phy.build: Build a novel phylogeny from existing data

In pez: Phylogenetics for the Environmental Sciences

Build a novel phylogeny from existing data

Description

Build a novel phylogeny from existing data

congeneric.impute sequentially add species to a phylogeny to form an _imputed_ bifurcating tree. Makes use of a result from Steel & Mooers (2010) that gives the expected branch-length under a Yule model whether the rate of diversification has been estimated. The intention of this is to approximate the method by which phylogenetic structure is sampled from the prior in BEAST; i.e., to approximate the standard Kuhn et al. (2011) method for imputing a phylogeny. When using congeneric.impute you should (1) repeat your analyses across many (if in doubt, thousands) of separate runs (see Kuhn et al. 2011) and (2) check for yourself that your trees are unbiased for your purpose - I make no guarantee this is appropriate, and in many cases I think it would not be. See also 'notes' below.

Usage

congeneric.merge(tree, species, split = "_", ...)

bind.replace(backbone, donor, replacing.tip.label, donor.length = NA)

congeneric.impute(tree, species, split = "_", max.iter = 1000, ...)

Arguments

tree	phylo phylogeny to have those species inserted into it
species	vector of species names to be bound into the tree if missing from it
split	the character that splits genus and species names in your phylogeny. Default is _, i.e. Quercus_robur.
...	ignored
backbone	backbone phylogeny (phylo) into which the donor is to be bound
donor	phylogeny (phylo) to bound into the backbone phylogeny
replacing.tip.label	the species in the donor phylogeny that's being replaced by the donor phylogeny
donor.length	how deep the donor phylogeny should be cut into the backbone phylogeny. If NA (default), then the bladj algorithm is followed (or, in plain English, it's put half-way along the branch)
max.iter	Sometimes the random draw for the new branch length to be added will be too large to allow it to be added to the tree. In such cases, congeneric.imput will randomly draw another branch length, and it will repeat this process max.iter times. See 'notes' for more on this.

Details

congeneric.merge Binds missing species into a phylogeny by replacing all members of the clade it belongs to with a polytomy. Assumes the tip.labels represent Latin binomials, split by the split argument. This code was originally shipped with phyloGenerator - this is the merge method in that program.

bind.replace Binds a phylogeny (donor) into a bigger phylogeny ('backbone'); useful if you're building a phylogeny a la Phylomatic. A version of this R code was shipped with phyloGenerator (Pearse & Purvis 2013). This is really an internal function for congeneric.merge, but hopefully it's of some use to you!

Value

phylo phylogeny

phylogeny (phylo)

Note

Thank you to Josep Padulles Cubino, who found that the genus name splitting in a previous version of this function could cause incorrect placement in oddly named cases. As with all phylogenetic construction tools, the output from congeneric.merge should be checked for accuracy before use.

Caveats for congeneric.impute: something I noticed is that BEAST randomly picks an edge to break when adding species (starting from a null tree), and this is the behaviour I have (attempted to) replicate here. It is not clear to me that this is unbiased, since a clade undergoing rapid diversification will have many edges but these will be short (and so cannot have an edge inserted into them following the method below). My understanding is this is a known problem, and I simply cannot think of a better way of doing this that doesn't incorporate what I consider to be worse pathology. Thus this method, even if it works (which I can't guarantee), it should tend to break long branches.

Author(s)

Will Pearse

Will Pearse

References

Pearse W.D. & Purvis A. phyloGenerator: an automated phylogeny generation tool for ecologists. Methods in Ecology and Evolution 4(7): 692–698.

Steel, M., & Mooers, A. (2010). The expected length of pendant and interior edges of a Yule tree. Applied Mathematics Letters, 23(11), 1315-1319.

Kuhn, T. S., Mooers, A. O., & Thomas, G. H. (2011). A simple polytomy resolver for dated phylogenies. Methods in Ecology and Evolution, 2(5), 427-436.

Examples

tree <- read.tree(text="((a_a:1,b_b:1):1, c_c:2):1;")
tree <- congeneric.merge(tree, c("a_nother", "a_gain", "b_sharp"))
tree <- read.tree(text="((a_a:1,b_b:1):1, c_c:2):1;")
tree <- congeneric.impute(tree, c("a_nother", "a_gain", "b_sharp"))

pez documentation built on Sept. 1, 2022, 1:09 a.m.