BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
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Abstract
Abstract Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release. Author summary Bayesian phylogenetic inference methods have undergone considerable development in recent years, and joint modelling of rich evolutionary data, including genomes, phenotypes and fossil occurrences is increasingly common. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing scientific software is increasingly crucial to advancement in many fields of biology. The challenges range from practical software development and engineering, distributed team coordination, conceptual development and statistical modelling, to validation and testing. BEAST 2 is one such computational software platform for phylogenetics, population genetics and phylodynamics, and was first announced over 4 years ago. Here we describe the full range of new tools and models available on the BEAST 2.5 platform, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.
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Methods for inferring latent phylogenetic trees are frustrated by long run times and poor scalability to large datasets.
“Methods for inferring these latent phylogenetic trees continue to be of substantial interest 92-94, but are frustrated by long run times and poor scalability to large datasets.”
From Learning the protein language: Evolution, structure, and function (2021) · cites this paper as [94]
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Evolutionary Rates and Hbv: Issues of Rate Estimation with Bayesian Molecular Methods
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Self-citationA Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics
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Self-citationPosterior Predictive Bayesian Phylogenetic Model Selection
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Uwamahoro, N., Qu, Y., Jeličić, B., Lo, T. L., Beaurepaire, C., Bantun, F., Quenault, T., Boag, P. R., Ramm, G., Callaghan, J. M., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002613 · Cited by 60 · see citing works
Phylogeography by diffusion on a sphere: whole world phylogeography
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Self-citationPseudo Dollo models for the evolution of binary characters along a treePreprint
Bouckaert, R., & Robbeets, M. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/207571 · Cited by 54 · see citing works
Self-citationInference of recombination maps from a single pair of genomes and its application to ancient samples
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Infectious disease: Tough choices to reduce Ebola transmission
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Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework
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Self-citationInferring Ancestral Recombination Graphs from Bacterial Genomic Data
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Self-citationBayesian Selection of Nucleotide Substitution Models and Their Site Assignments
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Self-citationBayesian inference of fine-scale recombination rates using population genomic data
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Phylodynamic Model Adequacy Using Posterior Predictive Simulations
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Self-citationDivergence Estimation in the Presence of Incomplete Lineage Sorting and Migration
Jones, G. R. (2018) · Systematic Biology · doi:10.1093/sysbio/syy041 · Cited by 38 · see citing works
Self-citationMüller, N. F., Dudas, G., & Stadler, T. (2019) · Virus Evolution · doi:10.1093/ve/vez030 · Cited by 36 · see citing works
Self-citationP3: Phylogenetic Posterior Prediction in RevBayes
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Self-citationNovel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales
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Self-citationLocal and relaxed clocks: the best of both worlds
Fourment, M., & Darling, A. E. (2018) · PeerJ · doi:10.7717/peerj.5140 · Cited by 21 · see citing works
Self-citationJoint inference of species histories and gene flowPreprint
Müller, N. F., Ogilvie, H. A., Zhang, C., Fontaine, M. C., Amaya-Romero, J.-E., Drummond, A. J., & Stadler, T. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/348391 · Cited by 18 · see citing works
Self-citationNovel Integrative Modeling of Molecules and Morphology across Evolutionary TimescalesPreprint
Ogilvie, H., Mendes, F. K., Vaughan, T. G., Matzke, N. J., Stadler, T., Welch, D., & Drummond, A. J. (2018) · ResearchSpace (University of Auckland) · doi:10.1101/242875 · Cited by 10 · see citing works
Self-citationCapturing heterotachy through multi-gamma site modelsPreprint
Bouckaert, R., & Lockhart, P. J. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/018101 · Cited by 6 · see citing works
Self-citationSynthetic Language Generation and Model Validation in BEAST2Preprint
Bradley, S. (2016) · arXiv (Cornell University) · doi:10.48550/arxiv.1607.07931 · Cited by 1 · see citing works
fkmendes/SSE: First release of SSE package
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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
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Self-citationEvaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
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Self-citationHyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
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Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
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Phylogenetic tree building in the genomic age
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Variant analysis of SARS-CoV-2 genomes
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Learning the protein language: Evolution, structure, and function
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COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
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Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
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Self-citationThe origins and spread of domestic horses from the Western Eurasian steppes
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Drivers and dynamics of a massive adaptive radiation in cichlid fishes
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Self-citationEmergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020Preprint
