Molecular Dating With Mean Path Lengths
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.
chronoMPL(phy, se = TRUE, test = TRUE)
- an object of class
- a logical specifying whether to compute the standard-errors
of the node ages (
- a logical specifying whether to test the molecular clock
at each node (
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
Absolute dating can be done by multiplying the edge lengths found by calibrating one node age.
- 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.
The present version requires a dichotomous tree.
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.
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")