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Diversitree: comparative phylogenetic analyses of diversification in R
Abstract
Summary: 1. The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary state speciation and extinction), MuSSE (a multistate extension of BiSSE), and QuaSSE (quantitative state speciation and extinction). Diversitree also includes methods for analysing trait evolution and estimating speciation/extinction rates independently. 2. In this note, I describe the features and demonstrate use of the package, using a new method, MuSSE (multistate speciation and extinction), to examine the joint effects of two traits on speciation. 3. Using simulations, I found that MuSSE could reliably detect that a binary trait that affected speciation rates when simultaneously accounting for additional thats that had no effect on speciation rates. 4. Diversitree is an open source and available on the Comprehensive R Archive Network (cran). A tutorial and worked examples can be downloaded from http://www.zoology.ubc.ca/prog/diversitree.
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Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Kass, R. E., & Raftery, A. E. (1995) · Journal of the American Statistical Association · doi:10.1080/01621459.1995.10476572 · Cited by 12,558
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793
The Design and Implementation of FFTW3
Frigo, M., & Johnson, S. G. (2005) · Proceedings of the IEEE · doi:10.1109/jproc.2004.840301 · Cited by 5,086
A likelihood approach to estimating phylogeny from discrete morphological character data
Lewis, P. O. (2001) · Systematic Biology · doi:10.1080/106351501753462876 · Cited by 2,929
Eastman, J. M., Alfaro, M. E., Joyce, P., Hipp, A. L., & Harmon, L. J. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01401.x · Cited by 240
Cited by
Phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)
Revell, L. J. (2024) · PeerJ · doi:10.7717/peerj.16505 · Cited by 1,244
A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models
Tung Ho, L. S., & Ané, C. (2014) · Systematic Biology · doi:10.1093/sysbio/syu005 · Cited by 1,085
Efficient comparative phylogenetics on large trees
Louca, S., & Doebeli, M. (2018) · Bioinformatics · doi:10.1093/bioinformatics/btx701 · Cited by 564
Detecting hidden diversification shifts in models of trait-dependent speciation and extinction
Beaulieu, J. M., & O’Meara, B. C. (2016) · Systematic Biology · doi:10.1093/sysbio/syw022 · Cited by 579
The unsolved challenge to phylogenetic correlation tests for categorical characters
Maddison, W. P., & FitzJohn, R. G. (2015) · Systematic Biology · doi:10.1093/sysbio/syu070 · Cited by 468
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Metadata
- Authors
- FitzJohn, R. G.
- Venue
- Methods in Ecology and Evolution
- Publisher
- Wiley
- Published
- 2012-08-06
- Volume
- 3
- Issue
- 6
- Pages
- 1084-1092
- ISSN
- 2041-210X (ISSN-L)
- OpenAlex
- W1482160415
- Cited by
- 941
- References
- 6
- FWCI
- 41.39
- Type
- journal article
- Language
- en
- Open access
- closed
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