Demographic history, geographic distance, and landscape features shape the genetic divergence of wild tigers in northeast India

Habitat fragmentation creates small, isolated populations vulnerable to inbreeding, genetic drift, and high genetic load. For conservation management, it is essential to distinguish contemporary landscape resistance from historical demographic processes as drivers of these genetic patterns, especially for conservation priority regions such as northeast India which intersects two major tiger conservation landscapes. We studied the genetic structure and landscape connectivity of tigers across four protected areas in northeast India: Kaziranga, Manas, Orang, and Nameri, using faecal samples. From 741 samples collected over two field seasons, we identified 654 confirmed tiger specimens. Using methylation-based enrichment and ddRAD-seq of 176 samples, we generated a high-quality dataset of 3091 SNPs across 44 individuals. Population structure analyses identified three genetically distinct clusters: Kaziranga-Nameri, Manas, and Orang. Isolation-by-distance and landscape resistance explained 13% and 17% of the observed genetic divergence, respectively, with human settlements influencing gene flow. Orang’s pronounced divergence from Kaziranga, despite geographic proximity and corridors, suggests a post-bottleneck founder effect, as evidenced by reduced heterozygosity (Ho = 0.24), nucleotide diversity (pi = 0.24), and effective population size (Ne = 1.3). These findings reveal that demographic and genetic recovery can decouple: Orang’s population has recently grown, yet genome-wide evidence shows ongoing genetic erosion that monitoring has not detected. Similar patterns have been reported in other Indian tiger populations, indicating that such decoupling may be systemic. Target 4 of the Kunming-Montreal Global Biodiversity Framework requires explicit genetic diversity monitoring; this study demonstrates that non-invasive genomics can operationalise that mandate at a conservation-relevant scale.