Detecting interspecific hybridization with Illumina SNP BeadChips: A case study based on the Spanish ibex

<b>Background</b> The Spanish ibex (<i>Capra pyrenaica</i>) is a wild goat species distributed in the Iberian Peninsula. Four subspecies have been defined: <i>C. p. hispanica</i> (CPH, south and east of the Iberian Peninsula), <i>C. p. victoriae</i> (CPV, center and northwest of the Iberian Peninsula), <i>C. p. lusitanica</i> (CPL, Galicia and north of Portugal) and <i>C. p. pyrenaica</i> (CPP, Pyrenees mountains). Hunting, epidemics and habitat loss caused the extinction of CPL (disappeared in the 19^th century) and CPP (extinct in the year 2000) as well as severe population bottlenecks decreasing the diversity of CPV and CPH. There are evidences that the coexistence of Spanish ibex populations with domestic goats raised in mountainous areas might have favoured the occurrence of hybridization events between both species. In the current work, we wanted to investigate these putative hybridization events by using genome-wide diversity data. We also wanted to evaluate whether the population bottleneck experienced by CPP resulted in the accumulation of deleterious mutations with harmful effects on viability and reproductive success. <b>Findings</b> By using a high throughput genotyping approach, we have identified the presence of Spanish ibexes introgressed with domestic goats in Tortosa-Beceite. Individual sequencing of one of the last CPP representatives (16× coverage) and Pool-sequencing (39× coverage) of 30 CPH and 23 CPV individuals revealed an extensive sharing of SNPs (74%) between the CPP individual and the extant CPV and CPH subspecies, Sequencing experiments also revealed that the genome of one of the last CPP representatives contains stop-gained mutations, with heterozygous genotypes, in the <i>WASF2</i>, <i>RBM17</i> and <i>SERPINB10</i> genes. The inactivation of WASF2 and RBM17 causes embryonic lethality, while SERPINB10 belongs to a family of serin proteases with key roles in immunity and other biological processes. <b>Conclusions</b> We have demonstrated that interspecific hybridization with domestic goats has been an important source of novel variability for Spanish ibexes living in Tortosa-Beceite. The presence of stop-gained mutations with highly harmful effects in the genome of one of the last representatives of the CPP subspecies suggests that its extinction might be partly explained by the progressive accumulation of mutations with adverse consequences on fitness and reproductive success.