Genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)

Improving the understanding of the causes and effects of anthropogenic
hybridization is fundamental to ensure species conservation, particularly
in the case of hybridization between wild species and their domestic
relatives. Knowledge is missing for many species also because of a lack of
appropriate tools for hybrid identification. Here, coupling genotype and
phenotype analysis, we carried out an extensive investigation of ongoing
hybridization in Alpine ibex Capra ibex, a mountain ungulate of
conservation concern from a genetic perspective. By genotyping at 63
diagnostic and 465 neutral SNPs 20 suspected hybrids and 126 Alpine ibex
without suspicious phenotype, representing eight populations across a
major part of the species distribution, we found evidence for ongoing
hybridization between Alpine ibex and domestic goat. We identified
different levels of hybridization including back crosses into both Alpine
ibex and domestic goat. Our results suggest a lack of reproductive
barriers between the two species and good survival and reproductive
success of the hybrids. Hybridization was locally intense, alike a hybrid
swarm, but not spread across the rest of the species distribution. Most of
the hybrids were discovered in two locations in the North-West of Italy,
while random sampling of individuals from different areas did not provide
evidence of recent hybridization. Our method, based on Amplicon sequencing
of 63 diagnostic SNPs specifically developed for this purpose, allowed us
to identify hybrids and back crosses up to the 4th-5thgeneration and was
suitable for genetic samples of different quality, although with varying
levels of certainty regarding the exact number of generations passed since
hybridization. Based on the paired analysis of genotype and phenotype, we
provide guidelines for a first identification of hybrids in the field and
suggest a procedure for the reliable identification of hybrids.