Flouri, Tomáš;
Huang, Jun;
Jiao, Xiyun;
Kapli, Paschalia;
Rannala, Bruce;
Yang, Ziheng;
(2022)
Bayesian phylogenetic inference using relaxed-clocks and the multispecies coalescent.
Molecular Biology and Evolution
10.1093/molbev/msac161.
(In press).
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Abstract
The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program BPP assumes a molecular clock and the Jukes-Cantor model, and is suitable for analyzing genomic data from closely related species. Here we extend our implementation to more general substitution models and relaxed clocks to allow the rate to vary among species. The MSCwith-relaxed-clock model allows the estimation of species divergence times and ancestral population sizes using genomic sequences sampled from contemporary species when the strict clock assumption is violated, and provides a simulation framework for evaluating species tree estimation methods. We conducted simulations and analyzed two real datasets to evaluate the utility of the new models. We confirm that the clock-JC model is adequate for inference of shallow trees with closely related species, but it is important to account for clock violation for distant species. Our simulation suggests that there is valuable phylogenetic information in the gene-tree branch lengths even if the molecular clock assumption is seriously violated, and the relaxed-clock models implemented in BPP are able to extract such information. Our Markov chain Monte Carlo (MCMC) algorithms suffer from mixing problems when used for species tree estimation under the relaxed clock and we discuss possible improvements. We conclude that the new models are currently most effective for estimating population parameters such as species divergence times when the species tree is fixed.
| Type: | Article |
|---|---|
| Title: | Bayesian phylogenetic inference using relaxed-clocks and the multispecies coalescent |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/molbev/msac161 |
| Publisher version: | https://doi.org/10.1093/molbev/msac161 |
| Language: | English |
| Additional information: | © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). |
| Keywords: | Multispecies coalescent, molecular clock, relaxed clock, BPP, species tree |
| UCL classification: | UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10153117 |
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