What This Document Is
This document is a laboratory exercise designed to accompany the Integrative Biology 200B (Ecology and Evolution) course at UC Berkeley. Specifically, Lab 2a focuses on the crucial topic of phylogenetic null models – a core concept in understanding evolutionary relationships and character distribution. It’s a hands-on guide intended to build practical skills in phylogenetic analysis using software like Mesquite. The lab explores methods for evaluating whether observed patterns in character traits are due to genuine evolutionary signal or simply the result of chance or tree topology.
Why This Document Matters
This lab is essential for students learning to interpret phylogenetic data and conduct rigorous evolutionary analyses. It’s particularly valuable for those interested in comparative methods, evolutionary biology, and ecological studies where understanding historical relationships is key. If you’re grappling with how to statistically test for phylogenetic signal, or are unsure how different tree structures influence character evolution, this resource will provide a foundational understanding. It’s best used *during* the lab session to guide your analysis and interpretation, and as a reference for future phylogenetic investigations.
Topics Covered
* Phylogenetic Signal Detection
* Discrete Character Evolution
* Null Model Generation (Yule, Equiprobable Trees, Uniform Speciation with Sampling)
* Parsimony Analysis
* Statistical Hypothesis Testing in Phylogenetics
* Character State Reconstruction
* Correlation between Discrete Characters
What This Document Provides
* A step-by-step framework for using Mesquite to analyze character distributions on phylogenetic trees.
* Guidance on generating and comparing different null models to assess the significance of observed patterns.
* Instructions for calculating and interpreting p-values to determine if phylogenetic signal is present.
* Exercises designed to help you understand the impact of tree shape and randomization techniques on evolutionary inferences.
* Questions to prompt critical thinking about the appropriate use of different null models in phylogenetic studies.
