chronoMPL: Molecular Dating With Mean Path Lengths

In ape: Analyses of Phylogenetics and Evolution

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)

Arguments

phy	an object of class "phylo".
se	a logical specifying whether to compute the standard-errors of the node ages (TRUE by default).
test	a logical specifying whether to test the molecular clock at each node (TRUE by default).

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.

Value

an object of class "phylo" with branch lengths as estimated by the function. There are, by default, two attributes:

stderr	the standard-errors of the node ages.
Pval	the P-value of the test of the molecular clock for each node.

Note

The present version requires a dichotomous tree.

Author(s)

Emmanuel Paradis

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")
layout(1)

ape documentation built on May 29, 2024, 10:50 a.m.