Selection and phylogenetics of salmonid MHC class I: wild brown trout (Salmo trutta) differ from a non-native introduced strain

• Published in: PLoS ONE
• Main Authors: O'Farrell, Brian, Benzie, John A. H., McGinnity, Philip, de Eyto, Elvira, Dillane, Eileen, Coughlan, Jamie P., Cross, Thomas F.
• Format: Article in Journal/Newspaper
• Language: English
• Published: Public Library of Science 2013
• Subjects: Major histocompatibility complex; Peptide binding region; Rainbow trout; Oncorhynchus mykiss; Atlantic salmon; Natural selection; Balancing selection; Transspecies polymorphism; Convergent evolution; Parasite resistance; Ula; Salmo salar
• Online Access: http://hdl.handle.net/10468/2379; https://doi.org/10.1371/journal.pone.0063035

We tested how variation at a gene of adaptive importance, MHC class I (UBA), in a wild, endemic Salmo trutta population compared to that in both a previously studied non-native S. trutta population and a co-habiting Salmo salar population ( a sister species). High allelic diversity is observed and allelic divergence is much higher than that noted previously for cohabiting S. salar. Recombination was found to be important to population-level divergence. The alpha 1 and alpha 2 domains of UBA demonstrate ancient lineages but novel lineages are also identified at both domains in this work. We also find examples of recombination between UBA and the non-classical locus, ULA. Evidence for strong diversifying selection was found at a discrete suite of S. trutta UBA amino acid sites. The pattern was found to contrast with that found in re-analysed UBA data from an artificially stocked S. trutta population.