Module 8: Phylogenetic Analysis

 

Introduction

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This module will discuss methods and tools available for the computational analysis of evolutionarily related genes. The topics in this module will be dealt in brief since there are other excellent WWW courses that consider them in more detail. (1. Computer Analysis of Genome Information course from the San Diego Supercomputing Center, 2. Bioinformatics and Computational Genetics course from the Weizmann Institute of Science, Israel, 3. Bioinformatics course from Stanford)

  • Study of phylogenetics: Evolution of species, as predicted by Charles Darwin, is due to variations in the genes of organisms by natural selection. Phylogeny is the study of evolutionary relationships between groups of organisms and leads to how various organisms are classified into "taxons" (taxonomy; "taxa" is the correct plural form of taxon). Phylogenetics is the new field of molecular evolution wherein changes (mutations) in DNA and protein sequences can be correlated with similarities and dissimilarities between related species. Computing tools are now available to analyze the sequence similarities/differences between related organisms and to calculate "molecular distances" of evolution between species. The smaller the number of differences in the DNA and/or protein sequences of similar genes from two related organisms, the less they have evolutionarily diverged from each other.

  • Phenetic and Cladistic methods: Evolutionary biologists use two different approaches to analyze and group organisms, species, proteins or genes within phylogenetic relationships. The common tool, in both approaches, is to build a phylogenetic "tree" with branches and leaves representing divergence and individual components respectively. (Figure of a Tree with Different Species of Jumping Spiders)

    The phenetic approach to building phylogenetic trees is based on a "molecular clock" which 'ticks' at a constant pace resulting in nucleic acid or amino acid sequence changes. In this method, only the current differences between two or more organisms are considered without giving any weight to their evolutionary history or assumptions based on that history. Algorithms based on this model generally rely on distance methods for building trees.

    The Cladistic approach takes into account both ancestral relationships between organisms and current data stored in their sequences. Here, morphological similarities/differences are also considered as part of the evolutionary history of organisms being compared. The software employed in this approach include parsimony and maximum likelihood methods.


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