geiger (version 1.3-1)

rc: Relative cladogenesis test

Description

Carries out relative cladogenesis test for all slices through the tree.

Usage

rc(phy, make.plot=TRUE, plot.bonf=FALSE, p.cutoff=0.05, cex=par("cex"))

Arguments

phy

Phylogenetic tree

make.plot

Plot tree with significant branches highlighted?

plot.bonf

Use bonferroni correction when highlighting significant branches on the tree plot? (see below for more details)

p.cutoff

Cutoff for significant p-values; only used when plotting

cex

A numeric value giving the factor scaling of the tip and node labels (Character EXpansion). The default is to take the current value from the graphical parameters.

Value

• Table of results with four columns: Number of ancestors, Maximum descendents, p-value, Bonferroni-corrected p-value

Details

A list of nodes is returned, along with the number of lineages alive just before that node, the maximum number of descendents that any of those lineages has at the present day, a p-value for this observation under the null hypothesis of a birth-death process (that is, given the null, what is the probability that one of these lineages had at least that many descendents), and the p-value after Bonferroni correction (given that a total of n-1 comparisons are made). If a plot is made, asterisks will mark significantly diverse clades. These asterisks appear just to the right of the MRCA of the diverse clade. The Bonferroni correction used here is exceedingly conservative for a tree of any reasonable size. I'm not sure that I recommend it, especially given the exploratory nature of this test and the non- independence of the comparisons. One will often see significant results "trickle down" nodes in the tree - that is, if one clade is expecially diverse, then one or more of its parent clades will also be diverse. I think the most parsimonious place to attribute this effect is to the most shallow significant branch - that is, the branch closest to the tips (see Moore et al. 2004).

References

Purvis, A., Nee, S. & Harvey, P. H. (1995) Proc. R. Soc. London Ser. B 260, pp. 329-333. Moore, B.R., K.M.A. Chan, and M.J. Donoghue. 2004. Detecting diversification rate variation in supertrees. In O.R.P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 487-533. Kluwer Academic, Dordrecht, the Netherlands.

Examples

data(geospiza)
attach(geospiza)

rc(geospiza.tree)