Background Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Results Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were con‑ sistently detected across different methods. Conclusions The repeated observation of genetically divergent lineages associated with mesophotic depths high‑ lights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.

Depth range
2- 127 m

Mesophotic “mentions”
60 x (total of 7804 words)

Classification
* Presents original data
* Focused on 'mesophotic' depth range
* Focused on 'mesophotic coral ecosystem'

Fields
Molecular ecology
Taxonomy

Focusgroups
Scleractinia (Hard Corals)

Locations
Australia - Coral Sea
Australia - Great Barrier Reef
Bonaire
Colombia - Caribbean Sea
Curaçao
Israel - Red Sea
USA - Hawaii
Bermuda

Platforms
Manned Submersible
Remotely Operated Vehicle (ROV)
SCUBA (open-circuit or unspecified)