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

Abstract

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 genetic drift in captive versus wild populations: an assessment of neutral and adaptive (MHC-linked) genetic variation in wild and hatchery brown trout (Salmo trutta) populations

“…Therefore, it is more likely that selection is a much stronger force than recombination in shaping the genetic diversity of MHC II β, similar to what was observed at a MHC I locus, outside an important recombination hotspot (O'Farrell et al 2013).…”

“…Since the MHC is highly recombinogenic in many species, including brown trout (Shum et al 2001;O'Farrell et al 2013), an additional Bayesian approach accounting for recombination was implemented in the software omegaMap 0.5 (Wilson and McVean 2006). The dN/dS ratios, posterior probabilities of selection and population recombination rate (ρ) were calculated for each codon separately (independent models of ρ & ω; details see Online Resource 1).…”

“…For salmonids, the genetic variability of MHC loci has been linked to kin discrimination (Olsén et al 1998), mate choice (Landry et al 2001;Forsberg et al 2007), embryo viability (Jacob et al 2010) and pathogen infections (Consuegra and Garcia de Leaniz 2008; Lamaze et al 2014), and also play an important role in the viability of invasive species or non-native strains (O'Farrell et al 2013;Monzón-Argüello et al 2014). The negative effects that stocking can have on immunogenetic traits (including MHC variability and expression) have also been documented in salmonids (Currens et al 1997;Lamaze et al 2014).…”

An Illumina approach to MHC typing of Atlantic salmon

“…Genomes of a large number of other salmonid species are becoming available (e.g. Chinook salmon Oncorhynchus tshawytscha (Christensen et al 2018a), Arctic char Salvelinus alpinus (Christensen et al 2018b), grayling Thymallus thymallus (Savilammi et al 2019)) making them prime candidates for inclusion in the IPD-MHC Database once MHC alleles are defined such as already initiated for brown trout Salmo trutta (O'Farrell et al 2013).…”

MHC class I evolution; from Northern pike to salmonids

“…Only Atlantic salmon has a duplicate annotated U lineage gene in the MHCIa region denoted ULA, a gene that lacks the transmembrane domain (Additional le 2-4) [26]. We know that the UBA loci from Atlantic salmon, rainbow trout, brown trout and sockeye salmon are classical MHCI loci with considerable polymorphism [15,17,[27][28][29][30]. There are currently 48 Atlantic salmon and rainbow trout UBA alleles registered in the IPD-MHC database [31] while 31 and 34 alleles have been de ned in brown trout and sockeye salmon.…”