identifying 60 individuals in an area of approximately 525 km2. We found that the Asiatic black bear population in the ACA has maintained high levels of genetic diversity (HE = 0.76) as compared to other bear populations from range countries. We did not detect a signature of population substructure among sampling localities and this suggests that animals are moving freely across the landscape within the ACA. We also detected a moderate population size that may increase with the availability of suitable habitat in the ACA, so bear-related conflict should be addressed to ensure the long-term viability of this expanding bear populations. Primers specific to bears were designed to amplify a 675 bp fragment of the mitochondrial control region from the collected samples. Three haplotypes were observed from the entire conservation area. The complete mitochondrial genome (16,771 bp), the first obtained from wild populations of the Himalayan black bear (U. t. laniger), was also sequenced to resolve the phylogenetic relationships of closely related subspecies of Asiatic black bears. The resulting phylogeny indicated that Himalayan black bear populations in Nepal are evolutionary distinct from other known subspecies of Asiatic black bears.

Wildlife Population Monitoring Study among Endangered Animals at Protected Areas in Nepal

“…Noninvasive genetic analysis technique is more safe and avoids the potential harmful effects from direct contacts with endangered wild animal species while performing research at protected areas [11]. In Nepal, more than dozens of previous studies on endangered wild animal species have been successfully recognized by applying the noninvasive genetic analysis insight into population structure, mitochondrial (mt) DNA of cytochrome b and D-loop control region sequencing, effective population size, phylogenetic inference, and other modeling [9,10,12, 13] approach as described in Table 1 [14][15][16][17][18][19][20][21].…”

Phylogenetic analysis of marginal Asiatic black bears reveals a recent Iranian–Himalayan divergence and has implications for taxonomy and conservation

“…S1). The smaller network that excluded all those likely mixed individuals with uncertainty in the locality of origin (from zoos, recovery centers, or introduced animals) recovered five well-distinguishable U. thibetanus clusters (subspecies groups), in accordance with Kadariya et al (2018) with the exception of differences in nominotypical subspecies (discussed below) (Fig. 2).…”

“…The origin on this sequence derives from Asiatic black bears collected from Sichuan Province Traditional Chinese Medicinal Materials Company and, therefore, may suggest either an unknown sample or cross contamination. Following these results, we did not name this subspecies in our analyses U. t. mupinensis (unlike analyses including its complete mitochondrial genome, Wu et al 2015;Kadariya et al 2018) and was excluded from the phylogenetic analyses.…”

“…As such, it is not surprising that the genetic status of these populations is still hardly known; in contrast, genetic tools have been widely employed to study the eastern Asian populations (e.g., Saitoh et al 2001;Ishibashi and Saitoh 2004;Ohnishi et al 2007Ohnishi et al , 2009Yasukochi et al 2009;Choi et al 2010;Kim et al 2011;Uno et al 2015;Wu et al 2015). To date, only one study (Kadariya et al 2018) has employed molecular markers to assess Asiatic black bear genetic diversity east from China. Interestingly, this study showed that the Nepalese Asiatic black bear population was in fact a distinct lineage and basal to all other mainland populations.…”

“…The Baluchistan black bear was long considered as a distinct subspecies, U. t. gedrosianus (Blanford 1877). However, the taxonomic validity of U. t. gedrosianus is uncertain and the affinity of this population with that of other populations has not been tested with molecular methods (Kadariya et al 2018). The latter can be particularly important since the taxonomy of Asiatic black bears below the species level remains uncertain, and there is no consensus with regard to either their systematics or their taxonomic nomenclature (Choi et al 2010;Wu et al 2015).…”