Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa) and uncover, through a comprehensive genomic and phenotypic assessment, that it comprises morphologically indistinguishable but ecologically divergent lineages. Demographic modeling based on whole-genome resequencing indi- cated that morphological crypsis (across micro- and macromorphological traits) was due to ancient morphological stasis rather than recent divergence. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid molecular assay revealed differenti- ation of their ecological distributions. Leveraging ‘‘common garden’’ conditions facilitated by the overlap- ping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate the presence of ecologically and phenotypically divergent coral species without substantial morphological differentiation and provide new leads into the potential mechanisms facilitating such divergence. More broadly, they indi- cate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

Depth range
7- 85 m

Mesophotic “mentions”
2 x (total of 2592 words)

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

Fields
Connectivity
Ecology
Molecular ecology
Reproduction

Focusgroups
Scleractinia (Hard Corals)

Locations
Australia - Coral Sea
Australia - Great Barrier Reef
Israel - Red Sea
Japan - Ryukyu Islands (Okinawa)
Papua New Guinea

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