Mapping predicted variation (below) shows putative local adaptation across the reef, primarily driven by depth and water chemistry.

Our findings suggest that temperature wasn’t a main driver of genetic divergence, but depth and water chemistry may be more important when transplanting corals.

We found 3 cryptic genetic lineages in each coral species, structured similarly by depth. Within each lineage, variation was better explained by depth and water chemistry than temperature.

Our results indicate that depth and water chemistry play a more significant role in coral adaptation in Florida than temperature. This underscores the need to consider a variety of environmental factors, rather than focusing solely on temperature, when selecting populations for assisted gene flow.

These findings are relevant for planning assisted gene flow and restoration efforts: not just any warmer reef would be an optimal source of transplants. For example, if choosing coral genotypes to repopulate the Marquesas Keys, the upper keys (circled) may be more suitable than Looe Key nearby.

Visualizing the predicted environment-associated genetic variation on a map suggests that these associations reflect adaptation to certain aspects of the inshore-offshore environmental gradient.

We applied RDAforest for detecting genotype-environment associations and found that within-lineage variation was cumulatively explained by water chemistry (nitrogen, phosphorus, silicate, and salinity). Thermal parameters were also consistently important but had a relatively low explanatory power.

Both species comprised three genetically distinct lineages distributed across depths in a remarkably similar way- hereby referred to as the yellow (shallow-specialist), blue (shallow-preferring) and indigo (depth-tolerant) lineages.