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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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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.
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pone-0063035-g004: 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.

Mentions: SPLITSTREE networks of Satr-UBA alleles incorporating the twenty one novel alleles described here and relevant salmonid UBA outgroups (Figure 4A) demonstrate some large loops, suggesting recombination and/or gene conversion events affecting the alleles connected by those loops. Eleven of 21 (52%) of the Satr-UBA alleles described here are recombinant alleles. Most of the loops can be explained by recombination at the intron between the exons coding for the α1 and α2 domains of the Satr-UBA as previously described for Atlantic salmon [12], [36]. Well-supported clades suggestive of conventional radiation by point mutation were also observed (e.g. clades including Satr-UBA*1101 and Satr-UBA*2301 Figure 4A). A neighbour-joining (NJ) tree of the same data presented for comparison (Figure 4B) shows broad agreement with the SPLITSTREE network. However, alleles which are involved in loops in the network appear to be incorrectly grouped in the NJ tree, e.g. Onmy-UBA*4401 (AY278452), Onmy-UBA*4701 (AY278449) and Onmy-UBA*4601 (AY278450), indicating the utility of the SPLITREE networks for better interpretation of data affected by recombination. Recombinant alleles from the Srahrevagh which are combinations of α1 and α2 lineages which appear to be new to all salmonids are Satr-UBA*1201 and Satr-UBA*1801 (α1 LI/α2 LIII); Satr-UBA*2601 (α1 LII/α2 LIII); and Satr-UBA*2801 (α1 LII/α2 LII). Ten of the 22 (45.4%) α1/α2 lineage combinations observed in all salmonid UBA data are observed in the single brown trout population from the Srahrevagh.


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0063035-g004: 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.
Mentions: SPLITSTREE networks of Satr-UBA alleles incorporating the twenty one novel alleles described here and relevant salmonid UBA outgroups (Figure 4A) demonstrate some large loops, suggesting recombination and/or gene conversion events affecting the alleles connected by those loops. Eleven of 21 (52%) of the Satr-UBA alleles described here are recombinant alleles. Most of the loops can be explained by recombination at the intron between the exons coding for the α1 and α2 domains of the Satr-UBA as previously described for Atlantic salmon [12], [36]. Well-supported clades suggestive of conventional radiation by point mutation were also observed (e.g. clades including Satr-UBA*1101 and Satr-UBA*2301 Figure 4A). A neighbour-joining (NJ) tree of the same data presented for comparison (Figure 4B) shows broad agreement with the SPLITSTREE network. However, alleles which are involved in loops in the network appear to be incorrectly grouped in the NJ tree, e.g. Onmy-UBA*4401 (AY278452), Onmy-UBA*4701 (AY278449) and Onmy-UBA*4601 (AY278450), indicating the utility of the SPLITREE networks for better interpretation of data affected by recombination. Recombinant alleles from the Srahrevagh which are combinations of α1 and α2 lineages which appear to be new to all salmonids are Satr-UBA*1201 and Satr-UBA*1801 (α1 LI/α2 LIII); Satr-UBA*2601 (α1 LII/α2 LIII); and Satr-UBA*2801 (α1 LII/α2 LII). Ten of the 22 (45.4%) α1/α2 lineage combinations observed in all salmonid UBA data are observed in the single brown trout population from the Srahrevagh.

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