RRphylo (version 2.5.0)

fix.poly: Resolving polytomies to non-zero length branches

Description

The function either collapses clades under a polytomy or resolves polytomous clades to non-zero length branches, dichotomous clades.

Usage

fix.poly(tree,type=c("collapse","resolve"),node=NULL)

Arguments

tree

a phylogenetic tree.

type

either 'collapse' to create or 'resolve' to resolve (fix) a polytomy to a specific node indicated by the argument node.

node

the node in the tree where a polytomy should be resolved of fixed, either. If type='resolve' and node is left unspecified all the polytomies present in the tree are resolved.

Value

A phylogenetic tree with randomly fixed (i.e. type='resolve') polytomies or created polytomies (i.e. type='collapse').

Details

Under type='resolve' polytomous clades are resolved adding non-zero length branches to each new node. The evolutionary time attached to the new nodes is partitioned equally below the dichotomized clade.

References

Castiglione, S., Serio, C., Piccolo, M., Mondanaro, A., Melchionna, M., Di Febbraro, M., Sansalone, G., Wroe, S., & Raia, P. (2020). The influence of domestication, insularity and sociality on the tempo and mode of brain size evolution in mammals. Biological Journal of the Linnean Society,in press. doi:10.1093/biolinnean/blaa186

See Also

fix.poly vignette;

Examples

# NOT RUN {
 require(ape)

 data("DataCetaceans")
 DataCetaceans$treecet->treecet

 # Resolve all the polytomies within Cetaceans phylogeny
 fix.poly(treecet,type="resolve")->treecet.fixed
 par(mfrow=c(1,2))
 plot(treecet,no.margin=TRUE,show.tip.label=FALSE)
 plot(treecet.fixed,no.margin=TRUE,show.tip.label=FALSE)

 # Resolve the polytomies pertaining the genus Kentriodon
 fix.poly(treecet,type="resolve",node=221)->treecet.fixed2
 par(mfrow=c(1,2))
 plot(treecet,no.margin=TRUE,show.tip.label=FALSE)
 plot(treecet.fixed2,no.margin=TRUE,show.tip.label=FALSE)

 # Collapse Delphinidae into a polytomous clade
 fix.poly(treecet,type="collapse",node=179)->treecet.collapsed
 par(mfrow=c(1,2))
 plot(treecet,no.margin=TRUE,show.tip.label=FALSE)
 plot(treecet.collapsed,no.margin=TRUE,show.tip.label=FALSE)
# }