What This Document Is
This document is a laboratory guide for an upper-level undergraduate course in Ecology and Evolution, specifically focusing on the principles of phylogenetic analysis at the molecular level. Lab 8, “Evolution at the Molecular Level,” explores how phylogenetic methods can be applied to investigate patterns and processes of gene evolution using DNA sequence data. It delves into statistical approaches for understanding evolutionary change within and between genes.
Why This Document Matters
This lab guide is essential for students seeking a practical understanding of molecular phylogenetics. It’s particularly valuable for those interested in applying computational tools to evolutionary questions, and for anyone needing to interpret the results of phylogenetic analyses. Students will benefit from working through this lab to solidify their understanding of how to test evolutionary hypotheses using real biological data. This resource is most useful when preparing for and completing the associated lab exercise, and as a reference for future work in molecular evolution.
Topics Covered
* Molecular evolution and phylogenetic inference
* Nucleotide substitution models and rate variation
* Intron vs. exon evolution
* Maximum Likelihood and Bayesian model testing methodologies
* Joint and marginal estimation in statistical analysis
* Markov Chain Monte Carlo (MCMC) methods
* Application of phylogenetic principles to gene evolution
What This Document Provides
* Background information on the importance of studying rate variation in gene evolution.
* Guidance on obtaining and setting up necessary software packages (RAXML and MrBayes).
* Instructions for accessing required data files for the lab exercise.
* An overview of nucleotide substitution models and transition matrices.
* A conceptual framework for understanding the relationship between branch lengths, transition matrices, and probabilities of nucleotide change.
* A foundation for understanding how probabilistic models are used in phylogenetic analysis.