In this example, we will calculate the ensemble consistency index (CI) and ensemble retention index (RI). The CI and RI both measure the degree of "tree-likeness" in data under a parsimony model for character change. We will use the free programs Mesquite (Maddison and Maddison 2006) and R (R Core Development Team 2010) to calculate CI and RI. If you did not yet install Mesquite, you can go here for download and installation instructions. You can download R from here.
Section 2.3 Contents
Lycett, S. J., M. Collard, and W. C. McGrew. 2010. Are behavioral differences among wild chimpanzee communities genetic or cultural? An assessment using tool-use data and phylogenetic methods. American Journal of Physical Anthropology. 142:461-467.
Maddison, W. P., and D.R. Maddison. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.75, http://mesquiteproject.org.
R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for
Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.