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Taxon ordering in phylogenetic trees: a workbench test.

Cerutti F, Bertolotti L, Goldberg TL, Giacobini M - BMC Bioinformatics (2011)

Bottom Line: Best results were obtained when taxa were reordered using geographic information.Improved representations of genetic and geographic relationships between samples were also obtained when merged matrices (genetic and geographic information in one matrix) were used.Our innovative method makes phylogenetic trees easier to interpret, adding meaning to the taxon order and helping to prevent misinterpretations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Production, Epidemiology and Ecology, Faculty of Veterinary Medicine, University of Torino, Grugliasco, Italy.

ABSTRACT

Background: Phylogenetic trees are an important tool for representing evolutionary relationships among organisms. In a phylogram or chronogram, the ordering of taxa is not considered meaningful, since complete topological information is given by the branching order and length of the branches, which are represented in the root-to-node direction. We apply a novel method based on a (λ + μ)-Evolutionary Algorithm to give meaning to the order of taxa in a phylogeny. This method applies random swaps between two taxa connected to the same node, without changing the topology of the tree. The evaluation of a new tree is based on different distance matrices, representing non-phylogenetic information such as other types of genetic distance, geographic distance, or combinations of these. To test our method we use published trees of Vesicular stomatitis virus, West Nile virus and Rice yellow mottle virus.

Results: Best results were obtained when taxa were reordered using geographic information. Information supporting phylogeographic analysis was recovered in the optimized tree, as evidenced by clustering of geographically close samples. Improving the trees using a separate genetic distance matrix altered the ordering of taxa, but not topology, moving the longest branches to the extremities, as would be expected since they are the most divergent lineages. Improved representations of genetic and geographic relationships between samples were also obtained when merged matrices (genetic and geographic information in one matrix) were used.

Conclusions: Our innovative method makes phylogenetic trees easier to interpret, adding meaning to the taxon order and helping to prevent misinterpretations.

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Related in: MedlinePlus

WNV trees. The original tree, as presented by Bertolotti et al. (A). The best trees obtained using the geographic (B), genetic (C) and combined (D) distances. The dashed line in C and D highlights the "C" shape acquired by the clades.
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Figure 4: WNV trees. The original tree, as presented by Bertolotti et al. (A). The best trees obtained using the geographic (B), genetic (C) and combined (D) distances. The dashed line in C and D highlights the "C" shape acquired by the clades.

Mentions: WNV is a positive-sense single-stranded RNA virus belonging to the family Flaviviridae, and it is transmitted primarily through the bite of infected mosquitoes to birds. Occasionally it infects horses and humans causing West Nile febrile illness and neurologic disease [16]. The original tree, from [13], shown in Figure 4a, was rearranged using a matrix of geographic distances, as described in the Methods section. In the case of WNV, the geographic arrangement of locations is not linear (Figure 5), as in the case of VSV. In the modified tree (Figure 4b), taxa nevertheless group by sampling location. Due to large sample size and constraints of tree topology, this grouping is less evident than in case of VSV.


Taxon ordering in phylogenetic trees: a workbench test.

Cerutti F, Bertolotti L, Goldberg TL, Giacobini M - BMC Bioinformatics (2011)

WNV trees. The original tree, as presented by Bertolotti et al. (A). The best trees obtained using the geographic (B), genetic (C) and combined (D) distances. The dashed line in C and D highlights the "C" shape acquired by the clades.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3050728&req=5

Figure 4: WNV trees. The original tree, as presented by Bertolotti et al. (A). The best trees obtained using the geographic (B), genetic (C) and combined (D) distances. The dashed line in C and D highlights the "C" shape acquired by the clades.
Mentions: WNV is a positive-sense single-stranded RNA virus belonging to the family Flaviviridae, and it is transmitted primarily through the bite of infected mosquitoes to birds. Occasionally it infects horses and humans causing West Nile febrile illness and neurologic disease [16]. The original tree, from [13], shown in Figure 4a, was rearranged using a matrix of geographic distances, as described in the Methods section. In the case of WNV, the geographic arrangement of locations is not linear (Figure 5), as in the case of VSV. In the modified tree (Figure 4b), taxa nevertheless group by sampling location. Due to large sample size and constraints of tree topology, this grouping is less evident than in case of VSV.

Bottom Line: Best results were obtained when taxa were reordered using geographic information.Improved representations of genetic and geographic relationships between samples were also obtained when merged matrices (genetic and geographic information in one matrix) were used.Our innovative method makes phylogenetic trees easier to interpret, adding meaning to the taxon order and helping to prevent misinterpretations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Production, Epidemiology and Ecology, Faculty of Veterinary Medicine, University of Torino, Grugliasco, Italy.

ABSTRACT

Background: Phylogenetic trees are an important tool for representing evolutionary relationships among organisms. In a phylogram or chronogram, the ordering of taxa is not considered meaningful, since complete topological information is given by the branching order and length of the branches, which are represented in the root-to-node direction. We apply a novel method based on a (λ + μ)-Evolutionary Algorithm to give meaning to the order of taxa in a phylogeny. This method applies random swaps between two taxa connected to the same node, without changing the topology of the tree. The evaluation of a new tree is based on different distance matrices, representing non-phylogenetic information such as other types of genetic distance, geographic distance, or combinations of these. To test our method we use published trees of Vesicular stomatitis virus, West Nile virus and Rice yellow mottle virus.

Results: Best results were obtained when taxa were reordered using geographic information. Information supporting phylogeographic analysis was recovered in the optimized tree, as evidenced by clustering of geographically close samples. Improving the trees using a separate genetic distance matrix altered the ordering of taxa, but not topology, moving the longest branches to the extremities, as would be expected since they are the most divergent lineages. Improved representations of genetic and geographic relationships between samples were also obtained when merged matrices (genetic and geographic information in one matrix) were used.

Conclusions: Our innovative method makes phylogenetic trees easier to interpret, adding meaning to the taxon order and helping to prevent misinterpretations.

Show MeSH
Related in: MedlinePlus