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. 2010 May 12:6:57-71.
doi: 10.4137/ebo.s4527.

An application of supertree methods to Mammalian mitogenomic sequences

Véronique Campbell  1 , François-Joseph Lapointe
Affiliations

An application of supertree methods to Mammalian mitogenomic sequences

Véronique Campbell et al. Evol Bioinform Online. .

Abstract

TWO DIFFERENT APPROACHES CAN BE USED IN PHYLOGENOMICS: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid missing data, since datasets that are analyzed separately do not need to represent identical taxa. However, the supertree approach and the corresponding consensus methods have been highly criticized for not providing valid phylogenetic hypotheses. In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing 93 mammal families. The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings. The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees. The most similar supertree method was the least congruent with the model trees. We conclude that some of the methods tested are worth considering in a phylogenomic context.

Keywords: DNA sequences; combined analysis; consensus; phylogenomics; separate analysis; supermatrix.

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Figures

Figure 1.
Figure 1.
First model tree (MT1) representing mitogenomic relationships among 93 mammalian families. Bootstrap values (BS) and Bayesian posterior probabilities (BPP) are indicated on branches (BS/BPP). Branches without values correspond to BS/BPP = 100/100.
Figure 2.
Figure 2.
Second model tree (MT2) representing mitogenomic relationships among mammalian families with eight extra polytomies added to MT1 to obtain a tree compatible with recent molecular studies. Bootstrap values (BS) and Bayesian posterior probabilities (BPP) are indicated on branches (BS/BPP). Branches without values correspond to BS/BPP = 100/100.
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