Niche marginality
As a measure of habitat quality, we used two approaches for assessing
niche marginality for each genetic clade as well as changes in niche
marginality from LGM to present. First, we calculated the present-day
marginality as the Mahalanobis distance between the centroid of the
niche ellipsoid from each clade to the centroid of the available
multivariate space in the PCA of current climatic conditions with the
“philentropy” package (Drost, 2018) in R. We also calculated the LGM
marginality as the Mahalanobis distance between the clade’s niche
centroid and the centroid of LGM available conditions in this same
multivariate space. We then compared the niche marginality (i.e.
Mahalonobis distances) between LGM and present by constructing a GLMM
that included time period (LGM vs present), clade location (north,
south, or unstructured), taxonomic group (mammal, plant, or reptile) and
elevation (highland or lowland) as factors, including taxon as a random
variable, and using a “gamma” distribution and “inverse” link
function.
For the second measurement of marginality, for each genetic clade we
obtained the suitability values for each cell from the raster
projections of the niche models onto geographic space with the
“raster” package (Hijmans, 2023) in R. We retained only values from
cells with suitability above the 10% omission rate threshold. Then,
each value was converted to niche marginality between 0 and 1, defined
as the inverse of suitability with the formula: