Environmental association analysis
All three EAA approaches found putatively adaptive SNPs for each of the
five climate variables (Table S2, tabs 1-5). The RDA approach identified
fewer candidate SNPs than BAYPASS and LFMM that identified similar
numbers (Figure 3; Table S1). The proportion of overlapped SNPs is
different for each variable (Figure 3). Overall, 2,336 unique SNPs were
flagged to be associated with at least one of the tested climate
variables across the three EAA approaches. RDA analysis (Figure S3)
identified between 16 (TSEAS) and 57
(TMAX) SNPs significantly associated with each of the
climate variables, for a total of 168 SNPs. All five climate variables
were shown to be significantly associated with variation in the RDA
(TSEAS: F = 3.98, p = 0.001;
TMAX: F = 2.26, p = 0.001;
TMIN: F = 2.11, p = 0.001;
PMA: F = 1.80 p = 0.001;
PWQ: F = 1.49, p = 0.001). LFMM identified
between 263 (PMA) and 411 (TMAX) SNPs
with significant correlations, with a total of 1,753 candidate SNPs.
BAYPASS identified between 284 (TMIN) and 888
(TMAX) SNPs with significant correlations, with a total
of 2,327 candidate SNPs. Candidates found for all environmental
variables from each EAA method were used in further analyses to predict
the distribution of adaptive SNPs, specifically the ones occurring in
genic regions (annotation) and have robust associations with climate
(GDM).