Transcript and module level signatures of adaptive evolution
At the per-transcript level, estimates of QST across both gardens ranged from 0 to 1 (Fig. 3), with a mean
(\(\pm\ 1\ sd)\) of 0.31 \(\pm\) 0.37 for the cold garden and 0.37\(\pm\) 0.38 for the warm garden. Approximately 50% of the transcripts
exhibited differentiation below 0.10 in the cold garden, while 40% were
below 0.10 in the warm garden. Only 20% of the transcripts exhibited
strong differentiation (> 0.90) in either garden. The
distribution of FST using genome-wide ddRADseq
markers was clustered around zero, with a multilocusFST of 0.015 (95% CI [0.06, 0.08]) (Fig.
S2.c). Using QST-FST comparisons,
we classified 234 transcripts as Cold-condA, 344 transcripts as
Warm-condA and 26 transcripts as Ad-Pl (Fig. 2) thus supporting H1 and
H2 at the per-transcript level.
At the cold garden, the co-expression network consisted of 22,757
transcripts, which were grouped into 31 modules (Methods S3, Fig S5),
with the number of transcripts per module ranging from 75 to 5,668. At
the warm garden, the co-expression network consisted of 23,468
transcripts, which were grouped into 26 modules, with the number of
transcripts per module ranging from 96 to 9,410 (Methods S3, Fig S5).
Using the eigengene values of each module, we identified 20 modules at
the warm garden and 21 at the cold garden that were strongly
differentiated across populations (Table S3). Of the 20 modules
identified at the warm garden, five were significantly enriched for
transcripts classified as Warm-condA (p < 0.05). Five
modules were significantly depleted for Warm-condA transcripts and did
not overlap with the 20 strongly differentiated modules (Fig. 4; Table
S3). Similarly, at the cold garden four of the 21 strongly
differentiated modules were significantly enriched (p <
0.05) for transcripts categorised under Cold-condA. Three modules were
significantly depleted (p < 0.05) for Cold-condA
transcripts and did not overlap with the 21 strongly differentiated
modules (Fig. 4; Table S3). At the warm garden, the number of
transcripts in enriched modules ranged from 125 to 3,439, while at the
cold garden they ranged from 139 to 5668. Q STenrichment or depletion was not associated with module size across
either garden (Cold garden: H = 4.78, df = 2, p =
0.09; Warm garden: H = 0.68, df = 2, p = 0.71).
These patterns of strong module level population differentiation noted
across both gardens render support for H1.