Tutorial on Phylogenetic Inference Part-2

Abstract

Phylogenetic Inference (PI) is a statistical technique to trace the evolutionary legacy of a wide range of subjects; including biological taxa (species), biomolecules, languages, ancient texts and so on. The first part 1 of this tutorial introduced a number of fundamental concepts including phenetics, cladistics, homology, homoplasy, synapomorphy, symplesiomorphy, orthology and paralogy. In this part, we will learn about models of molecular evolution, choosing the best model, overview of various genetic loci used in PI, methods of PI (including distance matrix method, NJ, and discrete data methods ML, MP and BI), issue of lineage sorting and conclude with a worked-out example.