This function calculates EDGE by combining evolutionary distinctiveness (ED; i.e., phylogenetic isolation of a species) with global endangerment (GE) status as defined by the International Union for Conservation of Nature (IUCN).
EDGE(x, phy, Redlist = "Redlist", species = "species", ...)a data.frame
a phylogenetic tree (object of class phylo).
column in the data frame with the IUCN ranks: LC,
NT, VU, EN, CR, and EX.
data frame column specifying the taxon
Further arguments passed to or from other methods.
Returns a dataframe of EDGE scores
EDGE is calculated as: $$log(1+ED) + GE*log(2)$$
where ED represents the evolutionary distinctiveness score of each
species (function evol_distinct), i.e. the degree of phylogenetic
isolation, and combining it with GE, global endangerment from IUCN
conservation threat categories. GE is calculated as the expected
probability of extinction over 100 years of each taxon in the phylogeny
(Redding & Mooers, 2006), scaled as follows: least concern = 0.001, near
threatened and conservation dependent = 0.01, vulnerable = 0.1,
endangered = 0.67, and critically endangered = 0.999.
Redding, D.W., & Mooers, A.Ø. (2006) Incorporating evolutionary measures into conservation prioritization. Conservation Biology 20: 1670–1678.
Isaac, N.J., Turvey, S.T., Collen, B., Waterman, C. & Baillie, J.E. (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE 2: e296.
data(africa)
y <- EDGE(x=africa$IUCN, phy=africa$phylo, Redlist="IUCN", species="Species")