BEAST 2: a software platform for Bayesian evolutionary analysis
Open accessAbstract
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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The model implemented in BEAST2 allows transitions between conserved and accelerated rates in both directions.
“The model implemented in BEAST2 allows transitions between conserved and accelerated rates in both directions.”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Bouckaert et al. 2014
The Results section, under “New evolutionary models in BEAST 2” (page not supplied), describes lower and faster site-rate categories, but does not say that a model permits transitions between conserved and accelerated rates in both directions. Searches for that phrasing and for switching between slow and fast evolutionary rates found no passage establishing the claimed behavior. (LLM, conf=0.72)
Experimental — accuracy not yet measuredIn the BEAST2 comparison, the accuracy of both methods increases as the ratio between accelerated and conserved rates increases.
“As seen in figure 3, the accuracy of both methods increases as the ratio between accelerated and conserved rates increases”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Bouckaert et al. 2014
In Results > New evolutionary models in BEAST 2 (page unavailable), Figure 3 concerns the effective reproduction number during a simulated epidemic, not a comparison of two methods. Searches for accuracy and for accelerated-versus-conserved rate ratios found no passage in our copy addressing the claimed trend. (LLM, conf=0.76)
Experimental — accuracy not yet measured
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Cites
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778 · see citing works
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works
BEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 12,898 · see citing works
Self-citationTamura, K., & Nei, M. (1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040023 · Cited by 11,267 · see citing works
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss075 · Cited by 9,991 · see citing works
Self-citationDating 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 · cited 1× · see citing works
“In particular it implements relaxed clocks [3], non-parametric coalescent analysis [4,5], multispecies coalescent inference [6], phylogeography [7,8] and others.”
MethodSelf-citationBayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
Drummond, A. J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi103 · Cited by 3,094 · see citing works
Self-citation(1986) · Cited by 2,570 · see citing works
Bayesian inference of species trees from multilocus data
Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453 · see citing works
Self-citationBayesian Phylogeography Finds Its Roots
Lemey, P., Rambaut, A., Drummond, A. J., & Suchard, M. A. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000520 · Cited by 1,790 · see citing works
Self-citationBeerli, P., & Felsenstein, J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.081068098 · Cited by 1,701 · see citing works
Baele, G., Lemey, P., Bedford, T., Rambaut, A., Suchard, M. A., & Alekseyenko, A. V. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss084 · Cited by 1,131 · see citing works
Self-citationBeerli, P., & Felsenstein, J. (1999) · Genetics · doi:10.1093/genetics/152.2.763 · Cited by 985 · see citing works
Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & RoyChoudhury, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss086 · Cited by 974 · see citing works
Self-citationComparison of Bayesian and maximum-likelihood inference of population genetic parameters
Beerli, P. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti803 · Cited by 928 · see citing works
Bayesian inference of population size history from multiple loci
Heled, J., & Drummond, A. J. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-289 · Cited by 739 · see citing works
Self-citationAyres, D. L., Darling, A. E., Zwickl, D. J., Beerli, P., Holder, M. T., Lewis, P. O., Huelsenbeck, J. P., Ronquist, F., Swofford, D. L., Cummings, M. P., et al. (2011) · Systematic Biology · doi:10.1093/sysbio/syr100 · Cited by 707 · see citing works
Self-citationDensiTree: making sense of sets of phylogenetic trees
Bouckaert, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq110 · Cited by 704 · see citing works
Self-citationPhylogeography Takes a Relaxed Random Walk in Continuous Space and Time
Lemey, P., Rambaut, A., Welch, J. J., & Suchard, M. A. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq067 · Cited by 688 · see citing works
Self-citationSmooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics
Minin, V. N., Bloomquist, E. W., & Suchard, M. A. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn090 · Cited by 680 · see citing works
Self-citationStadler, T., Kühnert, D., Bonhoeffer, S., & Drummond, A. J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207965110 · Cited by 515 · see citing works
Self-citationMany-core algorithms for statistical phylogenetics
Suchard, M. A., & Rambaut, A. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp244 · Cited by 417 · see citing works
Self-citationVARIABLE SELECTION IN REGRESSION MODELS
Rao, M. S., & M.Venkataramanaih, M. S. (2013) · International Journal of Research in Commerce, IT and Management · Cited by 402 · see citing works
van de Laar, T., Pybus, O. G., Bruisten, S. M., Brown, D. J., Nelson, M. R., Bhagani, S., Vogel, M., Baumgarten, A., Chaix, M., Fisher, M., et al. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.02.006 · Cited by 313 · see citing works
Molecular phylogeny and evolution of primate mitochondrial DNA.
