expandTaxonTree: Extrapolating Lower-Level Taxon Phylogenies from Higher-Level...

In paleotree: Paleontological and Phylogenetic Analyses of Evolution

Extrapolating Lower-Level Taxon Phylogenies from Higher-Level Taxon Trees

Description

This function takes a tree composed of higher-level taxa and a vector of lower-level taxa belonging to the set of higher-level taxa included in the input tree and produces a tree composed of the lower-level taxa, by treating the higher-level taxa as unresolved monophyletic polytomies. A user can also mark higher taxa as paraphyletic such that these are secondarily collapsed and do not form monophyletic clades in the output tree.

Usage

expandTaxonTree(
  taxonTree,
  taxaData,
  collapse = NULL,
  keepBrLen = FALSE,
  plot = FALSE
)

Arguments

taxonTree	A phylogeny as an object of class phylo, where tips represent some 'higher taxa' that is to be expanded at a lower taxonomic level.
taxaData	Character vector of higher taxa, with elements names equal to the lower taxa. See below.
collapse	Character vector containing names of non-monophyletic higher taxa to be collapsed.
keepBrLen	Logical, decides if branch lengths should be kept or discarded. FALSE by default. See details below.
plot	If TRUE, plots a comparison between input and output trees

Details

The output tree will probably be a rough unresolved view of the relationships among the taxa, due to the treatment of higher-level taxa as polytomies. This is similar to the methods used in Webb and Donoghue (2005) and Friedman (2009). Any analyses should be done by resolving this tree with multi2di in the ape package or via the various time-scaling functions found in this package (paleotree).

The taxaData vector should have one element per lower-level taxon that is to be added to the tree. The name of each element in the vector should be the names of the lower-level taxa, which will be used as new tip labels of the output lower-taxon tree. There should be no empty elements! Otherwise, expandTaxonTree won't know what to do with taxa that aren't being expanded.

By default, all higher-level taxa are treated as monophyletic clades if not otherwise specified. The collapse vector can (and probably should) be used if there is doubt about the monophyly of any higher-level taxa included in the input taxon-tree, so that such a group would be treated as a paraphyletic group in the output tree.

Also by default, the output tree will lack branch lengths and thus will not be dated, even if the input phylogeny is dated. If keepBrLen = TRUE, then the tree's edge lengths are kept and new taxa are added as zero length branches attaching to a node that represents the previous higher-taxon. This tree is probably not useful for most applications, and may even strongly bias some analyses. USE WITH CAUTION! The collapse argument, given as a vector, will cause such edges to be replaced by zero-length branches rather than fully collapsing them, which could have odd effects. If collapse is not NULL and keepBrLen = TRUE, a warning is issued that the output probably won't make much sense at all.

Value

Outputs the modified tree as an object of class phylo, with the higher-level taxa expanded into polytomies and the lower-level taxa as the tip labels.

Author(s)

David W. Bapst

References

Friedman, M. 2009 Ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction. Proceedings of the National Academy of Sciences 106(13):5218–5223.

Webb, C. O., and M. J. Donoghue. 2005 Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes 5(1):181–183.

See Also

multi2di, bind.tree

Examples

set.seed(444)
# lets make our hypothetical simulated tree of higher taxa
taxtr <- rtree(10)
# taxa to place within higher taxa
taxd <- sample(taxtr$tip.label, 30, replace = TRUE)	
names(taxd) <- paste(taxd,"_x", 1:30, sep = "")
coll <- sample(taxtr$tip.label,3)		#what to collapse?
expandTaxonTree(taxonTree = taxtr, taxaData = taxd, 
                collapse = coll, plot = TRUE)

paleotree documentation built on Aug. 22, 2022, 9:09 a.m.