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.

Figure 1. Selection and recombination in the Srahrevagh.

A) Model of the peptide binding region of the reference allele, Satr-UBA*0101. Sites under selection are labelled and colour coded according to their degree of statistical support (see key at bottom right of diagram. Higher p values indicate stronger statistical support). The sites with the highest ω estimates are Tyr113 (ω = 8.57), Ala42 (3.51), Lys156 (3.38), Phe94 (2.08) and Asn96 (2.05). The Lys156 residue appears to occur between the cleft and the so-called “gatekeeper” residue, Gln155. B, C) Plots of site-by-site mean posterior estimates of ω (B) and ρ (C) for Satr-UBA described in this study showing non-correspondence in their pattern of variation. Highest Posterior Density (HPD) 95% confidence intervals are seen in grey about the plot line. In B), the dashed red line indicates ω = 1, values above which indicate selection.

Figure 2. Selection in the Colorado.

A) Model showing selected sites in the UBA protein for the Colorado River S. trutta. For comparison, this information from the Srahrevagh River S. trutta population is also provided (inset, right, detail in Figure 1A). Clear differences in the distribution of selected sites in the peptide binding can be seen. B) Plot of ω for the Colorado River S. trutta. Highest Posterior Density (HPD) 95% confidence intervals are seen in grey about the plot line and are tight about means in all cases, suggesting confidence in the ω estimates.

Figure 3. Selected sites in UBA.

Venn diagram showing all sites under significant selection as identified in conjoint CODEML analysis of the three different taxa labelled. Sites in intersections are under selection in two or more species. Significance levels of selection on residues: p<0.001 (bold), p<0.01 (normal) and p<0.05 (italics).

Figure 4. Phylogenetics of UBA.

A) SPLITSTREE neighbor-net network of Satr-UBA alleles (blue) with relevant outgroup sequences from S. salar (green) and O. mykiss (red). Square nodes indicate the novel alleles identified from the Srahrevagh River, Co. Mayo. Parallel lines indicate splits in the network. Bootstrap support values (1000 replicates) are presented for the most relevant splits in the network. Large loops imply areas of phylogenetic uncertainty or reticulations. The frequency of these in the network implies that recombination is an important factor in the evolution of Satr-UBA, predominantly between the α1 and α2 domains. Conversely, good bootstrap support for splits involving several closely related Satr-UBA alleles is suggestive of conventional radiation by point mutation. Roman numerals (α1/α2) indicate the lineages to which each Satr-UBA allele's α1 and α2 sequence belongs (see also Figures 5 and 6). B) Neighbour-joining tree rooted on the midpoint for salmonid UBA amino acid sequences with bootstrap support (1,000 replicates) shown for nodes with 50% support or greater. Nodes in A) and B) highlighted with an orange triangle illustrate how SPLITSTREE is better able to visualise sequences affected by recombination.

Figure 5. Phylogenetics of the α1 domain.

A) Satr-UBA α1 sequences (blue) together with relevant outgroup sequences from S. salar (green) and O. mykiss (red). Novel Srahrevagh River sequences are represented by square nodes. Accession numbers are included in node labels. The number of plus signs after a sequences indicates the number of other Satr-UBA alleles which share this sequence in its entirety. α1 lineages are indicated using roman numerals. A C. idella UBA is included to highlight the distinct sub-lineages in L_V, not as an outgroup, and these networks are unrooted. B) Possible α1 intradomain recombination event between typical α1 L_III sequences and sequences more similar to Satr-UBA*1301 giving rise to Sasa-UBA*0301. The α1 L_I sequence is included as an outgroup. C) α1 L_V sequences from S. trutta, S. salar and O. mykiss. Loops are observed in the network, affecting L_Vb sequences primarily. Note also in this network the extent of trans-species polymorphism in L_Va sequences.

Figure 6. Phylogenetics of the α2 domain.

A) Satr-UBA α2 sequences with novel sequences described in this work represented by square nodes. The number of plus signs after a sequence indicates the number of other Satr-UBA alleles which share this sequence in its entirety and, therefore, are sequences which are likely to have been involved in recombination. Known α2 lineages are indicated using roman numerals. Note that a novel α2 lineage, L_IV, unique to S. trutta, which appears to have originated more recently from the α2 L_I lineage, is well supported with the additional data described in this work. The shape of the overall tree is distinct from that of α1 with fewer well-supported lineages and with evidence of extensive radiation within the ‘majority’ α2 L_I lineage.