Hayasaka, K., Gojobori, T., & Horai, S. (1988) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040524 · Cited by 179 · see citing works
Kühnert, D., Stadler, T., Vaughan, T. G., & Drummond, A. J. (2014) · Journal of The Royal Society Interface · doi:10.1098/rsif.2013.1106 · Cited by 131 · see citing works
Self-citationWagner and Dollo: A Stochastic Duet by Composing Two Parsimonious Solos
Alekseyenko, A. V., Lee, C. J., & Suchard, M. A. (2008) · Systematic Biology · doi:10.1080/10635150802434394 · Cited by 89 · see citing works
Self-citationEvolutionary Rates and Hbv: Issues of Rate Estimation with Bayesian Molecular Methods
Bouckaert, R., Alvarado-Mora, M. V., & Pinho, J. R. R. (2005) · Antiviral Therapy · doi:10.3851/imp2656 · Cited by 67 · see citing works
Self-citationA Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics
Vaughan, T. G., & Drummond, A. J. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst057 · Cited by 65 · see citing works
Self-citationBayesian Selection of Nucleotide Substitution Models and Their Site Assignments
Wu, C., Suchard, M. A., & Drummond, A. J. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss258 · Cited by 48 · see citing works
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- [27]Vaughan T, Kühnert D, Popinga A, Welch D, Drummond A (2013) Efficient sampling of multi-type trees for bayesian phylogenetic inference. In press.
Cited by
Sorted by citations
ModelFinder: fast model selection for accurate phylogenetic estimates
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017) · Nature Methods · doi:10.1038/nmeth.4285 · Cited by 18,449 · see citing works
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159 · see citing works
Self-citationYu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. (2016) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12628 · Cited by 4,821 · see citing works
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006650 · Cited by 4,556 · see citing works
Self-citationBayesian phylogenetic and phylodynamic data integration using BEAST 1.10
Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018) · Virus Evolution · doi:10.1093/ve/vey016 · Cited by 3,749 · see citing works
Self-citationRDP4: Detection and analysis of recombination patterns in virus genomes
Martin, D. P., Murrell, B., Golden, M., Khoosal, A., & Muhire, B. M. (2015) · Virus Evolution · doi:10.1093/ve/vev003 · Cited by 3,272 · see citing works
ASAP: assemble species by automatic partitioning
Puillandre, N., Brouillet, S., & Achaz, G. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13281 · Cited by 1,779 · see citing works
Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts
LaJeunesse, T. C., Parkinson, J. E., Gabrielson, P. W., Jeong, H. J., Reimer, J. D., Voolstra, C. R., & Santos, S. R. (2018) · Current Biology · doi:10.1016/j.cub.2018.07.008 · Cited by 1,647 · see citing works
Xie, J., Chen, Y., Cai, G., Cai, R., Hu, Z., & Wang, H. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad359 · Cited by 1,396 · see citing works
Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017
Nagasawa, K., Matsushima, Y., Motoya, T., Mizukoshi, F., Ueki, Y., Sakon, N., Murakami, K., Shimizu, T., Okabe, N., Nagata, N., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00001 · Cited by 1,258 · see citing works
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., et al. (2021) · Nature · doi:10.1038/s41586-021-03291-y · Cited by 1,097 · see citing works
bModelTest: Bayesian phylogenetic site model averaging and model comparison
Bouckaert, R., & Drummond, A. J. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0890-6 · Cited by 903 · see citing works
Self-citationHöhna, S., Landis, M. J., Heath, T. A., Boussau, B., Lartillot, N., Moore, B. R., Huelsenbeck, J. P., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syw021 · Cited by 815 · see citing works
