Evolutionary rate simulation
To illustrate the difference between evolutionary rate estimates based
on traditional coding schemes using a continuous measure of central
tendency measure (median environmental values at suitable sites) and our
coding scheme based on considering the range of suitable values
independent of their frequency across the landscape, we generated 4 sets
of 100 stochastic birth-death phylogenies (birth rate = 1, death rate =
0) with 6, 50, 100, and 490 tip taxa using the R package phytoolsv.0.6-99 (Revell, 2012). Then, we randomly assigned simulated cool niche
species to the tips of each tree. To characterize each species’ niche,
we used two methods: (i) a traditional approach that uses the median
cell value of suitable area within M to represent the species’
fundamental niche, and (ii) the midpoint bin value from ‘known’ bins
using our new coding method (representing a best-case scenario in which
all species have completely characterized niches. This same process was
then repeated for the warm niche species.
These two datasets simulate the simplest evolutionary scenario: a
completely conserved fundamental niche across the clade. However,
estimates of niche evolution based on realized niches may differ greatly
from this known value; as such, we compared rates of niche evolution
estimated from our two coding schemes (traditional and known-bin). To
estimate rates of niche evolution, we calculatedσ 2, the rate of Brownian motion (BM) evolution,
using the fitContinuous function in the R package geigerv.2.0.6 (Harmon et al. 2008).σ 2 is equal to the rate of variance
accumulation per unit of branch length
(Felsenstein 1985;
O’Meara et al. 2006), and has been
interpreted as a measure of the rate of ecological niche evolution
(Cooper et al. 2011). Smallerσ 2 values can be interpreted as representing
less niche evolution, and larger σ 2 values as
more niche evolution. σ 2 itself, however, does
not provide information on whether niches are conserved, but rather
informs about degrees of change among traits or groups
(Revell et al. 2008;
Cooper et al. 2011). Code for analyses can
be found in Supplement 3; annoted code with tables and figures provided
as an HTML document in Supplement 4.