What This Document Is
This is a laboratory exercise designed to accompany the Integrative Biology 200B (Ecology and Evolution) course at the University of California, Berkeley. Specifically, it focuses on the principles and practical application of phylogenetic analysis, with an emphasis on understanding how diversification patterns change over time. It’s a hands-on guide intended to build skills in computational phylogenetics using the R statistical environment. This lab explores methods for investigating evolutionary history and testing hypotheses about diversification rates.
Why This Document Matters
This lab is essential for students seeking a deeper understanding of macroevolutionary processes. It’s particularly valuable for those interested in quantitative approaches to studying evolutionary history, and for anyone planning to conduct research involving phylogenetic trees. Students will benefit from working through this material during or after lectures covering phylogenetic methods and diversification analysis. It’s ideal for reinforcing concepts and developing practical skills needed for independent research projects.
Topics Covered
* Lineage-through-time (LTT) plots and their interpretation
* Simulating phylogenetic trees using different models
* Birth-death processes and their application to diversification analysis
* Testing for shifts in diversification rates over time
* Utilizing R packages (ape, geiger) for phylogenetic analysis
* Pruning extinct lineages from phylogenetic trees
* Understanding the relationship between speciation, extinction, and diversification
What This Document Provides
* A step-by-step guide to simulating phylogenetic trees in R.
* Instructions for visualizing and interpreting tree structures.
* Guidance on using specific functions within R packages for phylogenetic analysis.
* A framework for comparing observed diversification patterns to null expectations.
* Code examples to facilitate practical application of the concepts.
* An introduction to likelihood-based methods for testing diversification rate changes.
