What This Document Is
This is a laboratory exercise designed to accompany the Principles of Phylogenetics: Ecology and Evolution course (INTEGBI 200B) at UC Berkeley. Specifically, this lab focuses on the intersection of phylogenetic analysis and community ecology – exploring how evolutionary relationships between species influence the structure and composition of ecological communities. It provides a practical application of theoretical concepts discussed in lectures.
Why This Document Matters
This lab is essential for students seeking to deepen their understanding of how evolutionary history shapes ecological patterns. It’s particularly valuable for those interested in quantitative approaches to ecology, biodiversity analysis, and conservation biology. Students will benefit from working through this lab during or immediately after covering phylogenetic trees and community ecology principles in their coursework, as it reinforces those concepts with hands-on data analysis.
Topics Covered
* Community phylogenetic structure
* Phylogenetic distance metrics
* Application of the picante R package
* Interpretation of NRI and NTI values
* Null model analysis in phylogenetic community ecology
* Visualizing phylogenetic relationships within communities
* Relating phylogenetic patterns to ecological observations
What This Document Provides
* A framework for calculating key community phylogenetic statistics.
* Guidance on utilizing a pre-existing ecological dataset for analysis.
* Instructions for visualizing community composition on a phylogenetic tree.
* A series of questions designed to promote critical thinking about the relationship between phylogeny and community structure.
* An introduction to different null models used in phylogenetic community ecology and their implications.
