Population Genetics of Fragmented Elephant Corridors

Abstract

Habitat fragmentation driven by agricultural expansion, human settlement, and linear infrastructure has isolated Asian
elephant (Elephas maximus) populations across their range, creating a patchwork of subpopulations connected by
increasingly narrow and degraded corridors whose effectiveness in maintaining genetic connectivity determines the
long-term viability of the species in fragmented landscapes. This study characterised the population genetic structure,
gene flow dynamics, and inbreeding status of 12 Asian elephant subpopulations across six corridor systems in southern
India and Sri Lanka using genotyping-by-sequencing (GBS) of 248 individuals, yielding 28,484 SNPs after filtering.
STRUCTURE analysis identified K = 6 genetic clusters corresponding broadly to the six corridor systems, with
FST(overall) = 0.184 (95% CI: 0.162-0.208), indicating substantial genetic differentiation consistent with substantially
restricted gene flow among subpopulations. Effective population sizes (Ne) estimated by linkage disequilibrium methods
ranged from 24.4 (most isolated subpopulation; single railway-bisected forest fragment) to 284.4 (largest connected
subpopulation; intact corridor), with 7 of 12 subpopulations showing Ne < 50 individuals, below the minimum viable
population threshold for long-term persistence. Relatedness analysis (KING estimator) identified significantly elevated
first- and second-degree relatedness in isolated subpopulations (mean r = 0.12 +- 0.04 vs. 0.04 +- 0.02 in connected
subpopulations; t = 8.42, p < 0.001). Corridor quality index (CQI; integrating width, land use, and infrastructure barriers)
was significantly positively correlated with inter-subpopulation genetic connectivity (EEMS estimated migration rates; r(S)
= +0.84, p < 0.001). These results identify three corridors requiring urgent restoration and two subpopulations at
immediate genetic rescue risk, providing a genomic evidence base for targeted elephant conservation investment under
the IUCN Species Survival Commission Asian Elephant Action Plan.