The Dark and Bright Sides of Phylogenetics and Comparative Methods

Five years ago at Evolution 2014, ‘The Dark Side of Phylogenetics’ symposium (organised by Natalie Cooper) explored some of the issues with phylogenetic comparative methods (PCMs). This year at Evolution 2019, Michael Landis and Rosana Zenil-Ferguson are organising a contrasting ‘Bright Side of Phylogenetics‘ spotlight session (featuring Michael Matschiner). They aim to promote research that has overcome these pitfalls and that explores innovations in phylogenetics. Clearly they found our lack of faith disturbing.

Natalie and Michael have created a Virtual Issue to complement the spotlight session: Phylogenetics and Comparative Methods: The Bright and Dark Sides. It highlights recent Methods in Ecology and Evolution papers that feature either the ‘Bright Side’ or ‘Dark Side’ of phylogenetics and comparative methods. This Virtual Issue also highlights the diversity of researchers around the world working on these exciting questions. We hope you have a good feeling about it!

The Dark Side of Phylogenetics and Comparative Methods

The Editors have roughly divided papers into ‘Dark Side’ (e.g. cautionary tales and sensitivity analyses) and ‘Bright Side’ (e.g. new tools and methods) themes. They’ve chosen to start the issue with an article based on the original ‘Dark Side of Phylogenetic Comparative Methods‘ symposium.

Other articles focus on how good our estimates of tip rates in diversification studies are, how non-random sampling influences our inferences from comparative studies, how we can assess model adequacy in studies of phyletic evolution of fossils, and the R package, sensiPhy, that provides methods for sensitivity analysis in PCMs.

The ‘Dark Side’ seems to have a weaker grip on phylogenetic inference. The specificity of phylogenetic marker identification is questioned. Otherwise, many newly developed methods shine a positive light on phylogenetic inference.

The Bright Side of Phylogenetics and Comparative Methods

The ‘Bright Side’ features the R package FossilSim which can simulate fossil occurrences to aid mechanistic modelling of fossil preservation and recovery rates, useful for PCM studies using fossil data. One of the authors of this article, Joëlle Barido-Sottani, is also presenting in the ‘Bright side of phylogenetics’ spotlight session. We also include the R package, ratematrix, which facilitates study of several integrated traits across phylogenies.

Large studies of phenotypic evolution are currently in vogue. So this Virtual Issue features two programmes and one method that can help anyone working in that area. The first is AutoMorph, which automates the processing of image data for morphometrics studies. Next up, we have the R package dispRity for estimating morphological diversity through space and time. Finally, there’s a new method for testing phenotypic evolutionary rate variation

On the ‘Bright Side’ of phylogenetic inference papers, we start with the Python package PyPHLAWD, which automates the compilation of phylogenetic datasets. Moving on, we find out how Bayesian phylogenetic inference can be facilitated with the R package babette. And Zhang et al. show how the whole phylogenomic workflow, from marker identification to phylogenetic inference, can now be automated with a new pipeline.

The sources of gene-tree discordance can be investigated with three new tools. A method based on likelihood calculations of models with various levels of gene flow is the first of these. The second is the clustering approach snapclust, implemented in the R package adegenet. To round off this section, we’ve got a new method for the inference of haplotype networks with the R package pegas.

With just a few papers left in the issue, we come to the R package Phangorn. The new functions of this package facilitate the comparison of trees and networks. Another new method allows the identification of the processes underlying correlated phylogenies of interacting groups of species (this paper won the 2018 Robert May prize). To bring the issue to a close, we have the TreeSimGM R package, which produces model simulations that can be used to compare shapes of phylogenetic trees.

All articles in the ‘Phylogenetics and Comparative Methods: The Bright and Dark Sides‘ Virtual Issue are freely available for a limited time.

For those of you at Evolution 2019, the Spotlight Session ‘​The bright side of phylogenetics‘ takes place at 09:30am on Sunday 23 June in Ballroom A.

1 thought on “The Dark and Bright Sides of Phylogenetics and Comparative Methods

  1. Pingback: Ultraconserved Elements are Widely Shared across the Tree of Life | methods.blog

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