Origin of angiosperms and the puzzle of the Jurassic gap
Li, H., Yi, T., Gao, L., Ma, P., Zhang, T., Yang, J., Gitzendanner, M. A., Fritsch, P. W., Cai, J., Luo, Y., et al. (2019) · Nature Plants · doi:10.1038/s41477-019-0421-0 · Cited by 810 · see citing works
HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
Pond, S. L. K., Poon, A. F. Y., Velazquez, R., Weaver, S., Hepler, N. L., Murrell, B., Shank, S. D., Magalis, B. R., Bouvier, D., Nekrutenko, A., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz197 · Cited by 724 · see citing works
Ancient hybridization fuels rapid cichlid fish adaptive radiations
Meier, J. I., Marques, D. A., Mwaiko, S., Wagner, C. E., Excoffier, L., & D, O. S. C. (2017) · Nature Communications · doi:10.1038/ncomms14363 · Cited by 717 · see citing works
High-level classification of the Fungi and a tool for evolutionary ecological analyses
Tedersoo, L., Ramirez, S. S., Kõljalg, U., Bahram, M., Döring, M., Schigel, D., May, T. W., Ryberg, M. K., & Abarenkov, K. (2018) · Fungal Diversity · doi:10.1007/s13225-018-0401-0 · Cited by 697 · see citing works
The global distribution and spread of the mobilized colistin resistance gene mcr-1
Wang, R., van Dorp, L., Shaw, L. P., Bradley, P., Wang, Q., Wang, X., Jin, L., Zhang, Q., Liu, Y., Rieux, A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03205-z · Cited by 677 · see citing works
Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes
Moura, A., Criscuolo, A., Pouseele, H., Maury, M. M., Leclercq, A., Tarr, C. L., Björkman, J., Dallman, T. J., Reimer, A. R., Enouf, V., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.185 · Cited by 666 · see citing works
Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot
Xing, Y., & Ree, R. H. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616063114 · Cited by 657 · see citing works
Wang, L.-G., Lam, T. T., Xu, S., Dai, Z., Zhou, L., Feng, T., Guo, P., Dunn, C. W., Jones, B. R., Bradley, T. C., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz240 · Cited by 621 · see citing works
Persistent HIV-1 replication maintains the tissue reservoir during therapy
Lorenzo-Redondo, R., Fryer, H. R., Bedford, T., Kim, E., Archer, J. P., Pond, S. L. K., Chung, Y., Penugonda, S., Chipman, J. G., Fletcher, C. V., et al. (2016) · Nature · doi:10.1038/nature16933 · Cited by 620 · see citing works
Self-citationEstablishment and cryptic transmission of Zika virus in Brazil and the Americas
Faria, N. R., Quick, J., Claro, I. M., Thézé, J., de Jesus, J. G., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., da Costa, A. C., et al. (2017) · Nature · doi:10.1038/nature22401 · Cited by 616 · see citing works
Self-citationEarly Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
Rasmussen, S., Allentoft, M. E., Nielsen, K. R., Orlando, L., Sikora, M., Sjögren, K.-G., Pedersen, A. G., Schubert, M., Dam, A. V., Kapel, C. M. O., et al. (2015) · Cell · doi:10.1016/j.cell.2015.10.009 · Cited by 557 · see citing works
Widespread natural variation of DNA methylation within angiosperms
Niederhuth, C. E., Bewick, A. J., Ji, L., Alabady, M., Kim, K. D., Li, Q., Rohr, N. A., Rambani, A., Burke, J. M., Udall, J. A., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1059-0 · Cited by 557 · see citing works
Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow
Malinsky, M., Svardal, H., Tyers, A. M., Miska, E. A., Genner, M. J., Turner, G. F., & Durbin, R. M. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0717-x · Cited by 557 · see citing works
Ancient orogenic and monsoon-driven assembly of the world’s richest temperate alpine flora
Ding, W., Ree, R. H., Spicer, R. A., & Xing, Y. (2020) · Science · doi:10.1126/science.abb4484 · Cited by 532 · see citing works
