Do we have SRS?
We have good support for SRS at the Nimpal (NMP) location: lower genome-wide genetic diversity in juveniles compared to adults (Fig. 1 F) along with the occurrence of close relatives among juveniles (Fig. 1 G), the latter being particularly hard to explain without invoking SRS. Yet, other results do not conform to the classical SRS hypothesis: we detect variation in genetic diversity not only in juveniles but also in adults (Fig. 1 F), and we don’t see the emergence of “chaotic genetic patchiness” sensu(Johnson and Black 1982) in juveniles (Fig. 1 E).
One possible reason why we detect variation in genetic diversity but not divergence between pop:age groups could be the difference in power of these two analyses. Our genetic diversity comparison benefits from 14-fold replication across chromosomes, and is capable of revealing very subtle differences on the order of 2% of the mean. The signal of SNP covariance (i.e. genetic divergence) generated by such a minor change may simply not be detectable. Generally, the SRS signal is expected to be weak in our case because all our pop:age groups, even juveniles, were likely pooled across several recruitment years, averaging out the SRS signature. In the future, to maximize the power of SRS detection, it would be advisable to ensure that the compared groups of corals truly represent same-year recruitment cohorts. This should not be too difficult for juveniles of broadcast-spawning corals that only recruit once a year: the youngest corals sampled shortly before the spawning season are very likely the same recruitment cohort from the previous year.
Why do we see variation in genetic diversity in every direction in both adults and juveniles (Fig. 1 F)? While it is tempting to once again invoke recruitment stochasticity (i.e. some form of SRS), another viable explanation would be environmental filtering that varies both in space and time. These alternatives (stochasticity versus selection) could not be resolved with our sparse 2bRAD data. One would need whole-genome resequencing to look for evidence of temporally- and spatially-varying selection in the form of regions of lower diversity forming extended haplotypes, rather than being distributed evenly across the genome as is expected in the case or recruitment stochasticity.
Even though the evidence for SRS is still inconclusive, we believe it would be prudent to keep the possibility of SRS in mind, especially when planning efforts aimed at preserving or restoring coral genetic diversity (Baums et al. 2019). While SRS does not seem to affect adaptive potential in long-lived corals (Fig. 1 A-C), likely because multiple recruitment events per generation help maintain genetic diversity (Fig. 2 E), it can have stronger effect on adaptive potential when recruitment is very infrequent (Dennis Hedgecock and Pudovkin 2011), like in Acropora and Orbicella in the Caribbean (van Woesik, Scott, and Aronson 2014; Kuffner and Toth 2016).