Distance-based phylogenetic analysis

Figure 8.4. An example of a user interface to a phylogenomic-oriented database (48). Relative distances, following black line paths, between nodes on the tree of phosphodiesterases indicate the similarity level between members of the family, based on the regions of the sequences selected for the phylogenetic analysis. Links to aligned domains permit the alignments themselves to be explored. The order in which the genes appear in the tree (the branching order) gives an indication of the homology relationship between members of the family. See Section 5.3.

Figure 18.2 Phylogenetic analysis segregates the human caspases into two major subfamilies, one based on caspase-1 previously referred to as ICE, for interleukin-converting enzyme, and the other based on similarities to the C. elegans cell death gene, ced-3. Further classification of the caspases is possible into those that mediate cytokine maturation that are involved in inflammation, those with a short prodomain involved in the effector phase of apoptosis (shown boxed), and those with a long prodomain that are involved in the initiator phase of apoptosis (not boxed). Note evolutionary distances are not accurately represented in this dendrogram. (Adapted from Nicholson, D.W. (1999). Caspase structure, proteolytic substrates, and function during apoptotic cell death. Cell Death Differ 6 1028-1042.)...

Figure 14.6. Simplified substitution rate matrix used in ML and distance phylogenetic analysis. The off-diagonal values a represent a product of an instantaneous rate of change, a relative rate between the different substitutions, and the frequency of the target base. In practice, the forward rates (upper triangular values) are presumed to equal the reverse rates (corresponding lower triangular values). The diagonal elements are nonzero, which effectively accounts for the possibility that more divergent sequences are more likely to share the same base by chance. In the simplest model of sequence evolution (the Jukes-Cantor model), all values of a are the same all substitution types and base frequencies are presumed equal.

Fig. 16.4. Phylogenetic trees or cladograms based on the sequence differences (SEQ) and three-dimensional structural differences (STR) of immunoglobulin fragments. The structural distance metric is a function of both the rms distance difference between superposed structures and the number of topologically equivalent positions in each pairwise comparison (taken from [11]). The lower part of the diagram shows a multidimensional scaling analysis based on structural differences. The constant (C) and variable (V) domains cluster together for the light (L) and heavy (H) chains of the immunoglobulin fragments...

Table 1. Examples of the phylogenetic distance of 16S rDNA clones to their nearest 16S rDNA sequence which are clone sequences (in percent similarity). Analysis is based on 1000 nucleotides.

Comparative sequence analysis and ERNA-3D software were used to model the three-dimensional structures of several signal recognition particle RNAs. RNA secondary structures were established by allowing only phylogenetically-supported base pairs. The folding of the RNA molecules was constrained further to include a pseudoknot and a tertiary interaction. Founded by the concept that all SRP RNAs must be shaped similarly in three dimensions, helical sections were oriented coaxially where a continuous helical stack was formed in the RNA of another species. Finally, RNA helices were placed at distances that preserved the connectivity of the molecule with the smallest number of single-stranded nucleotide residues as identified from the aligned sequences. Representative models of the three-dimensional structures of an eukaryote, an archaeon, and three bacterial SRP RNAs are presented. 

Minimum evolution and spectral analyses of LogDet distances of the type performed here should prove valuable for future phylogenetic analyses based on the rRNA gene family. Such an approach will allow inclnsion of seqnences of other deuterostomes and protostomes in an extensive analysis of metazoan relationships, even if their base frequencies are not uniform across the taxa, as will likely be the case. 

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