An empirical guide for producing a dated phylogeny with treePL in a maximum likelihood framework

treePL uses a penalised likelihood approach to produce a dated phylogeny in a maximum likelihood framework. Since its publication in 2012, few resources have been developed to explain how to use it properly. In this guide, I provide a step-by-step protocol for producing a dated phylogeny using treePL, based on my experience building a large dated phylogeny with it and conducting additional tests on a smaller phylogeny. I also provide the necessary data to reproduce one of the example phylogenies presented. I compare these treePL phylogenies to BEAST2-built counterparts. Even though I cannot explain precisely how treePL works, the evidence discussed in this guide suggest that the empirical protocol presented is reliable.

[1]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[2]  Koichiro Tamura,et al.  Fast and Accurate Estimates of Divergence Times from Big Data , 2017, Molecular biology and evolution.

[3]  Maxim Teslenko,et al.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.

[4]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[5]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

[6]  Pamela S Soltis,et al.  Origin of angiosperms and the puzzle of the Jurassic gap , 2019, Nature Plants.

[7]  M. Réjou‐Méchain,et al.  A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses , 2019, bioRxiv.

[8]  Brian C. O'Meara,et al.  treePL: divergence time estimation using penalized likelihood for large phylogenies , 2012, Bioinform..

[9]  Sebastián Duchêne,et al.  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis , 2018, bioRxiv.

[10]  Mark A. Miller,et al.  Creating the CIPRES Science Gateway for inference of large phylogenetic trees , 2010, 2010 Gateway Computing Environments Workshop (GCE).

[11]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[12]  Liam J. Revell,et al.  phytools: an R package for phylogenetic comparative biology (and other things) , 2012 .

[13]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[14]  Kévin J. L. Maurin.  A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences , 2020, PhytoKeys.