Phylogenetic Biology

Phylogenetic Biology is a rigorous, accessible introduction to the principles and practice of reconstructing evolutionary history and using phylogenies to answer biological questions.

Modern phylogenetic methods are built on mathematical models of evolution, but these models are often introduced in the context of inferring the past. This book takes a more intuitive approach: it first shows how evolutionary models generate data forward through time and then applies the same models to phylogenetic inference, hypothesis testing, ancestral reconstruction, and comparative analysis.

Beginning with tree structure, topology, rooting, branch lengths, and phylogenetic representation, the book develops a unified, model-centered framework for understanding the field. Readers progress from simulation and models of molecular evolution to maximum likelihood and Bayesian phylogenetic inference. The text then extends these foundations to practical molecular phylogenetics, model evaluation, statistical support, gene tree-species tree discordance, morphological and continuous characters, divergence-time estimation, ancestral character state reconstruction, and phylogenetic comparative methods.

Topics include:

• Reading, drawing, rooting, and representing phylogenetic trees
• Evolutionary models and the simulation of molecular data
• Maximum likelihood and Bayesian phylogenetic inference
• Model selection and model adequacy
• Gene trees and species trees
• Discrete morphological characters and continuous trait evolution
• Molecular clocks, fossil calibration, and divergence-time estimation
• Ancestral character state reconstruction
• Phylogenetic independent contrasts and phylogenetic generalized least squares

Worked examples and visual explanations connect statistical theory to practical analysis.

Developed for a Phylogenetic Biology course at Yale University, this book is suitable for advanced undergraduate and graduate courses, researchers entering the field, and self-directed learners.