Molecular Evolutionary Study: Phylogenetic Tree

AbstractThis chapter discusses mostly the molecular evolutionary studies with biodiversity analysis through phylogenetic tree construction. The commonly used software for phylogenetic tree construction are as follows: Phylip (general package, protdist, NJ, parsimony, maximum likelihood, etc.); PAUP (parsimony); PAML (maximum likelihood); TreePuzzle (quartet based); PhyML (maximum likelihood); MyBayes; MEGA (biologist-centric); DNASTAR; and Network analysis. Structurally, a phylogenetic tree may be classified in two types—rooted and unrooted. Functionally, the tree may be classified as based on distance or characters. Common techniques of a phylogenetic tree involve MAFFT, MEGA (Molecular Evolutionary Genetics Analysis), PHYLIP, reduced median network theory, and neighbor joining tree. The details of these techniques have been illustrated with suitable examples and diagrams. Some common indicators for effective population size have been discussed.KeywordsMolecular evolutionPhylogenetic treeMEGAPHYLIPMAFFTNetwork analysis