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 = mean 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
# NOT RUN {
### 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)
# }
Documentation reproduced from package ape, version 5.3, License: GPL (>= 2)

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