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

O'Farrell B, Benzie JA, McGinnity P, de Eyto E, Dillane E, Coughlan J, Cross TF - PLoS ONE (2013)

Bottom Line: Recombination was found to be important to population-level divergence.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.

View Article: PubMed Central - PubMed

Affiliation: Environmental Research Institute, University College Cork, Cork, Ireland. Eb.ofarrell@ucc.ie

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.

Show MeSH
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).
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pone-0063035-g003: 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).

Mentions: CODEML models allowing for ω>1 were more likely in likelihood ratio tests, for each taxon, indicating that selection occurs on UBA in each of the three species tested. Codons under selection [M8 (β and ω)] are summarised in Figure 3 with only two codons, Cys67 and Gln155, showed significant evidence of selection in all three salmonid species. Codons in two distinct regions of the protein, Phe94 and Asn96; and Tyr113 and Phe115 were under very highly significant selection in the Salmo species but not in O. mykiss. More codons are under selection in S. trutta UBA than in either of the other two species.


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

O'Farrell B, Benzie JA, McGinnity P, de Eyto E, Dillane E, Coughlan J, Cross TF - PLoS ONE (2013)

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).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646885&req=5

pone-0063035-g003: 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).
Mentions: CODEML models allowing for ω>1 were more likely in likelihood ratio tests, for each taxon, indicating that selection occurs on UBA in each of the three species tested. Codons under selection [M8 (β and ω)] are summarised in Figure 3 with only two codons, Cys67 and Gln155, showed significant evidence of selection in all three salmonid species. Codons in two distinct regions of the protein, Phe94 and Asn96; and Tyr113 and Phe115 were under very highly significant selection in the Salmo species but not in O. mykiss. More codons are under selection in S. trutta UBA than in either of the other two species.

Bottom Line: Recombination was found to be important to population-level divergence.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.

View Article: PubMed Central - PubMed

Affiliation: Environmental Research Institute, University College Cork, Cork, Ireland. Eb.ofarrell@ucc.ie

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.

Show MeSH