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).