Distance-based phylogenetic

There are several important philosophical differences between distance-based phylogenetic methods and character-based parsimony which should not be overlooked. First is the unappealing property of distance-based analyses that all information on evolutionary change is averaged into one number for each pair of taxa. Second, to paraphrase Swofford and Olsen (1990), the as stamptions involved in distance methods (such as additivity and clock-like evolution) are rarely evident or discussed and the justification of the algorithm itself often seems to be the objective of the study. On the contrary, in the case of methods will a well-defined optimality criterion such as parsimony, the objective is usually related to a (more or less) concrete set of assumptions. 

Phylogenetic analyses of sequences can be conducted by analyzing discrete characters (i.e., the nucleotides themselves) or by making pairwise comparisons of whole sequences (the distance approach). Deciding whether to use a distance-based or a character-based method depends on... 

The most widely used models of amino acid substitution include distance-based methods, which are based on matrixes such as PAM and BLOSUM. Again, such matrices are described fiuther in other chapters in this book. Briefly, Dayhoff s PAM 001 matrix (Dayhoff, 1979) is an empirical model that scales probabilities of change from one amino acid to another in terms of an expected 1% change between two amino acid sequences. This matrix is used to make a transition probability matrix that allows prediction of the probability of changing from one amino acid to another and also predicts equilibriiun amino acid composition. Phylogenetic distances are calculated with the assumption that the probabilities in the matrix are correct. The... 

Tree-building methods implemented in available software are discussed in detail in the literature (Saitou, 1996 Swofford et al., 1996 Li, 1997) and described on the Internet. This section briefly describes some of the most popular methods. Treebuilding methods can be sorted into distance-based vs. character-based methods. Much of the discussion in molecular phylogenetics dwells on the utility of distance-and character-based methods (e.g., Saitou, 1996 Li, 1997). Distance methods compute pairwise distances according to some measure and then discard the actual data, using only the fixed distances to derive trees. Character-based methods derive trees that optimize the distribution of the actual data patterns for each character. Pairwise distances are, therefore, not flxed, as they are determined by the tree topology. The... 

Phylogenetic inference methods can be broken into two categories, those that create trees based on genetic distances among taxa and those that create trees based on presence of shared character states (Felsenstein 1988, Swofford and Olsen 1990). Distance-based methods could be subdivided into... 

Fig. (7). Phylogenetic relationship of tomato subtilases. An unrooted phylogenetic tree is shown based on the amino acid sequences deduced from tomato subtilase genes and cDNAs. Numbers indicate PAM distances (accepted point mutations per 100 residues) between sequences. The figure was modified after (8).

Fig. 4. Phylogenetic tree of Basidiomycota based on the primary structure of the 18S rRNA gene. Alignment, distance matrix and calculation of phylogenetic distances were made by means of different programs as described in the legend of figure 1. Hmnan pathogenic genera are indicated by arrows. T = Teleomorphic species A = anamorphic species Y = yeasts or yeast stages.

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.

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