Title: General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa
Abstract:Inconsistency of phylogenetic estimations refers to the property of certain estimation methods to converge on the positively wrong estimate with increasing amounts of data. This property, at least wit...Inconsistency of phylogenetic estimations refers to the property of certain estimation methods to converge on the positively wrong estimate with increasing amounts of data. This property, at least with respect to the maximum parsimony method, has been given the catch phrase branches attract. It has also been suggested that this problem can be alleviated by inclusion of more taxa to break up the long branches. Unfortunately, these observations have been based on computations for trees with small numbers of taxa. Here, I present a decomposition equation that allows determination of inconsistency conditions for large numbers of taxa. I show by counterexamples that long branches are a poor predictor of inconsistent conditions and that even trees with equal branch lengths can produce inconsistent estimates. I also tested the idea of breaking up long branches with additional taxa. The addition of taxa alleviates the inconsistency problem only if the average rate of change in the added taxa is low. If the rate is high, the inconsistency problem can become worse. Sampling of random tree models indicates that the inconsistency problem becomes increasingly acute as the number of taxa becomes larger. Conclu- sions: (1) low rates of change are of paramount importance if the inconsistency problem is to be avoided, (2) if the evolutionary question of interest does not require large numbers of taxa, it seems best to use fewer taxa because larger trees are more likely to contain inconsistent branches, and (3) if taxa are added to counter inconsistency problems, the added taxa should have low rates of change and be close to the common ancestor of the clade (which may be measured by com- parison with the outgroup taxa). Longer branches require large numbers of added taxa, but such additions should only be used to resolve the particular branch of interest. Other parts of the tree, especially the branches within the added taxa, may still be inconsistently estimated. (Maximum parsimony; inconsistency; large phylogenies; long branches.)Read More
Publication Year: 1996
Publication Date: 1996-09-01
Language: en
Type: article
Indexed In: ['crossref']
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Cited By Count: 227
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