molloy-lab/ck-phylo-workshop

Coalescent Lab at 2024 Workshop on Phylogenomics @ Cesky Krumlov

Coalescent Lab

The goal of this lab is to learn (or reinforce) some of the core principles behind coalescent species tree methods, through hands-on experience.

During this lab, we will

• compute the probability of a (gene tree) topology given an MSC model species tree
• run quartet-based coalescent methods, including gene tree summary methods and site-based methods
• use quartet concordance factors (qCFs) to evaluate the pseudo-likelihood of a species tree (+ visualize goodness of fit)

and interpret the results of these analyses. We will utilize real and synthetic data for Palaeognathae (flightless birds), considering the effects of incomplete lineage sorting (ILS), gene tree estimation error (GTEE), and data type.

This study system was selected because concatenation (RaxML and ExaML) and coalescent methods (ASTRAL and MP-EST) have yielded different results with respect to the placement of Rheas [Cloutier et al. (2019)]. Additionally, the data for Palaeognathae are publicly available well-curated, cover several different marker types (ranging from UCEs to CR1 retrotransposon insertions), and are small enough to analyze with a variety of methods (there are 15 taxa so just 1365 subsets of 4 taxa need to be evaluated by methods that explicitly enumerate all quartets). The methods selected for this lab are unified by their use of quartets; see the slides for an incomplete list of other coalescent methods to check out.

• Go to Day 1 Lab.
• Go to Day 2 Lab.

Acknowledgements

This lab was created for the 2024 Workshop on Phylogenomics @ Cesky Krumlov; thanks to the organizers for inviting me.

The day 1 lab uses the coalescent simulation scripts by Cloutier et al. (2019) with some minor modifications. The day 2 lab uses data generated by Cloutier et al. (2019); also see Sackton et al. (2019). Thanks to Cloutier et al. (2019) for depositing their intermediate data files in Dryad, making the re-analysis highly accessible. The intermediate files include estimated alignments and gene trees for 3158 ultraconserved elements (UCEs), 5016 introns, and 12676 conserved non-exonic elements (CNEEs) as well as data for 4301 retrotransposon (CR1) insertions. These data have since been re-analyzed by Simmons et al. (2022) and Takezaki (2023). Simmons et al. (2022) identified 105 UCEs with homology errors and recovered an additional 44 CR1 retrotransposons; the day 2 lab benefits from the homology annotations and the extended CR1 data set.

All bird images were downloaded from PhyloPic.