Comparative methods on reticulate phylogenies

using JuliaPhylo

This repository contains materials compatible with PhyloNetworks v1 and PhyloTraits. It is an update of this 2023 workshop, which requires the older PhyloNetworks v0.16.

You can find and clone the tutorial material at this github repository.

Goal of the tutorial: learn to analyze trait data using phylogenetic comparative methods (PCMs) on reticulate phylogenies, modelled by phylogenetic networks –also named admixture graphs when modelling closely-related populations.

Comparative methods are meant to answer questions about trait evolution. In this tutorial, we will learn about methods on networks:

• to account for reticulation in the phylogeny, and
• to look at how reticulation might have affected trait evolution.

topics covered

• how to calibrate a network, if needed
• continuous response:
  • phylogenetic regression & phylogenetic ANOVA when the phylogeny is a network. Predictors can be continuous or discrete.
  • how account for within-species variation in the response trait
  • ancestral state reconstruction
  • how to measure the impact of gene flow
• discrete trait
  • ancestral state reconstruction
  • was the trait via gene flow?
• how to visualize the results