Hybridization load introduced by Alpine ibex hybrid swarms

Species restoration efforts can be threatened by the accumulation of deleterious mutations and inbreeding depression associated with the historic population contraction. However, even successfully restored species could face deleterious mutation swamping from hybridization with an abundant and closely related species. Here, we analyze this risk for Alpine ibex (Capra ibex), a flagship species of large mammal restoration in the Alps. The Alpine ibex faced near-extinction two centuries ago, resulting in exceptionally low genome-wide diversity and increased inbreeding, which facilitated the purging of severe deleterious mutation load. For this, we produced a highly contiguous chromosome-level genome assembly of the Alpine ibex capturing structural divergence from domestic goat (Capra hircus) and mapping immune-relevant MHC genes. Analyses of eight recent ibex-goat hybrids from two swarms in Northern Italy, combined with 29 non-hybrid Alpine ibex and 22 domestic goats, identified 215 masked loss-of-function (LOF) mutations introduced via hybridization. Yet, we found no evidence for counter-selection in early backcrosses. This exposes Alpine ibex to further backcrosses compounding the deleterious mutation load of the species by a factor of up to two. Our work provides one of the first direct estimates of hybridization load and guides conservation efforts to preserve endangered species gene pools.