PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.
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README.md

PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.

PyRate is licensed under a AGPLv3 License.

The program's documentation is available here:

  • Tutorials (work in progress; Older Wiki pages are still available, although updated documentation is being only added to the Tutorials)
  • Instructions to install the fastPyRateC library
  • For questions, suggestions or bugs contact us

The main methods are described here:

  • Silvestro D., Schnitzler J., Liow L.H., Antonelli A. and Salamin N. (2014) Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data. Systematic Biology, 63, 349-367.

  • Silvestro D., Salamin N., Schnitzler J. (2014) PyRate: A new program to estimate speciation and extinction rates from incomplete fossil record. Methods in Ecology and Evolution, 5, 1126-1131.

The MCDD model is described here:

  • Silvestro D., Antonelli A., Salamin N., Quental T. B. (2015) The role of clade competition in the diversification of North American canids. PNAS, 112, 8684-8689.

  • Silvestro D., Pires M. M., Quental T., Salamin N. (2017) Bayesian estimation of multiple clade competition from fossil data. Evolutionary Ecology Research, 18:41-59.

The DES model is described here:

  • Silvestro, D., Zizka A., Bacon C. D., Cascales-Minana B. and Salamin, N., Antonelli, A. (2016) Fossil Biogeography: A new model to infer dispersal, extinction and sampling from paleontological data. Philosophical Transactions of the Royal Society B 371:20150225.

The MBD model is described here:

  • Lehtonen S., Silvestro D., Karger D. N., Scotese C., Tuomisto H., Kessler M., Peña C., Wahlberg N., Antonelli A. (2017) Environmentally driven extinction and opportunistic origination explain fern diversification patterns. Scientific Reports, 7:4831.

The ADE model is described here:

  • Hagen O., Andermann T., Quental T. B., Antonelli A., Silvestro D. (in press) Estimating Age-dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Systematic Biology, doi: 10.1093/sysbio/syx082.