Continuous Ancestral Character Estimation
Continuous Ancestral Character Estimation
Question
Given a set of observations for a continuos trait (e.g. height, weight, yield,...) for a set of taxa with a known phylogenetic relationship, estimate the value of the trait (and its confidence intervals) in the ancestors of these taxa.
Implementation
R package ape (http://cran.r-project.org/web/packages/ape/index.html)
ace(x, phy, type = "continuous", method = "ML", CI = TRUE, model = "BM", scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1)
Method
The trait is assumed to evolve according to a Brownian motion process. Under this model, the expected difference between two taxa can be computed as a function of the time separating the taxa from their most recent common ancestor, which is obtained from the phylogenetic tree. Maximum Likelihood is then used to obtain the ancestors' trait values which minimize the sum of squared changes along the branches.
Output
The output is a table of ancestral trait values and the corresponding 95% confidence intervals. These value estimates can be plotted on the phylogenetic tree using a color gradient.
(Note: branches are usually colored with gradients)
Additionally, the function outputs an estimate of the Brownian motion parameter sigma2and the log likelihood of the model.
References
Schluter, D., Price, T., Mooers, A. O. and Ludwig, D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution, 51, 1699-1711.
Paradis, E., Claude, J. and Strimmer, K. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.