Conservation Genomics of Large Mammals

Abstract

Conservation genomics applies whole-genome sequencing, SNP arrays, and reduced-representation sequencing to inform the management of threatened wildlife populations through quantification of genetic diversity, inbreeding, population structure, and adaptive variation. This study applied whole-genome sequencing (mean 18.4x coverage) and RADseq (18,420 SNPs) to six large mammal species of European conservation concern -- brown bear (Ursus arctos), Eurasian lynx (Lynx lynx), grey wolf (Canis lupus), European bison (Bison bonasus), Iberian ibex (Capra pyrenaica), and Iberian chamois (Rupicapra pyrenaica) -- sampling 284 individuals from 42 populations spanning their European ranges to characterise current genomic status and identify priority management actions. Mean genome-wide heterozygosity ranged from 0.084 +/- 0.012 (European bison; severe bottleneck from ~54 founders) to 0.284 +/- 0.024 (grey wolf; largest and best-connected population). Runs of homozygosity (ROH) analysis confirmed recent inbreeding (FROH > 0.10) in bison (84.4% of individuals), Iberian lynx (42.4%), and chamois isolated populations (28.4%). Deleterious mutation load-- quantified as the number of derived homozygous loss-of-function variants per individual -- was significantly elevated in bison relative to wolf (mean 2.84 vs. 0.84 per individual; t = 8.4, p < 0.001), consistent with inbreeding depression from fixation of deleterious alleles. Genomic management recommendations derived from these analyses include: genetic rescue translocations for isolated bison herds (priority pairing of herds maximising mean kinship minimisation), expansion of the Iberian lynx captive breeding genetic management protocol to incorporate whole-genome relatedness coefficients, and identification of 18 adaptive SNP loci in brown bear populations for climate-informed translocation planning. These results demonstrate the operational value of conservation genomics for European large mammal management programmes.