Data from: Adaptation to reef habitats through selection on the coral animal and its associated microbiome

Spatially adjacent habitats on coral reefs can represent highly distinct
environments, often harbouring different coral communities. Yet, certain
coral species thrive across divergent environments. It is unknown whether
the forces of selection are sufficiently strong to overcome the
counteracting effects of the typically high gene flow over short
distances, and for local adaptation to occur. We screened the coral genome
(using restriction-site-associated sequencing [RAD-seq]), and
characterized both the dinoflagellate photosymbiont and tissue-associated
prokaryote microbiomes (using metabarcoding) of a reef flat and slope
population of the reef-building coral, Pocillopora damicornis, at two
locations on Heron Island in the southern Great Barrier Reef. Reef flat
and slope populations were separated by <100 m horizontally and ~5
m vertically and the two study locations were separated by ~1 km. For the
coral host, genetic divergence between habitats was much greater than
between locations, suggesting limited gene flow between the flat and slope
populations. Consistent with environmental selection, outlier loci
primarily belonged to the conserved, minimal cellular stress response,
likely reflecting adaptation to the different temperature and irradiance
regimes on the reef flat and slope. Similarly, the prokaryote community
differed across both habitat and, to a lesser extent, location, whereas
the dinoflagellate photosymbionts differed by habitat but not location.
The observed intra-specific diversity associated with divergent habitats
supports that environmental adaptation involves multiple members of the
coral holobiont. Adaptive alleles or microbial associations present in
coral populations from the environmentally-variable reef flat may provide
a source of adaptive variation for assisted evolution approaches, through
assisted gene flow, artificial cross-breeding or probiotic inoculations,
with the aim to increase climate resilience in the slope populations.