A Protocol for Phylogenetic Reconstruction

Abstract

The similarity of biological functions and molecular mechanisms in living organisms suggests their common origin. The inference of evolutionary relationships among the extant organisms is primarily based on structural, functional, and sequence data of biomolecules, such as DNA, RNA, and protein, and their relative changes over the course of time. To decipher evolutionary relationships, a variety of data can be used. The exponential growth of genomic data, spurred by advances in DNA sequencing, has enabled biologists to reconstruct the tree or network of life for a vast number of organisms dwelling in the earth. In addition of organismal relationships, phylogenetic analysis is often performed to characterize gene families, specifically to identify the orthologs and paralogs of a gene of interest and understand their varied functions in light of evolution. In this chapter, we describe a protocol for reconstructing a phylogenetic tree using maximum-likelihood approach. We demonstrate using an example dataset and a suite of publicly available programs.

Keywords: Maximum-likelihood; Phylogenetic analysis; Phylogenetic reconstruction; Phylogenetic tree.