By comparing genes and genomes across the tree of life, we can interpret Nature’s grand experiment over millions of years of evolution. By comparing genes and genomes across individuals within populations, we can study the same process over the last thousands of years. This information allows us to make key inferences about the past, such as identifying loci that have critical functions, and those that have mediated adaptations to the environment. Evolutionary methods allow us to make inferences about the functional significance of each single genomic position; they also allow us to unravel the evolutionary and adaptive histories of populations and species.

In this module, students will learn how comparing genomes across species to reconstruct genome evolution helps us understand species and their genomes. We will explore exciting new developments in comparative genomics, introduce modern bioinformatic tools and techniques of molecular evolution and phylogenetics, and learn about the connections between molecular evolution and population genetics. Students will become familiar with the latest methods in evolutionary genomics, including comparative genomics, phylogenomics and molecular evolution. They will also learn about applications of these methods to study the evolution of diverse species. At the end of the module they will have deep knowledge of the fundamental concepts in evolutionary genomics and population genetics, and a critical understanding of the strengths and limitations of different approaches. In the computer practical sessions students will learn to use some of the most widely used tools in phylogenetics and molecular evolution.

Learning objectives

During the course of the module, students will become familiar with the latest methods in evolutionary genomics, including comparative genomics, phylogenomics and molecular evolution. They will learn about the main applications of these methods to study the evolution of diverse species. At the end of the module they will have deep knowledge of the fundamental concepts in evolutionary genomics and population genetics, and a critical understanding of the strengths and limitations of different approaches. They will also learn about real-life applications of these methods, both theoretically and hands-in during the practical sessions.

Indicative lecture topics – based on module content in 2021/22

Introduction Data and Theory of Molecular Evolution
	The neutral theory of molecular evolution Gene structure, mutation and variation
	Comparison of nucleotide sequences
	Comparison of protein-coding genes
	Phylogeny reconstruction I: Overview, distance & parsimony, likelihood, Bayesian
	Reliability: Homoplasy and errors in phylogenetics
	Rare genetic changes and phylogeny interference
	The Mesozoa: A case study
	Coalescent theory and genealogies
	Molecular adaptation: theory and overview, case studies
	Detecting natural selection using population data
	Population differentiation and theta estimators
	Are flies closer to humans or to worms? A case study
	The origins of lactase persistence