Test for Punctuational Evolution and the Node-Density Artifact.

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This will hopefully be resolved shortly

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

  • The input tree(s) should be in Nexus format
  • The trees should be fully bifurcating

Outgroup and rooting

  • Trees must be inferred with an outgroup
  • Before analysis the trees must be rooted using the outgroup and the outgroup removed (see papers above for a detailed explanation of why this must be done).

The result and output

  • The first table of the results provide information about the input file
    • Tree file name
    • Number of tree in the Nexus file
    • Reference ID number
  • The second table shows the results of the test for the punctuational effect
    • Number (and percent) of trees with a significant β
    • Number (and percent) of trees with a significant β and δ < 1
    • Conclusion (whether there is a significant punctuational effect or node-density artifact is present of neither)

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.

  • The third table only appears if a significant punctuational effect is detected - It shows
    • Percentage of evolution in the tree attributable to punctuational effects
    • Punctuational effects contribution of the deviation from molecular clock (r2)

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