Map of the Terai Arc Landscape, Nepal.

<p>(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 (<i>n</i> = 78) in three populations across the Terai Arc Landscape revealing three (<i>k</i> = 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.</p

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.

<p>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 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193495#pone.0193495.ref036" target="_blank">36</a>] in ArcGIS 10.1.</p

Contemporary gene flow patterns for tigers inferred across the Terai Arc Landscape, Nepal, based on migration rates (M_c) estimated in BayesAss+[70].

<p>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.</p

Tiger species identification using mtDNA PCR assay.

<p>Tiger positive samples yielded 162bp PCR fragments.</p

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.

<p>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.</p

Pair-wise measures of the level of differentiation of tiger sub-populations in the Terai Arc Landscape, Nepal based on F_ST[55] and D_EST (in parentheses) [56] (below the diagonal).

<p>Pair wise geographical distance (in km) between core population (above diagonal).</p

Study area and sampling grids cells (15 X 15 km) used for collection of tiger scat samples across the Terai Arc Landscape, Nepal.

<p>We searched and collected tiger scats (<i>n</i> = 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.</p

Summary of PCR amplification success and genotyping accuracy (GA) for 8 microsatellite loci for all processed tiger samples (<i>n</i> = 401) detected across the three protected areas: Chitwan National Park, Bardia National Park, and Suklaphanta National Park across the Terai Arc Landscape, Nepal.

<p>Summary of PCR amplification success and genotyping accuracy (GA) for 8 microsatellite loci for all processed tiger samples (<i>n</i> = 401) detected across the three protected areas: Chitwan National Park, Bardia National Park, and Suklaphanta National Park across the Terai Arc Landscape, Nepal.</p

Sex identification of tiger species positive samples using Amelogenin gene PCR assay.

<p>Females have single band at 214 bp and males have bands at 194 bp and 214 bp.</p

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.

<p>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.</p