Module 8: Phylogenetic Analysis

 

Cladistic Methods

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  • Parsimony Analysis: This method seeks to build a tree with the smallest number of mutations compared to a common ancestral sequence. It allows the use of all known evolutionary information about the various branches and leaves of the presumptive tree for constructing the tree. Since this analysis may be highly computer-intensive to build a tree from sequences alone, one can start with a tree based on a distance method and use that as a basis to build the most parsimonious tree. PAUP (Phylogenetic Analysis Using Parsimony) is the most sophisticated parsimony program available.

  • Maximum Likelihood Method: This method assumes the independent evolution of each position in a sequence and each lineage (or generation) within a population. It also assumes that each mutation takes place at a constant rate of change (molecular clock). The computations involved in tree-building are based on, initially, figuring out the most probable ancestor for each neighboring pair of sequences (leaves) joined by a branch of the tree, and then, working similarly (by probability calculations) from the top of the tree to its root. MOLPHY is an example of a maximum likelihood software available on the web.


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SWBIC 2001