Bayesian Evolutionary Analysis with BEAST
Drummond, A. J., & Bouckaert, R. (2015) · Cambridge University Press eBooks · doi:10.1017/cbo9781139095112 · Cited by 518 · see citing works
Self-citationA RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
Miller, M. A., Schwartz, T., Pickett, B. E., He, S., Klem, E. B., Scheuermann, R. H., Passarotti, M., Kaufman, S., & O’Leary, M. A. (2015) · Evolutionary Bioinformatics · doi:10.4137/ebo.s21501 · Cited by 514 · see citing works
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · see citing works
Species Delimitation using Genome-Wide SNP Data
Leaché, A. D., Fujita, M. K., Minin, V. N., & Bouckaert, R. (2014) · Systematic Biology · doi:10.1093/sysbio/syu018 · Cited by 475 · see citing works
Self-citationStarBEAST2 brings faster species tree inference and accurate estimates of substitution rates
Ogilvie, H. A., Bouckaert, R. R., & Drummond, A. J. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx126 · Cited by 469 · see citing works
Self-citationTotal-Evidence Dating under the Fossilized Birth–Death Process
Zhang, C., Stadler, T., Klopfstein, S., Heath, T. A., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syv080 · Cited by 419 · see citing works
Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics
Zhang, S., Jin, J., Chen, S., Chase, M. W., Soltis, P. S., Li, H., Yang, J., Li, D.-Z., & Yi, T. (2017) · New Phytologist · doi:10.1111/nph.14461 · Cited by 393 · see citing works
The evolution of a tropical biodiversity hotspot
Harvey, M. G., Bravo, G. A., Claramunt, S., Cuervo, A. M., Derryberry, G. E., Battilana, J., Seeholzer, G. F., McKay, J., O’Meara, B. C., Faircloth, B. C., et al. (2020) · Science · doi:10.1126/science.aaz6970 · Cited by 391 · see citing works
A new time tree reveals Earth history’s imprint on the evolution of modern birds
Claramunt, S., & Cracraft, J. (2015) · Science Advances · doi:10.1126/sciadv.1501005 · Cited by 383 · see citing works
The abiotic and biotic drivers of rapid diversification in A ndean bellflowers (Campanulaceae)
Lagomarsino, L. P., Condamine, F. L., Antonelli, A., Mulch, A., & Davis, C. “. (2016) · New Phytologist · doi:10.1111/nph.13920 · Cited by 379 · see citing works
Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny
Pollock, F. J., McMinds, R., Smith, S. J., Bourne, D. G., Willis, B. L., Medina, M., Thurber, R. L. V., & Zaneveld, J. (2018) · Nature Communications · doi:10.1038/s41467-018-07275-x · Cited by 379 · see citing works
Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
Gavryushkina, A., Heath, T. A., Ksepka, D. T., Stadler, T., Welch, D., & Drummond, A. J. (2016) · Systematic Biology · doi:10.1093/sysbio/syw060 · Cited by 372 · see citing works
Self-citationEvolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus
Pu, J., Wang, S., Yin, Y., Zhang, G., Carter, R. A., Wang, J., Xu, G., Sun, H., Wang, M., Wen, C., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1422456112 · Cited by 371 · see citing works
Thomas, S., Izard, J., Walsh, E. K., Batich, K. A., Chongsathidkiet, P., Clarke, G. A., Sela, D. A., Muller, A. J., Mullin, J. M., Albert, K., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-16-2929 · Cited by 369 · see citing works
Palomo, A., Pedersen, A. G., Fowler, J., Dechesne, A., Sicheritz‐Pontén, T., & Smets, B. F. (2018) · The ISME Journal · doi:10.1038/s41396-018-0083-3 · Cited by 368 · see citing works
Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike
Yamasoba, D., Kimura, I., Nasser, H., Morioka, Y., Nao, N., Ito, J., Uriu, K., Tsuda, M., Zahradník, J., Shirakawa, K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.04.035 · Cited by 366 · see citing works
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
Gavryushkina, A. “., Welch, D., Stadler, T., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003919 · Cited by 365 · see citing works
