10th Anniversary Volume 3: Phylogenetics Editor’s Choice

To celebrate our 10th Anniversary, we are highlighting a key article from each of our volumes. For Volume 3, we selected ‘paleotree: an R package for paleontological and phylogenetic analyses of evolution‘ by David W. Bapst (2012).

In this post, three of our Associate Editors with expertise in phylogenetics Simone Blomberg, Will Pearse and Michael Matschiner share their favourite MEE papers in the field of phylogenetics and beyond.

Simone Blomberg, University of Queensland

Some of the most important macroevolution papers in MEE from the past 10 years include articles that have warned researchers and put caveats on what can be determined from various macroevolutionary models.

A particular favorite is the paper by Ho and Ané (2014), which points out that there are serious difficulties in the identifiability of Ornstein-Uhlenbeck models of trait evolution. This has not deterred publication of many papers that use or extend the Ornstein-Uhlenbeck model. Another is the paper by Cooper et al. (2016), who point out the pitfalls that often beset the unwary users of phylogenetic comparative methods. It is a call to users (watch out!) and to methods developers (be clearer!).

The field of macroevolution is particularly heavy on theory and methods but good, relevant data are harder to come by. The Special Feature of MEE devoted to uniting molecular and fossil approaches is an important resource for those interested in modelling the entire evolutionary history of a group (not just the extant taxa!).

Some of the most important papers in macroevolution have been MEE methods papers. A particular citation stand-out is Revell (2012), who continues to provide the field with much-needed analysis and visualisation tools in R. Other highly-cited papers include Yu et al. (2017) on flexible plotting of trees in R, and FitzJohn (2012) on state-dependent speciation and extinction models in R. In a field with complex data types, great tools for visualisation and analysis are always in demand. R is fast becoming the best pathway to access the latest methods.

Will Pearse, Imperial College London

Everyone knows MEE articles are uniformly brilliant (right?!) but not everyone knows just how good they are for helping graduate students teach themselves about topics. Below are a selection of the papers I find myself constantly flinging to interested students to help them find their feet and learn how to learn.

We spend so long telling undergraduates about classic brawls in the literature from hundreds of years ago that I think they mistakenly think scientists are curmudgeonly and hate everyone who disagrees with them. Do not log-transform data by O’Hara & Kotze (2010) and For testing the significance of regression coefficients, go ahead and log‐transform count data by Anthony R. Ives (2015) are written engagingly, fairly, and with good humour (read the acknowledgements of the first!) are two of my favourite ways to show students just how much fun the literature can be and how there is rarely “one right and true answer”:

Almost every month I send someone this classic guide to Mantel tests and their potential use in spatial analysis: Should the Mantel test be used in spatial analysis? by Legendre et al. (2015).

Phylogeny isn’t just useful for purely evolutionary studies, it’s also useful for community ecological studies too. This is a paper I read and immediately loved: a thoughtful introduction to modern phylogenetic methods in ecology that goes well beyond ‘the usual suspects’ of SESmpd and the like: The statistical need to include phylogeny in trait‐based analyses of community composition by Li & Ives (2017).

Finally, my pick for ‘future classic’, a thought-provoking essay on the use of priors in Bayesian analysis of ecological data. You don’t have to agree with everything in this wonderful paper, but I guarantee that by the end of it you’ll think differently about your analyses. Inferring extinction year using a Bayesian approach by Kodikara et al. (2020).

Michael Matschiner, University of Zurich

Among the Methods papers that were particularly influential for me are the following:

Revell LJ (2012) phytools: an R package for phylogenetic comparative biology (and other things). Phytools is the Swiss army knife for the analysis of phylogenetic trees. It allows tree manipulation (e.g. pruning taxa, merging trees), the application of a range of tests (e.g. for constant diversification), simulation, and plotting of lineage accumulation or trait diversification over time. The actively maintained associated blog http://blog.phytools.org, on which Liam Revell regularly informs about updates to Phytools and demonstrates the use of new functions is also extremely helpful.

Rabosky DL, Grundler M, Anderson C et al. (2014) BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. The programs BAMM and BAMMtools have been extremely influential for studies investigating diversification rates over time and among groups. The program has for example been used to support a correlation of rates of speciation and morphological evolution or a correlation of speciation rate with latitude in marine fishes. The webpage associated with BAMM and BAMMtools http://bamm-project.org is also very informative.

FitzJohn RG (2012) Diversitree: comparative phylogenetic analyses of diversification in R. The R package Diversitree was one of the first to implement the BiSSE and QuaSSE analyses for speciation-rate dependence on binary or quantitative traits, and introduced the MuSSE analysis as a multi-state extension of BiSSE. The implemented version of the BiSSE analysis can also account for incomplete taxon sampling, making it particularly useful for application to real-world datasets.

To find out about dating phylogenies containing fossil taxa, read about our article highlighted for Volume 3: paleotree: A Retrospective

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