The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“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
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“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
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
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 13,104
Self-citationTamura, K., & Nei, M. (1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040023 · Cited by 11,267
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 10,128
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
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×
“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
Self-citation(1986) · Cited by 2,570
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
Self-citation
Flagged first, then by citations
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
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
“2012), BEAST2 (Bouckaert et al. 2014), LAMARC (Kuhner 2006), Migrate (Beerli 2006), MrBayes (Ronquist et al.”
MethodSelf-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
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
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
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 3,338
ASAP: assemble species by automatic partitioning
Puillandre, N., Brouillet, S., & Achaz, G. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13281 · Cited by 1,834
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
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
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
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
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
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 840
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 820
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 767
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 733
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
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 703
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
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
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
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 653
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
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 589
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
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 568
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
Bayesian Evolutionary Analysis with BEAST
Drummond, A. J., & Bouckaert, R. (2015) · Cambridge University Press eBooks · doi:10.1017/cbo9781139095112 · Cited by 526
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 526
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
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 493
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
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
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 400
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 405
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
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
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 393
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
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
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 400
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 376
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
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 372
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 383
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 364
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 360
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 365
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 359
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
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 364
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
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 346
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 337
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 285
Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria
Hublin, J.-J., Sirakov, N., Aldeias, V., Bailey, S., Bard, E., Delvigne, V., Endarova, E., Fagault, Y., Fewlass, H., Hajdinjak, M., et al. (2020) · Nature · doi:10.1038/s41586-020-2259-z · Cited by 287
Jones, G. (2016) · Journal of Mathematical Biology · doi:10.1007/s00285-016-1034-0 · Cited by 312
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
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 320
Wright, A. M., & Hillis, D. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0109210 · Cited by 302
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
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 324
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 305
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
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 304
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 301
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 294
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 288
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 283
DensiTree 2: Seeing Trees Through the ForestPreprint
Bouckaert, R., & Heled, J. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/012401 · Cited by 267
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
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
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
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
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
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 269
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 266
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
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
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 256
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
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 254
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 250
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
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
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 251
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 239
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 241
Lloyd, G. T. (2016) · Biological Journal of the Linnean Society · doi:10.1111/bij.12746 · Cited by 227
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 236
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 225
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
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
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 228
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
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 228
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
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
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 222
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
Metadata
- 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
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