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Self-citationEpigenetic patterns in a complete human genome
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Widespread introgression across a phylogeny of 155 Drosophila genomes
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Incongruence in the phylogenomics era
Steenwyk, J. L., Li, Y., Zhou, X., Shen, X., & Rokas, A. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00620-x · Cited by 267 · see citing works
Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM
Acman, M., Wang, R., van Dorp, L., Shaw, L. P., Wang, Q., Luhmann, N., Yin, Y., Sun, S., Chen, H., Wang, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28819-2 · Cited by 256 · see citing works
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
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Self-citationiTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists
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Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2
Wu, H., Xing, N., Meng, K., Fu, B., Xue, W., Dong, P., Tang, W., Xiao, Y., Liu, G., Luo, H., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.11.005 · Cited by 224 · see citing works
Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics
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Towards reproducible computational drug discovery
Schaduangrat, N., Lampa, S., Simeon, S., Gleeson, M. P., Spjuth, O., & Nantasenamat, C. (2020) · Journal of Cheminformatics · doi:10.1186/s13321-020-0408-x · Cited by 208 · see citing works
Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer
Mattocks, J. A., Jung, J. J., Lin, C., Dong, Z., Yennawar, N. H., Featherston, E. R., Kang-Yun, C. S., Hamilton, T. A., Park, D. M., Boal, A. K., et al. (2023) · Nature · doi:10.1038/s41586-023-05945-5 · Cited by 208 · see citing works
Triangulation supports agricultural spread of the Transeurasian languages
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Self-citationIsabel, S., Graña-Miraglia, L., Gutierrez, J. M., Bundalovic-Torma, C., Groves, H. E., Isabel, M. R., Eshaghi, A., Patel, S. N., Gubbay, J. B., Poutanen, T., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-70827-z · Cited by 197 · see citing works
Tracking the COVID-19 pandemic in Australia using genomics
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Self-citationAdaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model
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Self-citationThe evolution and changing ecology of the African hominid oral microbiome
Yates, J. A. F., Velsko, I. M., Aron, F., Posth, C., Hofman, C. A., Austin, R. M., Parker, C., Mann, A. E., Nägele, K., Arthur, K. W., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021655118 · Cited by 176 · see citing works
Integrative approaches for species delimitation in Ascomycota
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Aphid Transmission of Potyvirus: The Largest Plant-Infecting RNA Virus Genus
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Self-citationThe dental proteome of Homo antecessor
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Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
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Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
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Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations
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Self-citationPhylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)
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Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences
Kim, Y.-K., Jo, S., Cheon, S.-H., Joo, M.-J., Hong, J.-R., Kwak, M., & Kim, K. J. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.00022 · Cited by 152 · see citing works
Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
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Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time
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Supergene origin and maintenance in Atlantic cod
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Phylogenomics and the flowering plant tree of life
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The source of the Black Death in fourteenth-century central Eurasia
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Self-citationInvestigating species boundaries in Colletotrichum
Bhunjun, C. S., Phukhamsakda, C., Jayawardena, R. S., Jeewon, R., Promputtha, I., & Hyde, K. D. (2021) · Fungal Diversity · doi:10.1007/s13225-021-00471-z · Cited by 153 · see citing works
Hufsky, F., Lamkiewicz, K., Almeida, A., Aouacheria, A., Arighi, C. N., Bateman, A. G., Baumbach, J., Beerenwinkel, N., Brandt, C., Cacciabue, M., et al. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa232 · Cited by 141 · see citing works
Self-citationPopulation genomics of apricots unravels domestication history and adaptive events
Groppi, A., Liu, S., Cornille, A., Decroocq, S., Bui, Q. T., Tricon, D., Cruaud, C., Arribat, S., Belser, C., Marande, W., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24283-6 · Cited by 139 · see citing works
A higher-rank classification for rust fungi, with notes on genera
Aime, M. C., & McTaggart, A. R. (2020) · Fungal Systematics and Evolution · doi:10.3114/fuse.2021.07.02 · Cited by 137 · see citing works
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Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous
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The origin and speciation of orchids
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Genome-enabled discovery of anthraquinone biosynthesis in Senna tora
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Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era
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The origin and early spread of SARS-CoV-2 in Europe
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Self-citationHerded and hunted goat genomes from the dawn of domestication in the Zagros Mountains
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StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent
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- Authors
- Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., Matschiner, M., Mendes, F. K., Müller, N. F., Ogilvie, H. A., du Plessis, L., Popinga, A., Rambaut, A., Rasmussen, D., Siveroni, I., Suchard, M. A., Wu, C.-H., Xie, D., Zhang, C., Stadler, T., & Drummond, A. J.
