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: