The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
Simulating Trees with a Fixed Number of Extant Species
Open accessAbstract
In this paper, I develop efficient tools to simulate trees with a fixed number of extant species. The tools are provided in my open source R-package TreeSim available on CRAN. The new model presented here is a constant rate birth-death process with mass extinction and/or rate shift events at arbitrarily fixed times 1) before the present or 2) after the origin. The simulation approach for case (2) can also be used to simulate under more general models with fixed events after the origin. I use the developed simulation tools for showing that a mass extinction event cannot be distinguished from a model with constant speciation and extinction rates interrupted by a phase of stasis based on trees consisting of only extant species. However, once we distinguish between mass extinction and period of stasis based on paleontological data, fast simulations of trees with a fixed number of species allow inference of speciation and extinction rates using approximate Bayesian computation and allow for robustness analysis once maximum likelihood parameter estimations are available.
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Cites
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Estimating a Binary Character's Effect on Speciation and Extinction
Maddison, W. P., Midford, P. E., & Otto, S. P. (2007) · Systematic Biology · doi:10.1080/10635150701607033 · Cited by 1,128
The conditioned reconstructed process
Gernhard, T. (2008) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2008.04.005 · Cited by 1,038
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Testing macro–evolutionary models using incomplete molecular phylogenies
Pybus, O. G., & Harvey, P. H. (2000) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.2000.1278 · Cited by 795
Rabosky, D. L. (2010) · Evolution · doi:10.1111/j.1558-5646.2009.00926.x · Cited by 589
Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved Phylogenies
FitzJohn, R. G., Maddison, W. P., & Otto, S. P. (2009) · Systematic Biology · doi:10.1093/sysbio/syp067 · Cited by 581
Density-Dependent Cladogenesis in Birds
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Rabosky, D. L., Chang, J., Title, P. O., Cowman, P. F., Sallan, L., Friedman, M., Kaschner, K., Garilao, C., Near, T. J., Coll, M., et al. (2018) · Nature · doi:10.1038/s41586-018-0273-1 · Cited by 933
The fossilized birth-death process for coherent calibration of divergence-time estimates
Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319091111 · Cited by 834
Self-citationA 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
“On the other hand, if multiple early lineages of Neornithes faced extinction during the K-Pg event, that may have created a false signal of rate increase in the reconstructed phylogenies, in which case the apparent increase is merely a consequence of missing lineages before the event (99, 100).”
BackgroundUyeda, J. C., & Harmon, L. J. (2014) · Systematic Biology · doi:10.1093/sysbio/syu057 · Cited by 339
RPANDA: an R package for macroevolutionary analyses on phylogenetic trees
Morlon, H., Lewitus, E., Condamine, F. L., Manceau, M., Clavel, J., & Drury, J. (2016) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12526 · Cited by 331
Metadata
- Authors
- Stadler, T.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-04-11
- Volume
- 60
- Issue
- 5
- Pages
- 676-684
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2129505888
- Cited by
- 264
- References
- 24
- FWCI
- 10.05
- Type
- journal article
- Language
- en
- Open access
- bronze
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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).
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