Genome-wide assessment reveals opposing patterns of vertical connectivity in two depth-generalist coral species.

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 consistently detected across different methods. Conclusions The repeated observation of genetically divergent lineages associated with mesophotic depths highlights 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.

Mesophotic coral communities are increasingly gaining attention for the unique and distinct biological species 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 rarely include mesophotic samples, and have long suffered from resolution issues associated with traditional sequence markers. Here, we used reduced-representation genome sequencing to provide a phylogenomic assessment of 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 substantial undescribed diversity (at least 24 molecular clades across the 8 species), including deep divergences within both genera and within current taxonomic species. Five of the eight focal species consisted of at least two sympatrically-occurring, genetically distinct clades, identified consistently across methods. The repeated observation of genetically divergent clades associated with mesophotic depths highlights that there are many more mesophotic-specialist coral species than currently acknowledged, and that an urgent assessment of this largely unstudied biological diversity is warranted.