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).We would like to thank Apolo Sánchez, Elías Martínez, Isidro Puga, Pepe López, Francisco Casado and Antonio Rodríguez for their assistance with the fieldwork in Sierra Nevada. We are also grateful to Miguel Ángel Habela, Santiago Lavín, Pelayo Acevedo, Eularico Fernández, Francisco Martínez, Juan Monje, Jaime Medina, Juan Antonio Funes, Antonio Serrano, Pepe Madrazo, Luis Alfonso Sarmiento and José Luis Chao for providing Iberian ibex samples.This study was partially funded by the Consejería de Medio Ambiente of the Junta de Andalucía (projects 173/2009/M/00 and 03/15/M/00) and the Ministerio de Economía y Competitividad of the Spanish Government (projects CGL2012–40043- C02–01, CGL2012–40043-C02–02 and CGL2016– 80543-P). The funding bodies did not contribute to the design of the study or collection, analysis and interpretation of data, or to the writing of the manuscript