Self-citationEarly human dispersals within the Americas
Moreno-Mayar, J. V., Vinner, L., Damgaard, P. D. B., Castro, C. D. L. F., Chan, J., Spence, J. P., Allentoft, M. E., Vimala, T., Racimo, F., Pinotti, T., et al. (2018) · Science · doi:10.1126/science.aav2621 · Cited by 365 · see citing works
Evolution of DNA Methylation across Insects
Bewick, A. J., Vogel, K. J., Moore, A. J., & Schmitz, R. J. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw264 · Cited by 356 · see citing works
Pearce, S. L., Clarke, D. F., East, P. D., Elfékih, S., Gordon, K. H. J., Jermiin, L. S., McGaughran, A., Oakeshott, J. G., Papanikolaou, A., Perera, O. P., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0402-6 · Cited by 356 · see citing works
Wyres, K. L., Wick, R. R., Judd, L. M., Froumine, R., Tokolyi, A., Gorrie, C. L., Lam, M. M. C., Duchêne, S., Jenney, A. W. J., & Holt, K. E. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008114 · Cited by 355 · see citing works
Genomic and epidemiological monitoring of yellow fever virus transmission potential
Faria, N. R., Kraemer, M. U. G., Hill, S. C., de Jesus, J. G., Aguiar, R. S., Iani, F. C. D. M., Xavier, J., Quick, J., du Plessis, L., Dellicour, S., et al. (2018) · Science · doi:10.1126/science.aat7115 · Cited by 348 · 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
A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
Kjær, K. H., Pedersen, M. W., Sanctis, B. D., Cahsan, B. D., Korneliussen, T. S., Michelsen, C., Sand, K. K. S., Jelavić, S., Ruter, A., Schmidt, A. M. A., et al. (2022) · Nature · doi:10.1038/s41586-022-05453-y · Cited by 338 · see citing works
Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131
Stoesser, N. E., Sheppard, A. E., Pankhurst, L. J., Maio, N. D., Moore, C. E., Sebra, R., Turner, P., Anson, L. W., Kasarskis, A., Batty, E. M., et al. (2016) · mBio · doi:10.1128/mbio.02162-15 · Cited by 332 · see citing works
Stable recombination hotspots in birds
Singhal, S., Leffler, E. M., Sannareddy, K., Turner, I., Venn, O., Hooper, D. M., Strand, A. I., Li, Q., Raney, B. J., Balakrishnan, C. N., et al. (2015) · Science · doi:10.1126/science.aad0843 · Cited by 327 · see citing works
Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes
Sun, H., Wu, S., Zhang, G., Jiao, C., Guo, S., Ren, Y., Zhang, J., Zhang, H., Gong, G., Jia, Z., et al. (2017) · Molecular Plant · doi:10.1016/j.molp.2017.09.003 · Cited by 324 · see citing works
Ancient pathogen genomics as an emerging tool for infectious disease research
Spyrou, M. A., Bos, K. I., Herbig, A., & Krause, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0119-1 · Cited by 313 · see citing works
Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria
Hublin, J., Sirakov, N., Aldeias, V., Bailey, S. E., Bard, É., Delvigne, V., Endarova, E., Fagault, Y., Fewlass, H., Hajdinjak, M., et al. (2020) · Nature · doi:10.1038/s41586-020-2259-z · Cited by 313 · see citing works
Jones, G. (2016) · Journal of Mathematical Biology · doi:10.1007/s00285-016-1034-0 · Cited by 312 · see citing works
Evolution of endemism on a young tropical mountain
Merckx, V. S. F. T., Hendriks, K. P., Beentjes, K. K., Mennes, C. B., Becking, L. E., Peijnenburg, K. T. C. A., Afendy, A., Arumugam, N., de Boer, H., Biun, A., et al. (2015) · Nature · doi:10.1038/nature14949 · Cited by 310 · see citing works
Evolution and comparative genomics of the most common Trichoderma species
Kubicek, C. P., Steindorff, A. S., Chenthamara, K., Manganiello, G., Henrissat, B., Zhang, J., Cai, F. M., Kopchinskiy, A. G., Kubicek, E. M., Kuo, A., et al. (2019) · BMC Genomics · doi:10.1186/s12864-019-5680-7 · Cited by 307 · see citing works
Wright, A. M., & Hillis, D. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0109210 · Cited by 302 · see citing works
