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

TL;DR

This paper provides a practical, step-by-step guide for using treePL to produce dated phylogenies within a maximum likelihood framework, including comparisons to BEAST2 results and reproducible examples.

Contribution

It offers the first comprehensive, empirically tested protocol for effectively applying treePL for dated phylogeny construction, with reproducible data and validation against other methods.

Findings

The protocol reliably produces dated phylogenies using treePL.

TreePL results are comparable to those from BEAST2.

The guide includes reproducible example data and tests.

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 suggest that the empirical protocol presented is reliable.