speciesTree

0th

Percentile

Species Tree Estimation

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

Keywords
models
Usage
speciesTree(x, FUN = min)
Arguments
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.
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 = sum gives the shallowest divergence tree of Maddison and Knowles (2006).

Value

  • an object of class "phylo".

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.

Aliases
  • speciesTree
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, 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
by MAXTREE")
plot(TSsha, "c", d = "u", y.lim = c(0, 0.17), font = 1)
axisPhylo(4); title("Species tree inferred
by Shallowest Divergence")
Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)

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