Phylogenetic Comparative Methods

A guide from first principles to working analyses

Phylogenetic comparative methods let us test evolutionary hypotheses by accounting for the shared history of species. Whether you are studying how body size evolves, mapping the origin of complex traits, or testing correlations between characters, the phylogeny is your map to understanding the data.

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Phylogenies

Before anything else, you need to know what a phylogeny is and how to read one. Learn to interpret the tree of life, understand branch lengths, and see why topology matters.

Foundational

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Continuous Traits

Body size, chromosome number, metabolic rate. How do we analyze traits that vary on a continuum? Learn Brownian motion, phylogenetic signal, and phylogenetic generalized least squares.

Intermediate

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Discrete Traits

Wings vs no wings. XY vs X0 sex determination. How do we model traits that come in distinct states? Learn the Mk model and ancestral state reconstruction.

Intermediate

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Discrete + Continuous

What happens when you need both types of data in the same analysis? Learn phylogenetic ANCOVA, threshold models, and how to integrate multiple types of data.

Advanced

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Birth-Death Simulator

Same rates, wildly different trees. Run paired birth-death simulations and see how stochastic macroevolution produces unpredictable diversity — even when underlying rates are identical.

Interactive