speciesTree: Species Tree Estimation
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) References Examples

This function calculates the species tree from a set of gene trees.

1	speciesTree(x, FUN = min)

`x`	a list of trees, e.g., an object of class `"multiPhylo"`.
`FUN`	a function used to compute the divergence times of each pair of tips.

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 = sum gives the shallowest divergence tree of Maddison and Knowles (2006).

an object of class "phylo".

Emmanuel Paradis

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.

### 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, sum) # shallowest divergence

layout(matrix(1:4, 1))
## playing with 'x.lim' is not so complicated
## but this will be improved someday
plot(tr1, "c", d = "u", y.lim = c(-0.07, 0.1), font = 1)
axisPhylo(4); title("Gene tree 1")
plot(tr2, "c", d = "u", y.lim = c(-0.05, 0.12), font = 1)
axisPhylo(4); title("Gene tree 2")
plot(TSmax, "c", d = "u", y.lim = c(-0.1, 0.07), font = 1)
axisPhylo(4); title("Species tree inferred\nby MAXTREE")
plot(TSsha, "c", d = "u", y.lim = c(0, 0.17), font = 1)
axisPhylo(4); title("Species tree inferred\nby Shallowest Divergence")