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Treelists, constraints and logfiles for: Relative time constraints improve molecular dating

Citation

Boussau, Bastien (2022), Treelists, constraints and logfiles for: Relative time constraints improve molecular dating, Dryad, Dataset, https://doi.org/10.5061/dryad.s4mw6m958

Abstract

Dating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. This is the case for instance for horizontal gene transfer events and ancient coevolutionary relationships such as (endo)symbioses, which can imply temporal relationships between two nodes in a phylogeny (Davin et al. 2018). This can be particularly helpful when the geological record is sparse, e.g. for microorganisms, which represent the vast majority of extant and extinct biodiversity. Here, we demonstrate that relative age constraints, when combined with fossil calibrations, can significantly improve both the accuracy and resolution of molecular clock estimates. We provide an implementation of relative age constraints in RevBayes (Hoehna et al. 2016) that can be combined in a modular manner with the wide range of molecular dating methods available in the software. To validate our method in a realistic data setting we apply it to two data sets of 40 Cyanobacteria and 62 Archaea respectively, and provide cross-validations of fossil calibrations and relative age constraints.

Methods

The data set contains, for both Archaea and Bacteria:

1. concatenated CAT GTR treelists used in approximating the phylogenetic likelihood, obtained using PhyloBayes
2. constraints used for the dating;
3. log files used in producing the plots in the paper

Funding

Centre National de la Recherche Scientifique

H2020 European Research Council, Award: 714774

NERC Environmental Bioinformatics Centre, Award: NE/P00251X/1