MaryELennon/PyRate

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

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)
• System requirements to run the program and 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.

• See tutorials 1 and 2

The RJMCMC algorithm is described here:

• Silvestro D., Antonelli A., Salamin N., Meyer X. (2018) Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework. bioRxiv, doi:10.1101/316992

• See tutorial 3

The MCDD and MBD models are 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.

• 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.

• See tutorial 4

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.

• See tutorial 5

The ADE model is described here:

• Hagen O., Andermann T., Quental T. B., Antonelli A., Silvestro D. (2017) Estimating Age-dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Systematic Biology, doi: 10.1093/sysbio/syx082.

• See tutorial 4

The BDC model is described here:

• Silvestro D., Warnock R., Gavryushkina A. & Stadler T. (2018) Closing the gap between palaeontological and neontological speciation and extinction rate estimates. Nature Communications, doi: 10.1038/s41467-018-07622-y.

• See tutorial 4