Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

[Background] Demographic bottlenecks erode genetic diversity and may increase endangered species’ extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species. We compared variation in the most variable exon of the MHCI and MHCII-DRB loci among the four species of the Lynx genus.[Results] The Iberian lynx was characterised by lower number of MHC alleles than its sister species (the Eurasian lynx). However, it maintained most of the functional genetic variation at MHC loci present in the remaining and genetically healthier lynx species at all nucleotide, amino acid, and supertype levels.[Conclusions] Species-wide functional genetic diversity can be maintained even in the face of severe population bottlenecks, which caused devastating whole genome genetic erosion. This could be the consequence of divergent alleles being retained across paralogous loci, an outcome that, in the face of frequent gene conversion, may have been favoured by balancing selection.Funding for this project was provided by the Spanish Dirección General de Investigación Científica y Técnica (CGL2010–21540/BOS and CGL2013–47755-P), project "Adaptive variation in declining species: Survey of MHC variation in Eurasian lynx populations at the western edge of its range" funded by the internal EBD proposal call “Microproyectos” financed by the Spanish Ministry of Economy and Competitiveness, through the Severo Ochoa Program for Centres of Excellence in R + D + I (SEV-2012-0262), and project 2014/15/B/NZ8/00212 funded by the National Science Center, Poland. Elena Marmesat received a JAE predoctoral grant from CSIC (Spanish National Research Council). We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Peer reviewe