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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 α1 domain.A) Satr-UBA α1 sequences (blue) together with relevant outgroup sequences from S. salar (green) and O. mykiss (red). Novel Srahrevagh River sequences are represented by square nodes. Accession numbers are included in node labels. The number of plus signs after a sequences indicates the number of other Satr-UBA alleles which share this sequence in its entirety. α1 lineages are indicated using roman numerals. A C. idella UBA is included to highlight the distinct sub-lineages in LV, not as an outgroup, and these networks are unrooted. B) Possible α1 intradomain recombination event between typical α1 LIII sequences and sequences more similar to Satr-UBA*1301 giving rise to Sasa-UBA*0301. The α1 LI sequence is included as an outgroup. C) α1 LV sequences from S. trutta, S. salar and O. mykiss. Loops are observed in the network, affecting LVb sequences primarily. Note also in this network the extent of trans-species polymorphism in LVa sequences.
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pone-0063035-g005: Phylogenetics of the α1 domain.A) Satr-UBA α1 sequences (blue) together with relevant outgroup sequences from S. salar (green) and O. mykiss (red). Novel Srahrevagh River sequences are represented by square nodes. Accession numbers are included in node labels. The number of plus signs after a sequences indicates the number of other Satr-UBA alleles which share this sequence in its entirety. α1 lineages are indicated using roman numerals. A C. idella UBA is included to highlight the distinct sub-lineages in LV, not as an outgroup, and these networks are unrooted. B) Possible α1 intradomain recombination event between typical α1 LIII sequences and sequences more similar to Satr-UBA*1301 giving rise to Sasa-UBA*0301. The α1 LI sequence is included as an outgroup. C) α1 LV sequences from S. trutta, S. salar and O. mykiss. Loops are observed in the network, affecting LVb sequences primarily. Note also in this network the extent of trans-species polymorphism in LVa sequences.

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 α1 domain.A) Satr-UBA α1 sequences (blue) together with relevant outgroup sequences from S. salar (green) and O. mykiss (red). Novel Srahrevagh River sequences are represented by square nodes. Accession numbers are included in node labels. The number of plus signs after a sequences indicates the number of other Satr-UBA alleles which share this sequence in its entirety. α1 lineages are indicated using roman numerals. A C. idella UBA is included to highlight the distinct sub-lineages in LV, not as an outgroup, and these networks are unrooted. B) Possible α1 intradomain recombination event between typical α1 LIII sequences and sequences more similar to Satr-UBA*1301 giving rise to Sasa-UBA*0301. The α1 LI sequence is included as an outgroup. C) α1 LV sequences from S. trutta, S. salar and O. mykiss. Loops are observed in the network, affecting LVb sequences primarily. Note also in this network the extent of trans-species polymorphism in LVa sequences.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0063035-g005: Phylogenetics of the α1 domain.A) Satr-UBA α1 sequences (blue) together with relevant outgroup sequences from S. salar (green) and O. mykiss (red). Novel Srahrevagh River sequences are represented by square nodes. Accession numbers are included in node labels. The number of plus signs after a sequences indicates the number of other Satr-UBA alleles which share this sequence in its entirety. α1 lineages are indicated using roman numerals. A C. idella UBA is included to highlight the distinct sub-lineages in LV, not as an outgroup, and these networks are unrooted. B) Possible α1 intradomain recombination event between typical α1 LIII sequences and sequences more similar to Satr-UBA*1301 giving rise to Sasa-UBA*0301. The α1 LI sequence is included as an outgroup. C) α1 LV sequences from S. trutta, S. salar and O. mykiss. Loops are observed in the network, affecting LVb sequences primarily. Note also in this network the extent of trans-species polymorphism in LVa sequences.
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