Drivers of adaptive evolution at the per-transcript level
Drought, freeze and geography associated variables jointly explained
50% of the expression variance for the Cold-condA category, 17% for
the Warm-condA category and 19% for the Ad-Pl category (Table 1). The
full model with all three predictors was significant only for the
Cold-condA category and this was driven by geography and drought on the
first RDA axis (p geo = 0.004,p drought = 0.011).
Estimates of genomic ancestry for the 30 maternal trees ranged from 0.18
to 1.00 (Fig. S2b), with 100% genomic ancestry from P. flexilisset at a value of 1.0. Survival estimates ranged from 0.37 to 1.00 at
the Cold garden and from 0.23 to 0.90 at the Warm garden. Across both
gardens, estimated survival of maternal trees was positively correlated
with their genomic ancestries (Pearson’s r ; Warm garden: r= 0.24, p = 0.18; Cold garden: r = 0.40, p = 0.02).
On average (± 1 sd), population-level expression values were weakly
correlated with population-level estimates of ancestry (-0.02 ± 0.31 in
Cold garden and 0.02 ± 0.31 in Warm garden). Correlation coefficients
for individual transcripts, however, ranged from -0.6 to 0.8 for
Cold-condA, from -0.8 to 0.8 for Warm-condA and from -0.6 to 0.4 for
Ad-Pl. The cumulative distribution of correlation coefficients between
ancestry and transcript abundance for all categories was not
significantly different from their respective matched background set of
transcripts (Cold-condA: D = 0.05, p = 0.702; Warm-condA:D = 0.03, p = 0.84; Ad-Pl: D = 0.13, p =
0.74). Several transcripts in the Warm-condA and Cold-condA categories
displayed significant associations with ancestry (p <
0.05), but none were significant after multiple test corrections. No
transcript in the Ad-Pl category was significantly associated with
ancestry.
Expression values on average (± 1 sd) were weakly correlated with
survival estimates (Cold garden: r = -0.008 ± 0.32; Warm garden:r = 0.029 ± 0.33). Correlation coefficients for individual
transcripts, however, ranged from r = -0.68 to 0.76 for
Cold-condA, from r = -0.89 to 0.73 for Warm-condA and fromr = -0.42 to 0.55 for Ad-Pl category. The cumulative
distributions of correlation coefficients for all categories were not
significantly different from their respective backgrounds (Cold-condA:D = 0.073, p = 0.817; Warm-condA: D = 0.065,p = 0.11; Ad-Pl: D = 0.17, p = 0.39). Similar to
the case of ancestry, we identified several transcripts for the
Warm-condA and Cold-condA categories as significantly associated with
survival (p < 0.05), although none passed the multiple
testing correction. No transcript in the Ad-Pl category was
significantly associated with survival.
While no GO terms were enriched in either Q STcategories, significant depletion was noted for GO terms related to
signal transduction and cell communication in Cold-condA, and for
hydrolase activity in Warm-condA (Table S2). Several transcripts related
to freeze and drought tolerance, as well as cell wall modulation were
classified under the Cold-condA category. These included VIN3 ,PPR , XTH and Aquaporins such as TIP1 (Sung &
Amasino, 2005; Raimund, 2015; Tucker et al ., 2018). Similarly,
the Warm-condA category contained transcripts related to drought stress
response and photosynthesis, including numerous ERF family genes,SWEET , WRKY, psbE and multiple auxin responsive elements,
such as ARF2 (Lata et al ., 2015; Zhang et al .,
2020). Transcripts classified in the Ad-Pl category, included auxin
responsive elements, such as SAUR50 (Sun et al ., 2016),
which is critical for light signaling, α-expansin and ABA
signaling pathway family genes, such as LPPD , which have known
roles in numerous plant developmental and stress response pathways
(Marowa et al ., 2016). Thus, even without clear relationships
between population-level transcript abundances, survival, and genomic
ancestry by QST category, there were several
notable examples of functionally sensible genes in eachQST category consistent with adaptive responses
to drought and freeze gradients. Together with the analyses presented in
the previous section these results provide support for hypothesis H1 and
H2 at the per-transcript level but render minimal support for H3.