speciesTree {ape} | R Documentation |
Species Tree Estimation
Description
This function calculates the species tree from a set of gene trees.
Usage
speciesTree(x, FUN = min)
Arguments
x |
a list of trees, e.g., an object of class
|
FUN |
a function used to compute the divergence times of each pair of tips. |
Details
For all trees in x
, the divergence time of each pair of tips is
calculated: these are then ‘summarized’ with FUN
to build a new
distance matrix used to calculate the species tree with a
single-linkage hierarchical clustering. The default for FUN
computes the maximum tree (maxtree) of Liu et al. (2010). Using
FUN = mean
gives the shallowest divergence tree of Maddison and
Knowles (2006).
Value
an object of class "phylo"
.
Author(s)
Emmanuel Paradis
References
Liu, L., Yu, L. and Pearl, D. K. (2010) Maximum tree: a consistent estimator of the species tree. Journal of Mathematical Biology, 60, 95–106.
Maddison, W. P. and Knowles, L. L. (2006) Inferring phylogeny despite incomplete lineage sorting. Systematic Biology, 55, 21–30.
Examples
### example in Liu et al. (2010):
tr1 <- read.tree(text = "(((B:0.05,C:0.05):0.01,D:0.06):0.04,A:0.1);")
tr2 <- read.tree(text = "(((A:0.07,C:0.07):0.02,D:0.09):0.03,B:0.12);")
TR <- c(tr1, tr2)
TSmax <- speciesTree(TR) # MAXTREE
TSsha <- speciesTree(TR, mean) # shallowest divergence
kronoviz(c(tr1, tr2, TSmax, TSsha), horiz = FALSE,
type = "c", cex = 1.5, font = 1)
mtext(c("Gene tree 1", "Gene tree 2", "Species tree - MAXTREE"),
at = -c(7.5, 4, 1))
mtext("Species tree - Shallowest Divergence")
layout(1)