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 `"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"`.

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)
```

[Package ape version 5.5 Index]