Fig 1.
Study area and sampling grids cells (15 X 15 km) used for collection of tiger scat samples across the Terai Arc Landscape, Nepal.
We searched and collected tiger scats (n = 770) from 54 grid cells (Protected Areas: 36 grids; Corridors: 18 grids) out of total 108 grid cells totaling 9,000 km2 of land area.
Fig 2.
Land use change (forest into agriculture and settlement) analysis, in the last 400 years in the Terai Arc Landscape using Anthrome 2.0 datasets at resolution of ~10 km pixel size [36] in ArcGIS 10.1.
Fig 3.
Tiger species identification using mtDNA PCR assay.
Tiger positive samples yielded 162bp PCR fragments.
Fig 4.
Sex identification of tiger species positive samples using Amelogenin gene PCR assay.
Females have single band at 214 bp and males have bands at 194 bp and 214 bp.
Table 1.
Summary of scat DNA analysis success rates for species and sex identification, and overall microsatellite genotyping based on putative tiger scat samples (n = 770) collected in the Terai Arc Landscape, Nepal.
Species identification was based on the total number of samples processed; sex identification was based on the total number of tiger positive samples; and genotyping success was based on the number of positive samples for species and sex identification. M, male; F, female.
Table 2.
Summary of PCR amplification success and genotyping accuracy (GA) for 8 microsatellite loci for all processed tiger samples (n = 401) detected across the three protected areas: Chitwan National Park, Bardia National Park, and Suklaphanta National Park across the Terai Arc Landscape, Nepal.
Table 3.
Genetic diversity estimates across 8 microsatellite loci for tigers studied in three protected areas across the Terai Arc Landscape, Nepal: Chitwan National Park, Bardia National Park, and Suklaphanta National Park.
Table 4.
Pair-wise measures of the level of differentiation of tiger sub-populations in the Terai Arc Landscape, Nepal based on FST[55] and DEST (in parentheses) [56] (below the diagonal).
Pair wise geographical distance (in km) between core population (above diagonal).
Fig 5.
Principal Coordinate Analysis of tiger genotypes obtained from “♦” Chitwan National Park, “○” Bardia National Park, and “▲” Suklaphanta National Park, in the Terai Arc Landscape, Ne pal, assessed through program GenAlEx.
Fig 6.
Map of the Terai Arc Landscape, Nepal.
(a) Protected areas (starting from left: Suklaphanta National Park, SuNP; Bardia National Park, BNP; Chitwan National Park, CNP; along with the spatial location of identified tiger-positive samples (black dots). (b) Pie charts showing the percentage of ancestry assigned to other identified genetic clusters in the populations (orange), and the resident population (blue). (c) STRUCTURE (non-spatially explicit) bar plot with each bar representing an individual tiger (n = 78) in three populations across the Terai Arc Landscape revealing three (k = 3) admixed sub-populations (represented by 3 different colors) along with five migrants (marked as “*’) identified across the population. (d) Bar plot showing three identified sub-populations analyzed in spatially-explicit assignment program TESS.
Fig 7.
Contemporary gene flow patterns for tigers inferred across the Terai Arc Landscape, Nepal, based on migration rates (Mc) estimated in BayesAss+[70].
Dashed lines in the center indicate direction of migration and line thickness represents the magnitude of estimates along with the migration rates. Figures within parentheses represent 95% CI for migration rates. Size of the circle represents the estimated size of breeding population. Broken lines around the periphery represent the spatial distances between the populations.
Fig 8.
Isolation-by-distance patterns for tigers in Terai Arc Landscape, Nepal assessed by plotting pairwise codominant genotypic distance versus pairwise geographic distances (km) including statistical significance using simple Mantel tests in GenAlEx, version 6.5.
Each point (diamond) represents a pair-wise comparison among individual tigers.
Table 5.
First-generation migrants between the 3 main core tiger populations in the Terai Arc Landscape-Nepal detected using programs STRUCTURE, Geneclass2 and BayesAss+; P value from Geneclass2.