title: Deep reefs are not universal refuges: Reseeding potential varies among coral species.
abstract: Deep coral reefs (that is, mesophotic coral ecosystems) can act as refuges against major disturbances affecting shallow reefs. It has been proposed that, through the provision of coral propagules, such deep refuges may aid in shallow reef recovery; however, this "reseeding" hypothesis remains largely untested. We conducted a genome-wide assessment of two scleractinian coral species with contrasting reproductive modes, to assess the potential for connectivity between mesophotic (40 m) and shallow (12 m) depths on an isolated reef system in the Western Atlantic (Bermuda). To overcome the pervasive issue of endosymbiont contamination associated with de novo sequencing of corals, we used a novel subtraction reference approach. We have demonstrated that strong depth-associated selection has led to genome-wide divergence in the brooding speciesAgaricia fragilis(with divergence by depth exceeding divergence by location). Despite introgression from shallow into deep populations, a lack of first-generation migrants indicates that effective connectivity over ecological time scales is extremely limited for this species and thus precludes reseeding of shallow reefs from deep refuges. In contrast, no genetic structuring between depths (or locations) was observed for the broadcasting speciesStephanocoenia intersepta, indicating substantial potential for vertical connectivity. Our findings demonstrate that vertical connectivity within the same reef system can differ greatly between species and that the reseeding potential of deep reefs in Bermuda may apply to only a small number of scleractinian species. Overall, we argue that the "deep reef refuge hypothesis" holds for individual coral species during episodic disturbances but should not be assumed as a broader ecosystem-wide phenomenon.
authors.affiliation: Global Change Institute, The University of Queensland, St. Lucia, Queensland 4072, Australia.; Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St. Lucia, Queensland 4072, Australia.
authors.forename: Pim
authors.identifier: 0000-0001-6747-6044
authors.initials: P
authors.lastname: Bongaerts
authors.affiliation: School of Biological Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Riginos
authors.affiliation: School of Biological Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia.; Faculty of Biology and Chemistry, University of Bremen, Bremen 28359, Germany.
authors.forename: Ramona
authors.identifier: 0000-0003-1734-8225
authors.initials: R
authors.lastname: Brunner
authors.affiliation: Global Change Institute, The University of Queensland, St. Lucia, Queensland 4072, Australia.; Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St. Lucia, Queensland 4072, Australia.; School of Biological Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia.
authors.forename: Norbert
authors.initials: N
authors.lastname: Englebert
authors.affiliation: Bermuda Aquarium, Museum and Zoo, Flatts FL 04, Bermuda.
authors.forename: Struan R
authors.initials: SR
authors.lastname: Smith
authors.affiliation: Global Change Institute, The University of Queensland, St. Lucia, Queensland 4072, Australia.; Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St. Lucia, Queensland 4072, Australia.
authors.forename: Ove
authors.initials: O
authors.lastname: Hoegh-Guldberg
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000145:classification / Q000502:physiology; D057894:Coral Reefs; D008954:Models, Biological
keywords: Coral reefs; RADseq; deep reef refuge hypothesis; divergent selection; endosymbiont contamination; mesophotic coral ecosystems; vertical connectivity