Phylogenetic analysis, steps

Phylogenetic analysis, steps of, 107, 108 Phylogenetic bone fusion, patterns on, 164 Phylogenetic cladistics, 107, 112 Phylogenetics, moleculai 268 Phylogenetic systematics character analysis, 109 logic of, 96... 

The five basic steps in phylogenetic analysis of sequences (Hillis et al., 1993) organized as shown in Figure 13.1 consist of ... 

Phylogenetic analysis of the quaternary arrangements and sequences of lumazine synthases and related pentameric riboflavin synthases derived from archaea, bacteria, plants, and fungi suggests a family of proteins composed of four different clades. These include the archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases. We could thus construct a picture of the evolution of the latter steps of riboflavin biosynthesis where initially there were two enzymes catalyzing the riboflavin synthase reaction. The archaeal riboflavin synthase evolved into the different lumazine synthases and the other enzyme evolved into the trimeric enzymes found in present day eubacterial and eukaryotic riboflavin synthases. This would explain how the two different enzymes can use two different diastereomeric intermediates in the generation of riboflavin. That the lumazine synthase evolved from the riboflavin synthases is supported by the finding that it still binds riboflavin. Perhaps the fact that two different enzymes have evolved for this last step in riboflavin reflects on the ease at which riboflavin is formed nonenzymatically. ... 

A straightforward phylogenetic analysis consists of foin steps ... 

The aligmnent step in phylogenetic analysis is one of the most important because it produces the data set on which models of evolution are used. 

It is very important to note that the methods implemented in computer programs replace only one of several steps of a phylogenetic analysis. The cladistic step is a purely deductive procedure that leads from a data matrix to one or more selected dendrograms. Phylogenetic cladistics, however, requires several other steps that are equally important and frequently... 

Many publications conclude by presenting the best cladogram. However, this is not a complete phylogenetic analysis. Further steps are needed ... 

In summary, it is clear from this work that KS domains from trans-AT PKSs do possess substrate specificity compatible with that proposed by phylogenetic analysis, and that this specificity is seen principally in the elongation step of the catalytic process. Encouragingly, mutagenesis of BaeL KS5 suggests that this specificity can be tuned to allow the elongation of non-natural substrates. 

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