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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 co-habiting  S. salar . Recombination was found to be important to population-level divergence. The α1 and α2 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.

Selection and Phylogenetics of Salmonid MHC Class I: Wild Brown Trout (Salmo trutta) Differ from a Non-Native Introduced Strain