Molecular Evolution & Phylogeny: What, When, Why & How?

Abstract

The endeavour for the classification and study of evolution of organisms, pioneered by Linneaus and Darwin on the basis of morphological and behavioural features of organisms, is now being propelled by the availability of molecular data. The field of evolutionary biology has experienced a paradigm shift with the advent of sequencing technologies and availability of molecular sequence data in the public domain databases. The post-genomic era provides unprecedented opportunities to study the process of molecular evolution, which is marked with the changes organisms acquire and inherit. The species are continuously subjected to evolutionary pressures and evolve suitably. These changes are observed in terms of variations in the sequence data that are collected over a period of time. Thus, the molecular sequence data archived in various databases are the snapshots of the evolutionary process and help to decipher the evolutionary relationships of genes/proteins and genomes/proteomes for a group of organisms. It is known that the individual genes may evolve with varying rates and the evolutionary history of a gene may or may not coincide with the evolution of the species as a whole. One should always refrain from discussing the evolutionary relationship between organisms when analyses are performed using limited/partial data. Thorough understanding of the principles and methods of phylogeny help the users not only to use the available software packages in an efficient manner, but also to make appropriate choices of methods of analysis and parameters so that attempts can be made to maximize the gain on huge amount of available sequence data. As compared to classical phylogeny based on morphological data, molecular phylogeny has distinct advantages, for instance, it is based on sequences (as descrete characters) unlike the morphological data, which is qualitative in nature. While the tree of life is depicted to have three major branches as bacteria, archaea and eukaryotes (it excludes viruses), the trees based on molecular data accounts for the process of evolution of bio-macromolecules (DNA, RNA and protein). The trees generated using molecular data are thus referred to as ‘inferred trees’, which present a hypothesized version of what might have happened in the process of evolution using the available data and a model. Therefore, many trees can be generated using a dataset and each tree conveys a story of evolution. The two main types of information inherent in any phylogenetic tree are the topology (branching pattern) and the branch lengths.