Resolving polytomies to non-zero length branches
The function either collapses clades under a polytomy or resolves polytomous clades to non-zero length branches, dichotomous clades.
fix.poly(tree,type=c("collapse","resolve"),node=NULL)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 |
the node in the tree where a polytomy should be resolved of
fixed, either. If |
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.
A phylogenetic tree with randomly fixed (i.e. type='resolve')
polytomies or created polytomies (i.e. type='collapse').
Pasquale Raia, Silvia Castiglione, Carmela Serio
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
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.