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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.

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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.
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pone-0063035-g002: 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.

Mentions: Re-analysis of the S. trutta UBA data from the Colorado river [12] showed no evidence of significant levels of selection at any amino acid site in the OMEGAMAP analysis of S. trutta (Figures 2A, 2B, S7). Mean ω was 0.48±0.022 for S. trutta in the Colorado River, which is lower than that found in the Srahrevagh. Mean ρ was slightly higher for S. trutta in the Colorado River (0.29±0.008). Curiously, there was no significant evidence for a high ρ estimate at the transition point between the α1 and α2 domains (Table 2).


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0063035-g002: 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.
Mentions: Re-analysis of the S. trutta UBA data from the Colorado river [12] showed no evidence of significant levels of selection at any amino acid site in the OMEGAMAP analysis of S. trutta (Figures 2A, 2B, S7). Mean ω was 0.48±0.022 for S. trutta in the Colorado River, which is lower than that found in the Srahrevagh. Mean ρ was slightly higher for S. trutta in the Colorado River (0.29±0.008). Curiously, there was no significant evidence for a high ρ estimate at the transition point between the α1 and α2 domains (Table 2).

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