Numerous genetic studies have shown that hybridization do not only occur more commonly than originally thought but also across the entire animal kingdom [1–4]. In particular, hybridization occurs between wild species and their domestic counterparts [5, 6], as well as between native and introduced species [4, 7, 8].
If the fitness of the hybrid-offspring is greater than that of the offspring from each parent species, hybridization on one hand may function as mode of speciation while on the other hand disrupt local adaptations, leading to population decline and loss of biodiversity [9, 10]. The list of consequences observed after hybridization between domestic and wild species is extensive and may include reduced fitness of F1 and F2 generations, accelerated growth rate with subsequent skeletal malformations, increased agonistic behaviour, decreased predator avoidance behaviour, and unpredictable effects on animals’ resistance to parasites [11–13].
While in the past hybridizations were considered to be rare events, nowadays they are increasingly detected because molecular methods often show hybridization despite unchanged phenotype . Because mammalian mitochondrial DNA (mtDNA) is maternally inherited, the detection of mtDNA haplotypes of one species in yet another, morphologically distinct species indicates introgression and thus past hybridization followed by numerous backcrosses [5, 10, 15, 16]. Nevertheless, mtDNA can only detect hybridization along matrilines while paternal hybrid offspring remains undetected. Moreover, mtDNA haplotypes may not be monophyletic within species because of ancestral lineage sorting in addition to hybridization . In the opposite case, Y-linked haplotype markers will only be useful to detect male hybrid offspring as they follow the paternal lineage  and thus, results inferred from mitochondrial DNA and Y-chromosome are sometimes discordant. Due to their biparental inheritance, microsatellites are thus better suited to detect hybridization events, and therefore have been established and used for many animal species [19, 20]. Nevertheless, for the eventual detection of hybridization, the use of microsatellites requires additional efforts such as standardization of allele lengths for both species and for the cross-species amplification in the hybrids . They also require the use of internal genotyping controls when performing PCR amplifications to overcome the possible lack of consistency in allele sizes across different analytical instruments and running conditions . A different approach, besides the use of mtDNA and microsatellite loci, is the exploration of the species specificity of coding sequences. To our knowledge, the genes of the Major Histocompatibility Complex (MHC) have not yet been used to detect hybridization events between vertebrate species.
In vertebrates, the MHC is vital for foreign antigen recognition and the immune response to infections . Some of its genes are among the most polymorphic loci of the vertebrate genomes  displaying high levels of allelic diversity . So far, at least six models have been suggested to explain the maintenance of MHC variability, the two most prominent ones being a) balancing selection and b) the rare allele model . Interestingly, domestic species often have higher than expected levels of MHC diversity, given their domestication history . On the other hand, many endangered species exhibit a low degree of MHC polymorphism caused by severe population bottlenecks in their history . Low MHC variability may also stem from the social organisation of a species , which may result in low transmission rates of infectious diseases  generating low selection pressure for high variability. Hence, hybridizations between species with high MHC allelic variability and species with low MHC variability may be detected by studying MHC allele distribution, given that there are no shared alleles.
There are several reports about hybridizations in caprine species. Hybrids between several wild caprine species have been reported and hybrids between domestic goat and wild caprine species were described as being fertile and having a reduced predator and human avoidance . In few cases, hybrids between the Alpine ibex (Capra ibex ibex) and domestic goats (Capra hircus) were reported for both crosses (wild male × domestic female; wild female × domestic male) and as occurring both in captivity  and in the wild . However, to our knowledge, neither a general report nor a molecular data based report has so far presented hybridization between Iberian ibex (Capra pyrenaica) and domestic goat in the wild.
In this paper we aim to (i) present the first cases of free-ranging Iberian ibex × domestic goat hybrids, and want to (ii) demonstrate the suitability of MHC loci (under certain conditions) as a molecular tool for the detection of hybridization between species with strongly differing allelic variability at these loci.