ape (version 3.0-3)

chronoMPL: Molecular Dating With Mean Path Lengths

Description

This function estimates the node ages of a tree using the mean path lengths method of Britton et al. (2002). The branch lengths of the input tree are interpreted as (mean) numbers of substitutions.

Usage

chronoMPL(phy, se = TRUE, test = TRUE)

Value

an object of class "phylo" with branch lengths as estimated by the function. There are, by default, two attributes:stderrthe standard-errors of the node ages.Pvalthe P-value of the test of the molecular clock for each node.

Details

The mean path lengths (MPL) method estimates the age of a node with the mean of the distances from this node to all tips descending from it. Under the assumption of a molecular clock, standard-errors of the estimates node ages can be computed (Britton et al. 2002).

The tests performed if test = TRUE is a comparison of the MPL of the two subtrees originating from a node; the null hypothesis is that the rate of substitution was the same in both subtrees (Britton et al. 2002). The test statistic follows, under the null hypothesis, a standard normal distribution. The returned P-value is the probability of observing a greater absolute value (i.e., a two-sided test). No correction for multiple testing is applied: this is left to the user.

Absolute dating can be done by multiplying the edge lengths found by calibrating one node age.

References

Britton, T., Oxelman, B., Vinnersten, A. and Bremer, K. (2002) Phylogenetic dating with confidence intervals using mean path lengths. Molecular Phylogenetics and Evolution, 24, 58--65.

See Also

chronopl

Examples

tr <- rtree(10)
tr$edge.length <- 5*tr$edge.length
chr <- chronoMPL(tr)
layout(matrix(1:4, 2, 2, byrow = TRUE))
plot(tr)
title("The original tree")
plot(chr)
axisPhylo()
title("The dated MPL tree")
plot(chr)
nodelabels(round(attr(chr, "stderr"), 3))
title("The standard-errors")
plot(tr)
nodelabels(round(attr(chr, "Pval"), 3))
title("The tests")