Genomic Diversity, Inbreeding Depression, and Conservation Unit Delineation in the Critically Endangered Mountain Gorilla: Whole-Genome Analysis of 224 Individuals From Bwindi and Virunga Populations

This study investigates genomic diversity, inbreeding coefficients, population structure, and conservation unit delineation in mountain gorillas from Bwindi Impenetrable Forest and Virunga Massif using whole-genome sequencing of 224 individuals within the context of conservation genetics and wildlife biology, an area of growing scientific importance given its implications for mountain gorilla conservation unit legal status, gene flow management between populations, and inbreeding mitigation via translocation policy. Using WGS at 20x coverage (Illumina NovaSeq), SNP calling (GATK HaplotypeCaller), runs of homozygosity (ROH) for inbreeding coefficient (FROH), Fst-based population differentiation, ADMIXTURE ancestry analysis, and effective population size (Ne) reconstruction via PSMC, we examine mountain gorilla critically endangered status (approximately 1,000 total individuals) creating strong genetic drift and inbreeding signals, with Bwindi and Virunga populations isolated by an 80-km geographic gap since approximately 400,000 years BP showing substantial Fst divergence supporting separate conservation units in 224 gorillas: 124 Bwindi (84 living in 24 social groups, 40 historical museum samples 1950-1990), 100 Virunga (72 living, 28 historical); 224 x 20x WGS generating 5.6 Tb sequence data; 4.8M high-quality SNPs after filtering drawn from Gorilla Doctors field teams in Bwindi and Virunga conducting non-invasive fecal sample collection (living individuals) and Smithsonian/RMCA museum collections (historical specimens); sequencing at Atlantic Conservation Institute genomics core. Results indicate that Bwindi and Virunga are genetically distinct populations (Fst=0.084, p<0.001), strongly supporting separate ESUs; mean FROH: Bwindi 0.084 (moderate inbreeding), Virunga 0.064; Ne Bwindi ~48 historical declining to ~28 current; historical specimens show 18.4% higher heterozygosity than contemporary (p < 0.001), with Fst=0.084; FROH Bwindi 0.084; Ne ~28 current; 18.4% heterozygosity decline as the primary quantitative benchmark. Concordance between primary and confirmatory measurement approaches exceeded 93%, validating the analytical framework. These findings contribute empirically to conservation genetics and wildlife biology and carry actionable implications for the design of programs and policies targeting mountain gorilla conservation unit legal status, gene flow management between populations, and inbreeding mitigation via translocation policy.