calcED: Calculate Evolutionary Distinctness
In DomBennett/MoreTreeTools: Tools for manipulating phylogenetic trees

Description Usage Arguments Details References See Also Examples

Calculate species evolutionary distinctness (ED) using one of three methods: Fair Proportion (FP), Equal Splits (ES) or Pendant Edge (PE).

1	calcED(tree, tips = "all", type = "FP")

`tree`	phylogenetic tree (ape class)
`tips`	vector of tips for which ED is calculated, else 'all'
`type`	method of ED calculation, either 'all', 'FP', 'ES' or 'PE' (default FP)

Evolutionary distinctness is a measure of how much independent evolution a species represents. Multiple methods exist for its calculation all of which require an ultrametric phylogenetic tree. The methods used here are Pendant Edge (PE) the length of a species branch that connects it to the tree (Altschul and Lipman, 1990), Fair Proportion (FP) the total proportion of the phylogenetic tree that a species represents where each branch is equally divided between all descdendants (Isaac et al. 2007) and Equal Splits (ES) where branch lengths are equally divided between descendents at every node in the tree (Redding and Mooers 2006)

No references yet! https://github.com/DomBennett/MoreTreeTools.

Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C. and Baillie, J.E.M. (2007). Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE, 2, e296.

Altschul, S., and Lipman, D. (1990). Equal animals. Nature.

Redding, D. W., and Mooers, A. Ø. (2006). Incorporating evolutionary measures into conservation prioritization. Conservation Biology : The Journal of the Society for Conservation Biology, 20(6), 1670–8.

evol.distinct, catarrhines

# Load catarrhine tree
data(catarrhines)
ed.vals <- calcED (catarrhines, type='all')
# Which Old World monkeys are the most distinct?
ed.vals[ed.vals$FP == min (ed.vals$FP), ]
ed.vals[ed.vals$ES == min (ed.vals$ES), ]
ed.vals[ed.vals$PE == min (ed.vals$PE), ]