Abstract
BackgroundFor the purposes of phylogenetic inference from molecular data sets many different methods are currently offered as alternatives for researchers in phylogenetic systematics. The vast majority of these methods are based on specific topological assumptions relating to the resultant genealogical tree. Each of these has been shown to perform effectively in special conditions and for specific data sets while yielding less reliable results in other instances. Moreover, the majority of the methods include information from homoplastic characters in spite of a universally accepted agreement in their ineffectiveness for phylogenetic inference, which may often lead to inaccuracy and inconsistency. As an alternative to such methods, a strict mutational compatibility consensus tree building method as a universally applicable and reliable method is reported.ResultsThe analysis of a data set from a previously published experimental phylogeny demonstrates the accuracy of the strict mutational compatibility consensus tree building method and illustrates its potential for obtaining unambiguous and precise results with full resolution.ConclusionThe universal applicability of a simplified compatibility method in its algorithmic form for phylogenetic inference is described. Firstly, dismissal of topological assumptions creates a general potential for agreement of inferred with true phylogeny. Second, exclusion of irregular characters from analysis repeatably enables construction of consistent phylogeny. Third, a direct calculation of bootstrap proportion values for individual nodes of the resulting tree is possible rather than their empirical estimation. Finally, guidance is given for empirical assessment of the sample size necessary for full genealogical resolution and significant bootstrap proportions.ReviewersThis article was reviewed by Yuri I. Wolf (nominated by Eugene Koonin), Arcady Mushegian and Martijn Huynen.
Highlights
For the purposes of phylogenetic inference from molecular data sets many different methods are currently offered as alternatives for researchers in phylogenetic systematics
Is there a guarantee that all possible tree topologies are considered in the first place? If not, there is no guarantee that the tree chosen will be the one that absolutely fits to the data
Looking at the topological assumptions made by the current phylogenetic methods, three of them are commonplace in most cases: a) Analysed taxa are placed exclusively at the terminal nodes of a tree, b) Each node is labelled by exactly one taxon, and c) The tree is strictly a bifurcating one
Summary
For the purposes of phylogenetic inference from molecular data sets many different methods are currently offered as alternatives for researchers in phylogenetic systematics. The general strategy of current character-based methods for an appropriate tree reconstruction from a homologous sequence set relies in the first place on an assumed tree for a given set of taxa. This tree is fitted by various optimality criteria to the partition of character states of an individual character on the taxa, the procedure is repeated for each character and a tree is used which best fits all of the characters taken together [1,4]. Instead of first assuming a tree and finding its fitness to the data, one should start from the data, keeping initial assumptions at a minimum and let the data create the tree themselves without any further inference from the analyst
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