Hidden MHC genetic diversity in the Iberian ibex (Capra pyrenaica)

Abstract

Background: Defining hidden genetic diversity within species is of great significance when attempting to maintain the evolutionary potential of natural populations and conduct appropriate management. Our hypothesis is that isolated (and eventually small) wild animal populations hide unexpected genetic diversity due to their maintenance of ancient polymorphisms or introgressions.

Results: We tested this hypothesis using the Iberian ibex (Capra pyrenaica) as an example. Previous studies based on large sample sizes taken from its principal populations have revealed that the Iberian ibex has a remarkably small MHC DRB1 diversity (only six remnant alleles) as a result of recent population bottlenecks and a marked demographic decline that has led to the extinction of two recognized subspecies. Extending on the geographic range to include non-studied isolated Iberian ibex populations, we sequenced a new MHC DRB1 in what seemed three small isolated populations in Southern Spain (n = 132). The findings indicate a higher genetic diversity than previously reported in this important gene. The newly discovered allele, MHC DRB1*7, is identical to one reported in the domestic goat C. aegagrus hircus. Whether or not this is the result of ancient polymorphisms maintained by balancing selection or, alternatively, introgressions from domestic goats through hybridization needs to be clarified in future studies. However, hybridization between Iberian ibex and domestic goats has been reported in Spain and the fact that the newly discovered allele is only present in one of the small isolated populations and not in the others suggests introgression. The new discovered allele is not expected to increase fitness in C. pyrenaica since it generates the same protein as the existing MHC DRB1*6. Analysis of a microsatellite locus (OLADRB1) near the new MHC DRB1*7 gene reveals a linkage disequilibrium between these two loci. The allele OLADRB1, 187 bp in length, was unambiguously linked to the MHC DRB1*7 allele. This enabled us to perform a DRB-STR matching method for the recently discovered MHC allele.

Conclusions: This finding is critical for the conservation of the Iberian ibex since it directly affects the identification of the units of this species that should be managed and conserved separately (Evolutionarily Significant Units).

Keywords: Capra aegagrus hircus; Capra pyrenaica hispanica; Capra pyrenaica victoriae; DRB-STR method; Linkage disequilibrium; MHC DRB1; Major histocompatibility complex (MHC); OLADRB1; Segura and las Villas Natural Park; Sierras de Cazorla; Spain.

Fig. 1

Map of the Iberian Peninsula showing the current Iberian ibex (Capra pyrenaica) distribution and the location of the studied populations. The MHC DRB1alleles are shown in red (DRB1*1 = 1, DRB1*2 = 2, DRB1*3 = 3, DRB1*5 = 5, DRB1*6 = 6, and DRB1*7 = 7). The populations in the Sierra Nevada National Park (10), Puertos de Tortosa and Beceite National Hunting Reserve (12), and Batuecas-Sierra de Francia Natural Park (13) have previously been studied by Alasaad et al. [23]

Fig. 2

Best maximum likelihood (ML) tree for the MHC (257 bp) gene fragment. Capra pyrenaica haplotypes are marked in red and their clades in blue. An asterisk (*) on nodes denotes posterior probabilities (Pp) recovered from the Bayesian analysis and bootstrap support from the ML bipartition tree (≥ 95%), respectively