The rapid development of phylogenetic network methods allows evolutionary biologists to infer reticulate relationships between species or their common ancestors. Given the notable levels of hybridization in plants relative to other groups, phylogenetic networks have the potential to elucidate complex evolutionary histories of speciation and trait evolution in addition to explaining historically contentious nodes in the Tree of Life. This workshop will connect method developers with empirical botanists to discuss models, misconceptions, and best practices on network estimation and downstream applications. A combination of theoretical lectures and hands-on computational exercises will provide an overview of the field and exposure to cutting-edge tools. Workshop participants are encouraged to bring their own data as there will be opportunity for analysis and discussion with speakers outside of guided activities.

Specific topics include estimating networks using multi-locus nuclear data, evaluating robustness of networks to different sources of error, and testing hypotheses of trait evolution on networks. Software used during the workshop will focus on PhyloNetworks and BPP, but other tools may be used as well through exercises. Lectures and computational exercises will demonstrate a range of strategies that fit different data types and taxon sampling scenarios. The assumptions and limitations of various methods will be discussed. No prior experience is expected, and speakers will provide the necessary theoretical background and real-time guidance through exercises.

Learning Goals

  • Understand how molecular sequence data can be used to estimate phylogenetic networks
  • Understand the appropriateness of different models of gene flow for different biological problems
  • Develop strategies for estimating species networks with many loci
  • Evaluate confidence in phylogenetic network estimates
  • Develop strategies for communicating and visualizing phylogenetic networks
  • Compare trait evolution on networks versus binary trees

Learning Outcomes

  • Estimate phylogenetic networks from gene tree topologies and sequences
  • Evaluate support statistics for networks
  • Test multiple competing gene flow hypotheses
  • Test trait evolution hypotheses with morphological models on networks
  • A solid theoretical understanding of the multispecies coalescent and models of gene flow

Registration

The link to a google form used for registration can be found on the Registration page.

Preparing for the Workshop

Information on installation steps that are needed to be performed prior to the workshop are on the Pre-workshop page. All analyses will be facilitated by institutional compute clusters at the host organizations.