A biologist’s guide to Bayesian phylogenetic analysis
Open accessAbstract
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use.
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Significant effort has been dedicated to understanding protein sequences as emerging from tree-structured evolutionary processes over time or coalescent processes in reverse time.
“However, significant effort has been dedicated to understanding protein sequences as emerging from tree-structured evolutionary processes over time or coalescent processes in reverse time 90,91.”
From Learning the protein language: Evolution, structure, and function (2021) · cites this paper as [90]
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Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687 · see citing works
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · see citing works
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
Meredith, R. W., Janečka, J. E., Gatesy, J., Ryder, O. A., Fisher, C. A., Teeling, E. C., Goodbla, A., Eizirik, E., Simão, T. L. L., Stadler, T., et al. (2011) · Science · doi:10.1126/science.1211028 · Cited by 1,464 · see citing works
Estimating the rate of evolution of the rate of molecular evolution
Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317 · see citing works
Estimating the pattern of nucleotide substitution
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178256 · Cited by 1,076 · see citing works
Self-citationA Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., & Rasnitsyn, A. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys058 · Cited by 930 · see citing works
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2016) · Nature · doi:10.1038/nature19417 · Cited by 928 · see citing works
Inferring speciation times under an episodic molecular clock
Rannala, B., & Yang, Z. (2007) · Systematic Biology · doi:10.1080/10635150701420643 · Cited by 475 · see citing works
Self-citationUncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales
dos Reis, M., Thawornwattana, Y., Angelis, K., Telford, M. J., Donoghue, P. C. J., & Yang, Z. (2015) · Current Biology · doi:10.1016/j.cub.2015.09.066 · Cited by 471 · see citing works
Self-citationBayesian molecular clock dating of species divergences in the genomics era
dos Reis, M., Donoghue, P. C. J., & Yang, Z. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.8 · Cited by 339 · see citing works
Self-citationIdentifiability of Parameters in MCMC Bayesian Inference of Phylogeny
Rannala, B. (2002) · Systematic Biology · doi:10.1080/10635150290102429 · Cited by 190 · see citing works
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Learning the protein language: Evolution, structure, and function
Bepler, T., & Berger, B. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.017 · Cited by 483 · see citing works
- Authors
- Nascimento, F. F., Reis, M. D., & Yang, Z.
- Affiliations
- University of Oxford (GB)
- Queen Mary University of London (GB)
- University College London (GB)
- Corresponding author
- Nascimento, Fabrícia F.
- Yang, Ziheng
- Venue
- Nature Ecology & Evolution
- Published
- 2017-09-21
- Volume
- 1
- Issue
- 10
- Pages
- 1446-1454
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC5624502
- OpenAlex
- W2746487413
- Cited by
- 212
- References
- 11
- Citations by year
- 2026: 9 · 2025: 23 · 2024: 21 · 2023: 30 · 2022: 22 · 2021: 28 · 2020: 47 · 2019: 22 · 2018: 9 · 2017: 1
- FWCI
- 2.02
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
- Funders
- British Academy
- Royal Society
- Biotechnology and Biological Sciences Research Council (BB/P006493/1, BB/K000896/1, BB/N000609/1)
- Natural Environment Research Council (NE/C509974/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Physical Sciences › Mathematics › Statistics and Probability › Markov Chains and Monte Carlo Methods
- Keywords
- Bayesian phylogenetics, Markov chain Monte Carlo, prior specification, substitution models, data partitioning, molecular phylogeny
- MeSH terms
- Bayes Theorem, Markov Chains, Models, Genetic, Monte Carlo Method, Phylogeny, Software, Evolution, Molecular
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