The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
The BPP program for species tree estimation and species delimitation
Open accessAbstract
This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis.
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Cites
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys029 · Cited by 27,843
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
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Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Monte Carlo Statistical Methods
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Monte Carlo Statistical Methods
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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
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
Self-citationHow to fail at species delimitation
Carstens, B. C., Pelletier, T. A., Reid, N. M., & Satler, J. D. (2013) · Molecular Ecology · doi:10.1111/mec.12413 · Cited by 1,248
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Cited by
StarBEAST2 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
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
Flouri, T., Jiao, X., Rannala, B., & Yang, Z. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy147 · Cited by 445
Self-citationChen, N., Cai, Y., Chen, Q., Li, R., Wang, K., Huang, Y., Hu, S., Huang, S., Zhang, H., Zheng, Z., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04737-0 · Cited by 403
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
Self-citationGene tree discordance causes apparent substitution rate variation
Mendes, F. K., & Hahn, M. W. (2016) · Systematic Biology · doi:10.1093/sysbio/syw018 · Cited by 189
Metadata
- Authors
- Yang, Z.
- Venue
- Current Zoology
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-10-01
- Volume
- 61
- Issue
- 5
- Pages
- 854-865
- ISSN
- 1674-5507 (ISSN-L)
- 2396-9814
- OpenAlex
- W2345712966
- Cited by
- 772
- References
- 38
- FWCI
- 42.97
- Type
- journal article
- Language
- en
- Open access
- diamond
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