Isolation By Distance
As an initial test of IBD, we implemented various classical statistics
based on Fst values (Slatkin 1993; Rousset 1997;
Hutchison and Templeton 1999; Diniz-Filho et al. 2013). We calculated
pairwise Fst using the approach of Weir and
Cockerham (1984) for individuals, populations, and lineages. For
individuals, we used a Mantel test with 999 permutations to evaluate
significance of the overall relationship between geographic and genetic
distance. For populations, we examined between- and within-lineage
slopes to estimate the relative prominence of local versus regional
structure. Finally, we calculated overall fixation between lineages as a
basic estimator for potentially species-level divergence (Roux et al.
2016). For individual and population-based analyses, we used linearizedFst =Fst /1-Fst.
As an additional test of both IBD and isolation by environment (IBE), we
used generalized dissimilarity modeling (GDM) in the R package ‘gdm’
(Ferrier et al. 2007; Mokany et al. 2022). We used the pairwiseFst matrix by site as our measure of genetic
dissimilarity, and the 9 continuous ecological variables, elevation, and
geographic distance (lat/long; see SI for list) as the environmental
predictors. We fit a GDM to these data and assessed variable inclusion
using estimated coefficients greater than zero, and variable importance
and significance using 1,000 permutations. We also evaluated model
significance and percent deviance explained.