Phylogenetic signal

The sequence variability in the sample contains phylogenetic signal adequate to resolve the problem of interest. 

Once sequences have been aligned, some assessment of the presence of phylogenetic signal is necessary. If all the sequences are identical, there is obviously no point in additional analysis. At the other extreme, the sequences may be so divergent that they have been randomized with respect... 

Assess evolutionary processes, constraints, and phylogenetic signal... 

If phylogenetic signal is present in a matrix of sequences, then the third step is selecting a method of phylogenetic inference. Some of the following questions must be answered to make an informed choice among the... 

Another way of detecting the presence of phylogenetic signal in a given data set is to examine the shape of the tree-length distribution that results from a parsimony analysis of all possible trees or a random subset of all... 

Several procedures are available that evaluate the phylogenetic signal in the data and the robustness of trees (Swofford et al., 1996 Li, 1997). The most popular of the former class are tests of data signal versus randomized data (skewness and permutation tests). The latter class includes tests of tree support from resampling of observed data (nonparametric bootstrap). The likelihood ratio test provides a means of evaluating both the substitution model and the tree. 

Characters are used that may contain more noise than phylogenetic signal (characters of low probability of homology) and are not weighted to express their value. For example, reduction of epidermal microvilli, reductions of motile cilia and reductions of endodermal cilia are considered to be synapomorphies of the Ecdysozoa (Zrzavy et al., 1998). Simple reductions of this type are not very specific characters and occur frequently in unrelated organisms. 

Lyons-Weiler, J., Hoelzer, G.A., and Tausch, R.J., Relative apparent synapomorphy analysis (RASA). I. The statistical measurement of phylogenetic signal, Mol. Biol. Evol., 13,749-757, 1996. 

Burleigh, J. G. and Mathews, S. (2004). Phylogenetic signal in nucleotide data from seed plants implications for resolving the seed plant tree of life. American Journal of Botany, 91, 1599-1613. 

Combined evidence yields 288 MPTs from two free islands. The deletion of all OTUs except the rhizogonian mosses and pleurocarps reduces the number of MPTs to four, and results in an increase of I/N. This suggests that the detectable phylogenetic signal is concentrated within 34 rhizogonian and pleurocarp exemplars. 

Hillis, D. M. (1991) Discriminating between phylogenetic signal and random noise in DNA sequences. In Phylogenetic Analysis of DNA Sequences (ed. M. M. Miyamoto and J. Cracraft). Oxford University... 

Vertebrate phylogeny limits of inference of mitochondrial genome and nuclear rDNA sequence data due to an adverse phylogenetic signal/noise ratio... 

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