eDNA data set from 63 locations of Okinawa Island

Coral reefs have the highest biodiversity of any marine ecosystem in
tropical and subtropical oceans. However, scleractinian corals, keystone
organisms of reef productivity, are facing a crisis due to climate change
and anthropogenic activities. A broad survey of reef-building corals is
essential for world-wide reef preservation. To this end, direct
observations made by coral-specialist divers can be supported by a more
convenient method. We improved a recently devised environmental DNA (eDNA)
metabarcoding method to identify more than 43 scleractinian genera by
sampling 2 L of surface seawater above reefs. Together with direct
observations by divers, we assessed the utility of eDNA at 63 locations
spanning ~250 km near Okinawa Island. Slopes of these islands are
populated by diverse coral genera, whereas shallow “moats” sustain fewer
and less varied coral taxa. Major genera recorded by divers included
Acropora, Pocillopora, Porites, and Montipora, the presence of which was
confirmed by eDNA analyses. In addition, eDNA identified more genera than
direct observations and documented the presence of new species. This
scleractinian coral-specific eDNA method promises to be a powerful tool to
survey coral reefs broadly, deeply, and cost-effectively.