Filtered SNP tables - Rangewide, Hamilton, Tejon, and Madera transects

Understanding how the environment shapes genetic variation provides
critical insight about the evolution of local adaptation in natural
populations. At multiple spatial scales and multiple geographic contexts
within a single species, such information could address a number of
fundamental questions about the scale of local adaptation and whether or
not the same loci are involved at different spatial scales or geographic
contexts. We used landscape genomic approaches from three local
elevational transects and range-wide sampling to 1) identify genetic
variation underlying local adaptation to environmental gradients in the
California endemic oak, Quercus lobata, 2) examine whether putatively
adaptive SNPs show signatures of selection at multiple spatial scales, and
3) map putatively adaptive variation to assess the scale and pattern of
local adaptation. Of over 10k single-nucleotide polymorphisms (SNPs)
generated with genotyping-by-sequencing, we found signatures of natural
selection by climate or local environment at over 600 SNPs (536 loci),
some at multiple spatial scales across multiple analyses. Candidate SNPs
identified with gene–environment tests (LFMM) at the range-wide scale also
showed elevated associations with climate variables compared to the
background at both range-wide and elevational transect scales with
gradient forest analysis. Some loci overlap with those detected in other
oak species, raising the question of whether the same loci might be
involved in local climate adaptation in different congeneric species that
inhabit different geographic contexts. Mapping landscape patterns of
adaptive versus background genetic variation identified regions of marked
local adaptation and suggests nonlinear association of candidate SNPs and
environmental variables. Taken together, our results offer robust evidence
for novel candidate genes for local climate adaptation at multiple spatial
scales.