Coral populations in the world’s warmest reefs, the Persian/Arabian Gulf
(PAG), represent an ideal model system to understand the evolutionary
response of coral populations to past and present environmental change
and to identify genomic loci that contribute to elevated thermal
tolerance. Here, we use population genomics of the brain coral Platygyra daedalea
to show that corals in the PAG represent a distinct subpopulation that
was established during the Holocene marine transgression, and identify
selective sweeps in their genomes associated with thermal adaptation. We
demonstrate the presence of positive and disruptive selection and
provide evidence for selection of differentially methylated haplotypes.
While demographic analyses suggest limited potential for genetic rescue
of neighboring Indian Ocean reefs, the presence of putative targets of
selection in corals outside of the PAG offers hope that loci associated
with thermal tolerance may be present in the standing genetic variation.