The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent
Open accessAbstract
The focus of this article is a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using molecular sequences from multiple loci. The species delimitation requires no a priori assignment of individuals to species, and no guide tree. The method is implemented in a package called STACEY for BEAST2, and is a extension of the author’s DISSECT package. Here we demonstrate considerable efficiency improvements by using three new operators for sampling from the posterior using the Markov chain Monte Carlo algorithm, and by using a model for the population size parameters along the branches of the species tree which allows these parameters to be integrated out. The correctness of the moves is demonstrated by tests of the implementation. The practice of using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data (Olave et al. in Syst Biol 63:263–271. doi:10.1093/sysbio/syt106, 2014). The same simulated data set is used to demonstrate the accuracy and improved convergence of the present method. We also compare performance with *BEAST for a fixed delimitation analysis on a large data set, and again show improved convergence.
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Cites
Inference of Population Structure Using Multilocus Genotype Data
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000) · Genetics · doi:10.1093/genetics/155.2.945 · Cited by 33,908
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
PEAKALL, R., & SMOUSE, P. E. (2006) · Molecular Ecology Notes · doi:10.1111/j.1471-8286.2005.01155.x · Cited by 16,589
BEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527
CODA: convergence diagnosis and output analysis for MCMC
Plummer, M., Best, N., Cowles, K., & Vines, K. (2006) · Open Research Online (The Open University) · Cited by 3,317
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
Gene tree discordance, phylogenetic inference and the multispecies coalescent
Degnan, J. H., & Rosenberg, N. A. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2009.01.009 · Cited by 1,958
Bayesian species delimitation using multilocus sequence data
Yang, Z., & Rannala, B. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913022107 · Cited by 1,405
Rannala, B., & Yang, Z. (2003) · Genetics · doi:10.1093/genetics/164.4.1645 · Cited by 1,131
Is a new and general theory of molecular systematics emerging?
Edwards, S. V. (2009) · Evolution · doi:10.1111/j.1558-5646.2008.00549.x · Cited by 1,040
Hey, J., & Nielsen, R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611164104 · Cited by 968
Cited by
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-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
Petzold, A., & Hassanin, A. (2020) · PLOS ONE · doi:10.1371/journal.pone.0217956 · Cited by 60
Metadata
- Authors
- Jones, G.
- Venue
- Journal of Mathematical Biology
- Published
- 2016-06-10
- Volume
- 74
- Issue
- 1-2
- Pages
- 447-467
- ISSN
- 0303-6812 (ISSN-L)
- 1432-1416
- OpenAlex
- W2408898951
- Cited by
- 316
- References
- 24
- FWCI
- 23.97
- Type
- journal article
- Language
- en
- Open access
- green
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