Reconstructing the genome of the most recent common ancestor of flowering plants
Murat, F., Armero, A. A., Pont, C., Klopp, C., & Salse, J. (2017) · Nature Genetics · doi:10.1038/ng.3813 · Cited by 302 · see citing works
Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline
Rascovan, N., Sjögren, K.-G., Kristiansen, K., Nielsen, R., Willerslev, E., Desnues, C., & Rasmussen, S. (2018) · Cell · doi:10.1016/j.cell.2018.11.005 · Cited by 301 · see citing works
Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis
Lee, J. Y. H., Monk, I. R., da Silva, A. G., Seemann, T., Chua, K., Kearns, A., Hill, R., Woodford, N., Bartels, M. D., Strommenger, B., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0230-7 · Cited by 299 · see citing works
Origins and genetic legacy of prehistoric dogs
Bergström, A., Frantz, L., Schmidt, R., Ersmark, E., Lebrasseur, O., Girdland-Flink, L., Lin, A. T., Storå, J., Sjögren, K.-G., Anthony, D., et al. (2020) · Science · doi:10.1126/science.aba9572 · Cited by 297 · see citing works
Bayesian inference of ancestral dates on bacterial phylogenetic trees
Didelot, X., Croucher, N. J., Bentley, S. D., Harris, S. R., & Wilson, D. J. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky783 · Cited by 295 · see citing works
A 4000-species dataset provides new insight into the evolution of ferns
Testo, W., & Sundue, M. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.09.003 · Cited by 293 · see citing works
Sequence capture of ultraconserved elements from bird museum specimens
McCormack, J. E., Tsai, W. L. E., & Faircloth, B. C. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12466 · Cited by 286 · see citing works
Guidelines for DNA taxonomy, with a focus on the meiofauna
Fontaneto, D., Flot, J., & Tang, C. Q. (2015) · Marine Biodiversity · doi:10.1007/s12526-015-0319-7 · Cited by 277 · see citing works
Asymptomatic transmission and the resurgence of Bordetella pertussis
Althouse, B. M., & Scarpino, S. V. (2015) · BMC Medicine · doi:10.1186/s12916-015-0382-8 · Cited by 275 · see citing works
DensiTree 2: Seeing Trees Through the ForestPreprint
Bouckaert, R., & Heled, J. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/012401 · Cited by 267 · see citing works
Self-citationPhylogenetic evidence for Sino-Tibetan origin in northern China in the Late Neolithic
Zhang, M., Yan, S. L., Pan, W., & Li, J. (2019) · Nature · doi:10.1038/s41586-019-1153-z · Cited by 266 · see citing works
Ctenophore relationships and their placement as the sister group to all other animals
Whelan, N. V., Kocot, K. M., Moroz, T. P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L. L., & Halanych, K. M. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0331-3 · Cited by 263 · see citing works
Neotropical forest expansion during the last glacial period challenges refuge hypothesis
Leite, Y. L. R., Costa, L. P., Loss, A. C., Rocha, R. G., Batalha‐Filho, H., Bastos, A. C., Quaresma, V. D. S., Fagundes, V., Paresque, R., Passamani, M., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1513062113 · Cited by 262 · see citing works
Dated language phylogenies shed light on the ancestry of Sino-Tibetan
Sagart, L., Jacques, G., Lai, Y., Ryder, R., Thouzeau, V., Greenhill, S. J., & List, J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817972116 · Cited by 262 · see citing works
Givnish, T. J., Zuluaga, A., Spalink, D., Gomez, M. S., Lam, V. K. Y., Saarela, J. M., Sass, C., Iles, W. J. D., de Sousa, D. J. L., Leebens‐Mack, J., et al. (2018) · American Journal of Botany · doi:10.1002/ajb2.1178 · Cited by 260 · see citing works
MERS-CoV spillover at the camel-human interface
Dudas, G., Carvalho, L. M., Rambaut, A., Bedford, T., Somily, A. M., Barry, M., Subaie, S. S. A., BinSaeed, A. A., Alzamil, F. A., Zaher, W., et al. (2018) · eLife · doi:10.7554/elife.31257 · Cited by 260 · see citing works
