4. Discussion
We found no evidence of genome-wide parallelism in genetic divergence,
with possible exceptions of two strong outliers shared between the two
CO2 adaptation cases (Figure 3 and 4). At the same time,
we see evidence of pervasive sharing of up- and down-regulated genes
between three or more contrasts (Figure 6), suggesting common regulatory
response to all the studied environmental contrasts. This result is
encouraging because it suggests the lack of tradeoffs between various
acclimatization responses, which in turn suggests that corals would be
able to successfully handle diverse future challenges at the same time.
There was no greater-than-expected overlap of the regulatory responses
with the generalized stress response reported by Dixon et al., 2020,
despite the fact that most of the contrasts here can be interpreted as
stress-related (CO2 seep proximity, thermal variability,
latitudinal gradient). This lack of overlap may be due to time scale
difference: our study involved corals acclimatizing to lifelong stress
in their natural habitat, while Dixon et al., 2020 summarized
experiments within much shorter time frames (e.g., 24 hours, 72 hours, 5
weeks). If so, this result would emphasize the point that long-term
acclimatization and/or adaptation rarely involve the same mechanisms as
the short-term stress response ().
Since our observed gene regulation patterns do not match genetic
divergences, as would have been predicted in the case ofcis -regulatory evolution, what could be the driver of those
changes? At the face value, our results seem to suggest that corals
handle environmental variation exclusively via gene expression
plasticity, which contradicts multiple studies demonstrating that
genetics also plays a role (). One way to reconcile these results is to
assume that adaptation to environmental variation in corals is highly
polygenic and, moreover, genetically redundant, such that the same
phenotypic result can be achieved through genetic changes in multiple
alternative ways. In that case, even repeated adaptation to the same
stressor based on the same pool of standing genetic variation is
unlikely to yield similar genetic patterns (Yeaman 2022). This is
perhaps the reason why genetic determinants of coral bleaching tolerance
proved to be hard to identify ().