Test for Punctuational Evolution and the Node-Density Artifact.

Nexus tree file

Detect and if present quantify the contribution of punctuational molecular evolution and test for the node density artifect

This program implements the methods out lined in the following papers:

Pagel, M., Venditti, C. and Meade, A. 2006. Large Punctuational contribution of speciation to evolutionary divergence at the molecular level. Science. 314: 199-121

Venditti, C., Meade, A., Pagel, M. 2006. Detecting the node-density artifact in phylogeny reconstruction. Systematic Biology 55: 637-643

Webster, A. J., Payne, R. J. and Pagel, M. 2003. Molecular phylogenies link rates of evolution and speciation. Science 301:478.

The Punctuated Evolution program can detect significant punctuated molecular evolution from phylogenetic trees inferred from sequence data. Where the punctuational effect is present the program will report the proportion of evolution attributable to speciation events (nodes). It also reports the deviation from the molecular clock caused by punctuational effects. (See papers above for methodological details)

A recognised artifact of phylogeny reconstruction known as the node-density effect can mimic punctuational effects. However, the node density artifact can be tested for statistically (See papers above). If the artifact is present the program reports it.

Input Tree File

Outgroup and rooting

The result and output

NB the output is simple if a single tree is analyzed, however, see See papers above for how we determine the presents of the punctuational effect and the node density artifact integrating over a Bayesian sample of phylogenies.

NB again this is simple if a single tree is analyzed. See papers above for how we integrate over a Bayesian sample.