publication . Preprint . 2020

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

Maurin, Kévin J. L.;
Open Access English
  • Published: 16 Aug 2020
Abstract
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...
Subjects
free text keywords: Quantitative Biology - Populations and Evolution
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1. Bouckaert R, Heled J, Kühnert D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 2014; 10:e1003537. [OpenAIRE]

2. Ronquist F, Teslenko M, Van Der Mark P, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 2012; 61:539-542 [OpenAIRE]

3. Mello B, Tao Q, Tamura K, et al. Fast and accurate estimates of divergence times from big data. Molecular Biology and Evolution 2017; 34:45-50.

4. Janssens SB, Couvreur TL, Mertens A, et al. A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses. Biodiversity Data Journal 2020; 8:e39677.

5. Li H-T, Yi T-S, Gao L-M, et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants 2019; 5:46.

6. Smith SA, O'Meara BC. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 2012; 28:2689-2690.

7. Bouckaert R, Vaughan TG, Barido-Sottani J, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology 2019; 15:e1006650.

8. Maurin KJL. A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S-26S repeat region sequences. PhytoKeys 2020; 155:15-32. [OpenAIRE]

9. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312-1313. [OpenAIRE]

10. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: 2010 gateway computing environments workshop (GCE). 2010; 1-8.

11. Revell LJ. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 2012; 3:217-223.

12. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria 2019.

Abstract
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...
Subjects
free text keywords: Quantitative Biology - Populations and Evolution
Download from

1. Bouckaert R, Heled J, Kühnert D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 2014; 10:e1003537. [OpenAIRE]

2. Ronquist F, Teslenko M, Van Der Mark P, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 2012; 61:539-542 [OpenAIRE]

3. Mello B, Tao Q, Tamura K, et al. Fast and accurate estimates of divergence times from big data. Molecular Biology and Evolution 2017; 34:45-50.

4. Janssens SB, Couvreur TL, Mertens A, et al. A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses. Biodiversity Data Journal 2020; 8:e39677.

5. Li H-T, Yi T-S, Gao L-M, et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants 2019; 5:46.

6. Smith SA, O'Meara BC. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 2012; 28:2689-2690.

7. Bouckaert R, Vaughan TG, Barido-Sottani J, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology 2019; 15:e1006650.

8. Maurin KJL. A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S-26S repeat region sequences. PhytoKeys 2020; 155:15-32. [OpenAIRE]

9. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312-1313. [OpenAIRE]

10. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: 2010 gateway computing environments workshop (GCE). 2010; 1-8.

11. Revell LJ. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 2012; 3:217-223.

12. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria 2019.

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