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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 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, LIV, unique to S. trutta, which appears to have originated more recently from the α2 LI 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 LI lineage.
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pone-0063035-g006: 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, LIV, unique to S. trutta, which appears to have originated more recently from the α2 LI 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 LI lineage.

Mentions: 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.


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 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, LIV, unique to S. trutta, which appears to have originated more recently from the α2 LI 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 LI lineage.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3646885&req=5

pone-0063035-g006: 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, LIV, unique to S. trutta, which appears to have originated more recently from the α2 LI 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 LI lineage.
Mentions: 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.

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