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 ().