Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape

Abstract

With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal’s first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (He = 0.61, AR = 3.51) and genetic differentiation (FST = 0.14) across the landscape. We detected 3–7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale land-use change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.

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].…”

Species, sex and geo-location identification of seized tiger (Panthera tigris tigris) parts in Nepal—A molecular forensic approach

“…Two microsatellite markers (FCA205 and PttA2) were included in the PCR multiplex but were not considered in the individual identification as one (Locus FCA205) did not amplify in the majority of samples and the other (PttA2) was not polymorphic. Similarly, the mean allelic dropout rate was 2.46% and false alleles were around 15.85% [ 44 ].…”

“…The molecular assay we have used in our baseline tiger genetic database and forensic samples have high probability of identification (P ID ; 1.5E-06) and probability of identification among siblings (P ID (sibs) ; 3.2E-03) with eight microsatellite loci showing high polymorphism [ 38 ]. Similarly, our species and sex identification PCR assay was highly effective [ 44 ].Other studies have shown that assignment tests can be very effective and accurate when pairwise F st values between source populations exceed 0.05, which was true in our study[ 44 , 65 ]. Using our analysis framework, we were able to assign 9 of the 14 individuals to a source population in Nepal.…”

“…NTGP created Nepal’s first comprehensive tiger reference genetic database by collecting and analyzing fecal samples ( n = 770;CNP = 420, BNP = 116, SWR = 79, PWR and wildlife corridors = 155) across the TAL region of Nepal ( Fig 1 and S2 Table ). This database includes species, sex and individual DNA microsatellite profiles of 120 wild tigers[ 44 ].…”

Humans Are Animals, Too: Critical Commonalities and Differences Between Human and Wildlife Forensic Genetics

“…Populations with F st values of 0.00–0.05 have little to no variation, 0.05–0.15 moderate variation, 0.15–0.25 great variation, and greater than 0.25 very great differentiation. Table compares Θ values for various wildlife species to humans, illustrating a wide range of Θ values .…”