Self-citationReconstructing the genetic history of late Neanderthals
Hajdinjak, M., Fu, Q., Hübner, A., Petr, M., Mafessoni, F., Grote, S., Skoglund, P., Narasimham, V., Rougier, H., Crèvecoeur, I., et al. (2018) · Nature · doi:10.1038/nature26151 · Cited by 258 · see citing works
The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps
Simões, T. R., Caldwell, M. W., Tałanda, M., Bernardi, M., Palci, A., Vernygora, O. V., Bernardini, F., Mancini, L., & Nydam, R. L. (2018) · Nature · doi:10.1038/s41586-018-0093-3 · Cited by 256 · see citing works
The delayed and geographically heterogeneous diversification of flowering plant families
Ramírez‐Barahona, S., Sauquet, H., & Magallón, S. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1241-3 · Cited by 253 · see citing works
The draft genome of tropical fruit durian (Durio zibethinus)
Teh, B. T., Lim, K. J., Yong, C. H., Ng, C. C. Y., Rao, S. R., Rajasegaran, V., Lim, W. K., Ong, C. K., Chan, K. C., Cheng, V. K. Y., et al. (2017) · Nature Genetics · doi:10.1038/ng.3972 · Cited by 250 · see citing works
Ayres, D. L., Cummings, M. P., Baele, G., Darling, A. E., Lewis, P. O., Swofford, D. L., Huelsenbeck, J. P., Lemey, P., Rambaut, A., & Suchard, M. A. (2019) · Systematic Biology · doi:10.1093/sysbio/syz020 · Cited by 249 · see citing works
Self-citationNarrow thermal tolerance and low dispersal drive higher speciation in tropical mountains
Polato, N. R., Gill, B. A., Shah, A. A., Gray, M. M., Casner, K. L., Barthelet, A., Messer, P. W., Simmons, M. P., Guayasamin, J. M., Encalada, A. C., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1809326115 · Cited by 245 · see citing works
Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks
Didelot, X., Fraser, C., Gardy, J. L., & Colijn, C. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw275 · Cited by 244 · see citing works
New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation
Maio, N. D., Wu, C., O’Reilly, K. M., & Wilson, D. J. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005421 · Cited by 240 · see citing works
Self-citationVision using multiple distinct rod opsins in deep-sea fishes
Musilová, Z., Cortesi, F., Matschiner, M., Davies, W. I. L., Patel, J. S., Stieb, S. M., de Busserolles, F., Malmstrøm, M., Tørresen, O. K., Brown, C. J., et al. (2019) · Science · doi:10.1126/science.aav4632 · Cited by 237 · see citing works
Reconstruction of ancient microbial genomes from the human gut
Wibowo, M. C., Yang, Z., Borry, M., Hübner, A., Huang, K. D., Tierney, B. T., Zimmerman, S. E., Barajas-Olmos, F. M., Contreras-Cubas, C., Garcia‐Ortíz, H., et al. (2021) · Nature · doi:10.1038/s41586-021-03532-0 · Cited by 237 · see citing works
Species boundaries in the human pathogen Paracoccidioides
Turissini, D. A., Gómez, O. M., Teixeira, M. D. M., McEwen, J. G., & Matute, D. R. (2017) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2017.05.007 · Cited by 236 · see citing works
Evolution of the immune system influences speciation rates in teleost fishes
Malmstrøm, M., Matschiner, M., Tørresen, O. K., Star, B., Snipen, L. G., Hansen, T. F., Baalsrud, H. T., Nederbragt, A. J., Hanel, R., Salzburger, W., et al. (2016) · Nature Genetics · doi:10.1038/ng.3645 · Cited by 235 · see citing works
Lloyd, G. T. (2016) · Biological Journal of the Linnean Society · doi:10.1111/bij.12746 · Cited by 224 · see citing works
Ancient goat genomes reveal mosaic domestication in the Fertile Crescent
Daly, K. G., Delser, P. M., Mullin, V. E., Scheu, A., Mattiangeli, V., Teasdale, M. D., Hare, A. J., Bürger, J., Verdugo, M. P., Collins, M. J., et al. (2018) · Science · doi:10.1126/science.aas9411 · Cited by 223 · see citing works
