Minimum conflict: a divide-and-conquer approach to phylogeny estimation.

MOTIVATION: Fast and reliable phylogeny estimation is rapidly gaining importance as more and more genomic sequence information is becoming available, and the study of the evolution of genes and genomes accelerates our understanding in biology and medicine alike. Branch attraction phenomena due to unequal amounts of evolutionary change in different parts of the phylogeny are one major problem for current methods, placing the species that evolved fast in one part of the phylogenetic tree, and the species that evolved slowly in the other. RESULTS: We describe a way to avoid the artifactual attraction of species that evolved slowly, by detecting shared old character states using a calibrated comparison with an outgroup. The corresponding focus on shared novel character states yields a fast and transparent phylogeny estimation algorithm, by application of the divide-and-conquer principle, and heuristic search: shared novelties give evidence of the exclusive common heritage (monophyly) of a subset of the species. They indicate conflict in a split of all species considered, if the split tears them apart. Only the split at the root of the phylogenetic tree cannot have such conflict. Therefore, we can work top-down, from the root to the leaves, by heuristically searching for a minimum-conflict split, and tackling the resulting two subsets in the same way. The algorithm, called "minimum conflict phylogeny estimation" (MCOPE), has been validated successfully using both natural and artificial data. In particular, we reanalyze published trees, yielding more plausible phylogenies, and we analyze small "undisputed" trees on the basis of alignments considering structural homology. AVAILABILITY: MCOPEis available via http://bibiserv.techfak.uni-bielefeld.de/mcope/. CONTACT: fuellen@alum.mit.edu

Evolution of ITS1 rDNA in the Digenea (Platyhelminthes: trematoda): 3' end sequence conservation and its phylogenetic utility.

A comparison of ribosomal internal transcribed spacer 1 (ITS1) elements of digenetic trematodes (Platyhelminthes) including unidentified digeneans isolated from Cyathura carinata (Crustacea: Isopoda) revealed DNA sequence similarities at more than half of the spacer at its 3' end. Primary sequence similarity was shown to be associated with secondary structure conservation, which suggested that similarity is due to identity by descent and not chance. Using an analysis of apomorphies, the sequence data were shown to produce a distinct phylogenetic signal. This was confirmed by the consistency of results of different tree reconstruction methods such as distance approaches, maximum parsimony, and maximum likelihood. Morphological evidence additionally supported the phylogenetic tree based on ITS1 data and the inferred phylogenetic position of the unidentified digeneans of C. carinata met the expectations from known trematode life-cycle patterns. Although ribosomal ITS1 elements are generally believed to be too variable for phylogenetic analysis above the species or genus level, the overall consistency of the results of this study strongly suggests that this is not the case in digenetic trematodes. Here, 3' end ITS1 sequence data seem to provide a valuable tool for elucidating phylogenetic relationships of a broad range of phylogenetically distinct taxa.

Molecular characteristation of digenetic trematodes associated with Cyathura carinata (Crustacea: Isopoda) with a note on the utility of 18S ribosomal DNA for phylogenetic analysis in the Digenea (Platyhelminthes: Trematoda).

Analysis of 18S rDNA sequences isolated from Cyathura carinata (Crustacea: Isopoda) indicate that two different species of the Digenea (Platyhelminthes: Trematoda) parasitize this isopod species for which parasitic associations have previously been unknown. Phylogenetic analysis, based on the largest data set of digenetic 18S rDNA sequences published to date, also suggests that 18S rDNA is unsuitable for the reconstruction of phylogenetic relationships of the major digenetic lineages either due to rapid radiation of these lineages or the presence of homoplasy at this level.

A priori estimation of phylogenetic information conserved in aligned sequences.

A new phenomenological approach to explorative data analysis, the estimation of spectra of supporting positions, allows the search for conserved tracks left by phylogeny in DNA sequences. Spectra of supporting positions can be generated without reference to a tree topology or a model of sequence evolution and are therefore an ideal tool for a priori estimation of information content of data sets. Analysis of published 18S rDNA alignments shows that signal to noise relationship varies greatly in a way not detected by conventional tree-construction methods.