To quote Hughes and piontkivska: "phylogenetic analyses of available sequences in 42 protein families gene generally supported monophyly of the genus Trypanosoma. One possible explanation for these conflicting results is poor taxon sampling in the case of protein coding genes, most of which have been sequenced for only a few species of Trypanosomatidae."
And another explanation is that their analysis of 18S sequences is flawed and that the overwhelming evidence from protein coding genes is, in fact, correct ...
Competing interests
None declared
Explanation of Contradictory Phylogenies
Austin Hughes, University of South Carolina
28 November 2003
Dr. Stevens's comment re-states the obvious: that either the phylogenies showing Trypanosma to be monophyletic are incorrect or the phylogenies showing this genus to be paraphyletic are incorrect. Since smaller numbers of sequences are available for protein-coding genes, it is possible that the results for these genes have been affected by relatively poor taxon sampling. However, we still do not have very good general knowledge of how taxon sampling affects phylogenetic reconstruction.
As regards the 18S rRNA phylogeny, it is really not helpful to assert that it might be "flawed." We used all widely used methods of phylogeny reconstruction (minimum evolution, maximum parsimony, maximum likelihood, Bayesian); and none supported monophyly of the genus Trypanosoma. It seems hard to believe that the problem lies in the methods of reconstruction. However, the 18S rRNA gene is just one gene; and stochastic error can cause the phylogeny of a single gene not to match that of the species.
Thus, what is needed to resolve this question is a phylogeny using multiple genes with adequate taxon sampling.
Viewed from another angle...
6 November 2003
To quote Hughes and piontkivska: "phylogenetic analyses of available sequences in 42 protein families gene generally supported monophyly of the genus Trypanosoma. One possible explanation for these conflicting results is poor taxon sampling in the case of protein coding genes, most of which have been sequenced for only a few species of Trypanosomatidae."
And another explanation is that their analysis of 18S sequences is flawed and that the overwhelming evidence from protein coding genes is, in fact, correct ...
Competing interests
None declared
Explanation of Contradictory Phylogenies
28 November 2003
Dr. Stevens's comment re-states the obvious: that either the phylogenies showing Trypanosma to be monophyletic are incorrect or the phylogenies showing this genus to be paraphyletic are incorrect. Since smaller numbers of sequences are available for protein-coding genes, it is possible that the results for these genes have been affected by relatively poor taxon sampling. However, we still do not have very good general knowledge of how taxon sampling affects phylogenetic reconstruction.
As regards the 18S rRNA phylogeny, it is really not helpful to assert that it might be "flawed." We used all widely used methods of phylogeny reconstruction (minimum evolution, maximum parsimony, maximum likelihood, Bayesian); and none supported monophyly of the genus Trypanosoma. It seems hard to believe that the problem lies in the methods of reconstruction. However, the 18S rRNA gene is just one gene; and stochastic error can cause the phylogeny of a single gene not to match that of the species.
Thus, what is needed to resolve this question is a phylogeny using multiple genes with adequate taxon sampling.
Competing interests
None declared