- Affiliations
- University of Auckland (NZ)
- SIB Swiss Institute of Bioinformatics (CH)
- The University of Melbourne (AU)
- University of Technology Sydney (AU)
- University of Otago (NZ)
- University of Gothenburg (SE)
- Max Planck Institute of Geoanthropology (DE)
- University of Basel (CH)
- Rice University (US)
- University of Edinburgh (GB)
- North Carolina State University (US)
- Imperial College London (GB)
- University of California, Los Angeles (US)
- University of Oxford (GB)
- Chinese Academy of Sciences (CN)
- Corresponding author
- Bouckaert, Remco
- Vaughan, Timothy G.
- Duchêne, Sebastián
- Fourment, Mathieu
- Gavryushkina, Alexandra
- Heled, Joseph
- Jones, Graham
- Kühnert, Denise
- Matschiner, Michael
- Mendes, Fábio K.
- Müller, Nicola F.
- Ogilvie, Huw A.
- Popinga, Alex
- Rambaut, Andrew
- Rasmussen, David
- Siveroni, Igor
- Suchard, Marc A.
- Wu, Chieh-Hsi
- Xie, Dong
- Zhang, Chi
- Stadler, Tanja
- Drummond, Alexei J.
- ORCID
- Bouckaert, Remco
- Vaughan, Timothy G.
- Barido-Sottani, Joëlle
- Duchêne, Sebastián
- Fourment, Mathieu
- Gavryushkina, Alexandra
- Heled, Joseph
- Jones, Graham
- Kühnert, Denise
- De Maio, Nicola
- Matschiner, Michael
- Mendes, Fábio K.
- Müller, Nicola F.
- Ogilvie, Huw A.
- Popinga, Alex
- Rambaut, Andrew
- Rasmussen, David
- Siveroni, Igor
- Suchard, Marc A.
- Wu, Chieh-Hsi
- Xie, Dong
- Zhang, Chi
- Stadler, Tanja
- Drummond, Alexei J.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2019-04-08
- Volume
- 15
- Issue
- 4
- Pages
- e1006650
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC6472827
- OpenAlex
- W2901954177
- Cited by
- 4,556
- References
- 130
- Citations by year
- 2026: 607 · 2025: 744 · 2024: 694 · 2023: 667 · 2022: 721 · 2021: 638 · 2020: 435 · 2019: 47 · 2018: 1 · 2014: 2
- FWCI
- 152.40
- Type
- journal article
- Language
- en
- Update notices
- new_version (2019-04-18)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository for Publications and Research Data (ETH Zurich) (publishedVersion, cc-by)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- ePrints Soton (University of Southampton) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- UTS ePRESS (University of Technology Sydney) (submittedVersion)
- UTS ePRESS (University of Technology Sydney) (submittedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Rice Research Repository (Rice University) (submittedVersion, cc-by)
- ResearchSpace (University of Auckland) (submittedVersion, cc-by)
- Spiral (Imperial College London) (submittedVersion, other-oa)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Marsden Fund (16-UOA-277)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- BEAST2, Bayesian phylogenetics, model hierarchy, software design, model compatibility, genome sequence, sampling date, radiocarbon dates, fossil occurrences, phenotypic data
- MeSH terms
- Animals, Bayes Theorem, Computer Simulation, Biological Evolution, Humans, Markov Chains, Models, Genetic, Monte Carlo Method, Phylogeny, Software, Evolution, Molecular, Computational Biology
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