Portik, D. M., Leaché, A. D., Rivera, D., Barej, M. F., Burger, M., Hirschfeld, M., Rödel, M., Blackburn, D. C., & Fujita, M. K. (2017) · Molecular Ecology · doi:10.1111/mec.14266 · Cited by 221 · see citing works
MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees
Puttick, M. N. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz554 · Cited by 221 · see citing works
RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses
Warren, D. L., Geneva, A. J., & Lanfear, R. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw279 · Cited by 219 · see citing works
Ancient hepatitis B viruses from the Bronze Age to the Medieval period
Mühlemann, B., Jones, T. C., Damgaard, P. D. B., Allentoft, M. E., Shevnina, I., Logvin, A., Usmanova, E. R., Панюшкина, И. П., Boldgiv, B., Bazartseren, T., et al. (2018) · Nature · doi:10.1038/s41586-018-0097-z · Cited by 218 · see citing works
A rapid rate of sex-chromosome turnover and non-random transitions in true frogs
Jeffries, D. L., Lavanchy, G., Sermier, R., Sredl, M. J., Miura, I., Borzée, A., Barrow, L. N., Canestrelli, D., Crochet, P., Dufresnes, C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06517-2 · Cited by 218 · see citing works
Macroecology and macroevolution of the latitudinal diversity gradient in ants
Economo, E. P., Narula, N., Friedman, N. R., Weiser, M. D., & Guénard, B. (2018) · Nature Communications · doi:10.1038/s41467-018-04218-4 · Cited by 217 · see citing works
Global emergence of the widespread Pseudomonas aeruginosa ST235 clone
Treepong, P., Kos, V. N., Guyeux, C., Blanc, D., Bertrand, X., Valot, B., & Hocquet, D. (2017) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2017.06.018 · Cited by 215 · see citing works
A biologist’s guide to Bayesian phylogenetic analysis
Nascimento, F. F., Reis, M. D., & Yang, Z. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0280-x · Cited by 212 · see citing works
Zakour, N. L. B., Alsheikh-Hussain, A. S., Ashcroft, M. M., Nhu, N. T. K., Roberts, L. W., Stanton-Cook, M. J., Schembri, M. A., & Beatson, S. A. (2016) · mBio · doi:10.1128/mbio.00347-16 · Cited by 210 · see citing works
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
- Authors
- Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J.
- Affiliations
- University of Auckland (NZ)
- University of California, Los Angeles (US)
- University of Edinburgh (GB)
- Corresponding author
- Bouckaert, Remco
- Drummond, Alexei J.
- ORCID
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-04-10
- Volume
- 10
- Issue
- 4
- Pages
- e1003537
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC3985171
- OpenAlex
- W2026062398
- Cited by
- 6,527
- References
- 31
- Citations by year
- 2026: 364 · 2025: 464 · 2024: 509 · 2023: 492 · 2022: 588 · 2021: 745 · 2020: 801 · 2019: 784 · 2018: 724 · 2017: 484 · 2016: 302 · 2015: 213 · 2014: 44 · 2013: 3
- FWCI
- 131.24
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository for Publications and Research Data (ETH Zurich) (publishedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, 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)
- Figshare (submittedVersion, cc-by)
- ResearchSpace (University of Auckland) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Funders
- National Science Foundation (1264153, 0856099)
- National Evolutionary Synthesis Center
- Wellcome Trust (095831)
- Royal Society
- Royal Society Te Apārangi
- National Institutes of Health
- National Human Genome Research Institute (R01HG006139)
- 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, Markov chain Monte Carlo, package management, extensibility, phylodynamics, model averaging, substitution models, XML file format, open source software
- MeSH terms
- Bayes Theorem, Biological Evolution, Programming Languages, Software
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