Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent

Flouri，Tomáš1; Huang，Jun1,2; Jiao，Xiyun1,3; Kapli，Paschalia1; Rannala，Bruce4; Yang，Ziheng1

2022-08-01

10.1093/molbev/msac161

MOLECULAR BIOLOGY AND EVOLUTION   Impact Factor & Quartile

0737-4038

1537-1719

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 MSC-with-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 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.

bpp molecular clock multispecies coalescent relaxed clock species tree

SCI

English

Others

Biotechnology and Biological Sciences Research Council[BB/P006493/1];Biotechnology and Biological Sciences Research Council[BB/R016240/1];Biotechnology and Biological Sciences Research Council[BB/R016240/1];National Institutes of Health[GM123306];

WOS:000838809000002

MOLECULAR BIOLOGY & GENETICS

2-s2.0-85135990661

Scopus

1.Department of Genetics Evolution and Environment,University College London,London,Gower Street,WC1E 6BT,United Kingdom
2.School of Biomedical Engineering,Capital Medical University,Beijing,100069,China
3.Department of Statistics and Data Science,China Southern University of Science and Technology,Guangdong,Shenzhen,518055,China
4.Department of Evolution and Ecology,University of California,Davis,95616,United States

Flouri，Tomáš,Huang，Jun,Jiao，Xiyun,et al. Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent[J]. MOLECULAR BIOLOGY AND EVOLUTION,2022,39(8).

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,39(8).

Flouri，Tomáš,et al."Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent".MOLECULAR BIOLOGY AND EVOLUTION 39.8(2022).