Bongaerts et al. 2017

scientific article | Science Advances | open access Open access small aa108fa7f478951c693af64a05bc4b46e6711dbb69a20809512a129d4d6b870f

Deep reefs are not universal refuges: Reseeding potential varies among coral species

Bongaerts P, Riginos C, Brunner R, Englebert N, Smith SR, Hoegh-Guldberg O

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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 species Agaricia 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 species Stephanocoenia 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.

Behind the science
Travel Norbert Processing
Stormy bermuda2 Emilyspinnacles1 christophe bailhache David transect
Research sites

10.1126   sciadv.1602373
Depth range
10- 42 m

Mesophotic “mentions”
50 x (total of 7469 words)

Molecular ecology Connectivity

Research focus
Scleractinia (Hard Corals)


Research platforms
Diving - Technical Open-Circuit
Author profiles
Pim Bongaerts ( 24 pubs)
Norbert Englebert ( 8 pubs)