Tutorial on phylogenetic inference — 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 part1 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 bestmodel, overview of various genetic loci used inPI,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.