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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 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.
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pone-0063035-g001: 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.

Mentions: OMEGAMAP showed that codons for 20 amino acid positions were under significant positive selection in Satr-UBA from the Srahrevagh trout (Figures 1A, 1B, S7). Fourteen of these were in the α1 domain and six were in the α2 domain. Mean ω for the entire Satr-UBA region was 0.65±0.062 (Table 2), ranging from 0.051 (Asp173)–8.570 (Tyr113). Low background ω rates suggest that most of the UBA gene is under purifying selection (Table 2). Evidence for strong positive or diversifying selection was found to occur at a discrete set of codons, (Figure 1A, 1B). Despite more codons being under selection in α1, those under the strongest selection were found within the α2 domain. The ω estimate for Tyr113 was thirteen times the mean ω, and that for Lys156 was five times the mean.


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 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.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0063035-g001: 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.
Mentions: OMEGAMAP showed that codons for 20 amino acid positions were under significant positive selection in Satr-UBA from the Srahrevagh trout (Figures 1A, 1B, S7). Fourteen of these were in the α1 domain and six were in the α2 domain. Mean ω for the entire Satr-UBA region was 0.65±0.062 (Table 2), ranging from 0.051 (Asp173)–8.570 (Tyr113). Low background ω rates suggest that most of the UBA gene is under purifying selection (Table 2). Evidence for strong positive or diversifying selection was found to occur at a discrete set of codons, (Figure 1A, 1B). Despite more codons being under selection in α1, those under the strongest selection were found within the α2 domain. The ω estimate for Tyr113 was thirteen times the mean ω, and that for Lys156 was five times the mean.

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