Signal, Noise, and Reliability in Molecular Phylogenetic Analyses

Abstract

DNA sequences and other molecular data compared among organisms may contain phylogenetic signal, or they may be randomized with respect to phylogenetic history. Some method is needed to distinguish phylogenetic signal from random noise to avoid analysis of data that have been randomized with respect to the historical relationships of the taxa being compared. We analyzed 8,000 random data matrices consisting of 10-500 binary or four-state characters and 5-25 taxa to study several options for detecting signal in systematic data bases. Analysis of random data often yields a single most-parsimonious tree, especially if the number of characters examined is large and the number of taxa examined is small (both often true in molecular studies). The most-parsimonious tree inferred from random data may also be considerably shorter than the second-best alternative. The distribution of tree lengths of all tree topologies (or a random sample thereof) provides a sensitive measure of phylogenetic signal: data matrices with phylogenetic signal produce tree-length distributions that are strongly skewed to the left, whereas those composed of random noise are closer to symmetrical. In simulations of phylogeny with varying rates of mutation (up to levels that produce random variation among taxa), the skewness of tree-length distributions is closely related to the success of parsimony in finding the true phylogeny. Tables of critical values of a skewness test statistic, g1, are provided for binary and four-state characters for 10-500 characters and 5-25 taxa. These tables can be used in a rapid and efficient test for significant structure in data matrices for phylogenetic analysis.

Towards a phylogenetic framework for the evolution of shakes, rattles, and rolls in Myiarchus tyrant-flycatchers (Aves: Passeriformes: Tyrannidae)

“…These values are comparable with those reported by Hunt et al (2001) for Caribbean mimids (33.9, 30.7%, respectively). Mean tree length of 10,000 random trees was 3164.22 AE 95.88 and the data contained significant phylogenetic signal (g 1 ¼ À0:32, p < 0:01; Hillis and Huelsenbeck, 1992). GenBank accession numbers of the sequences used in this study are listed in Appendix A.…”

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum–Neofusicoccum ribis species complex

“…1000 bootstrap replicates (Felsenstein, 1985) were done to assess the support for branching and isolates of Neofusicoccum australe were used as the outgroup. Estimated levels of homoplasy and phylogenetic signal (retention and consistency indices and g1-value) (Hillis and Huelsenbeck, 1992) were also determined using PAUP.…”

Aurifilum, a new fungal genus in the Cryphonectriaceae from Terminalia species in Cameroon

“…The support of the branches for the most parsimonious trees was assessed with a 1000 bootstrap replications (Felsenstein 1985). Other measures noted were tree length, consistency index, rescaled consistency index, and retention index (Hillis and Huelsenbeck 1992). A partition homogeneity test of 500 replicates was conducted in PAUP to assess the possibility of combining the ITS and β-tub data sets.…”