Introgression with domestic goats has expanded the genetic variability of the Spanish ibex

Abstract

The Spanish ibex (Capra pyrenaica) is a wild goat species distributed in the Iberian Peninsula. Based on phenotypic criteria, 4 subspecies have been defined: C. p. hispanica (CPH, south and east of the Iberian Peninsula), C. p. victoriae (CPV, center and northwest of the Iberian Peninsula), C. p. lusitanica (CPL, Galicia and north of Portugal) and C. p. pyrenaica (CPP, Pyrenees mountains). Hunting, epidemics and habitat loss caused the extinction of CPL (disappeared in the 19th century) and CPP (extinct in the year 2000) as well as severe population bottlenecks decreasing the diversity of CPV and CPH. By using a high throughput genotyping approach, we have demonstrated that interspecific hybridization with domestic goats has been an important source of novel variability for Spanish ibexes living in Tortosa-Beceite. Individual sequencing of one of the last CPP representatives ( × 16.6 coverage) and Pool-sequencing ( × 39 coverage) of 30 CPH and 23 CPV individuals revealed an extensive sharing of SNPs (96%) between the CPP individual and the extant CPV and CPH subspecies, thus suggesting that the extinction of CPP did not cause a major loss of diversity in Capra pyrenaica. Sequencing experiments also revealed that the genome of one of the last CPP representatives contains stop-gained mutations, with heterozygous genotypes, in the WASF2, RBM17 and SERPINB10 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. Our results suggest that the dramatic reduction of the CPP population during the19th-20th centuries led to the progressive accumulation of mutations with harmful effects (genomic meltdown) that probably contributed to its extinction by limiting fitness and reproductive success.