evol.distinct function

Species' evolutionary distinctiveness

Calculates evolutionary distinctiveness measures for a suite of species by: a) equal splits (Redding and Mooers 2006) b) fair proportions (Isaac et al., 2007). Returns a datafram with species identifiers and species scores. 1.1

evol.distinct(tree, type = c("equal.splits", "fair.proportion"),
    scale = FALSE, use.branch.lengths = TRUE)

Arguments

• tree: an object of class phylo
• type: a) equal splits (Redding and Mooers 2006) or b) fair proportions (Isaac et al., 2007)
• scale: The scale option refers to whether or not the phylogeny should be scaled to a depth of 1 or, in the case of an ultrametric tree, scaled such that branch lengths are relative.
• use.branch.lengths: If use.branch.lengths=FALSE, then all branch lengths are changed to 1.

References

Redding, D.W. and Mooers, A.O. (2006). Incorporating evolutionary measures into conservation prioritisation. Conservation Biology, 20, 1670-1678.

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.

Mark Vellend, William K. Cornwell, Karen Magnuson-Ford, and Arne Mooers. In press. Measuring phylogenetic biodiversity. In: Biological diversity: frontiers in measurement and assessment. Edited by Anne Magurran and Brian McGill.

Author(s)

Karen Magnuson-Ford, Will Cornwell, Arne Mooers, Mark Vellend

Note

This function will return a vector of evolutionary distinctivenss for every species in the given tree. If only a subset of values are needed there are two, concetually distinct options: either prune the tree first and then pass the tree in or subset the resulting vector. These two options will provide very different outputs.