Pagel’s Tree Transformations

This applet illustrates the effects of Pagel’s (1999) three transformations on rooted trees: lambda, delta, and kappa. A lambda value of 0.2 reduces the height of internal nodes to 20% of their original height. A delta value of 0.2 raises the height of every node (including leaf nodes) to the power 0.2. Finally, a kappa value of 0.2 raises every edge length to the power 0.2. Section 6.2 of Luke Harmon’s book provides a good explanation of these transformations in the context of comparative methods.

Use the left/right arrow keys to cycle among the three parameters and the up/down arrow keys to increase/decrease the current parameter value. Note that the left/right arrow keys reset the parameter value to 1.0, which is the unmodified tree. Hold down Shift when using the arrow keys to avoid scrolling while changing parameter values. The Simulate button simulates a new tree using a pure birth model scaled to have total height 100.

Literature Cited

M Pagel. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884. DOI:10.1038/44766

Acknowledgements

This applet makes use of the excellent d3js javascript library.

Licence

Creative Commons Attribution 4.0 International. License (CC BY 4.0). To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.