Genotyping Reveals Significance of Mesophotic Reefs for Florida Keys’ Coral Recovery

Coral cover on shallow reef systems (0 to 30 meters) in the Florida Keys has declined over the past several decades, punctuated by severe losses during coral disease outbreaks and bleaching events. However, some areas within the Florida Keys, especially the Dry Tortugas and many upper mesophotic habitats (30 to 60 meters), have maintained relatively healthy coral communities, even in the face of recent severe and widespread coral disease outbreaks.

Relatively little is known about the genetic connectivity of corals among these sites or the potential for mesophotic sites to serve as refuges by contributing to metapopulation recovery and persistence. No previous studies have characterized or compared the genetic structure between paired shallow and upper mesophotic depth zones of the stony coral species, Montastraea cavernosa, across reef habitats throughout the Florida Keys. It is believed that mesophotic reefs, by nature of their depth and distance from land, may be inherently buffered from environmental stressors that more severely impact shallow coral communities.

Using a single-nucleotide polymorphism (SNP) genotyping approach, researchers from Florida Atlantic University’s Harbor Branch Oceanographic Institute quantified and compared the genetic structure and genomic diversity of paired shallow and upper mesophotic sites in the Northern and Southern Dry Tortugas and the Lower and Upper Keys.

Results of the study, published in the journal Coral Reefs, suggest that while vertical connectivity between paired shallow and mesophotic populations can vary, certain mesophotic coral populations are likely important for maintaining the long-term survival of this ecologically important coral species throughout the Florida Keys and should be considered in future management strategies.

A high-resolution restriction site-associated DNA sequencing technique termed 2bRAD was employed to generate a suite of thousands of SNP markers dispersed throughout the genome. A genetic dataset based on a suite of more than 9,000 SNP loci indicated that the level of vertical genetic connectivity between paired shallow and upper mesophotic populations varied significantly based on location. Shallow and upper mesophotic M. cavernosa populations in the Northern Dry Tortugas and the Upper Keys were genetically similar to one another. In contrast, populations were significantly differentiated across depth in the Lower Keys and Southern Dry Tortugas. While upper mesophotic populations in the Lower Keys and Southern Dry Tortugas were distinct from their shallow counterparts, there was evidence of relatively high levels of genetic connectivity to both the shallow and upper mesophotic populations downstream in the Upper Keys.

“Ultimately, this genetic characterization of a dominant species across the Florida Keys can inform management efforts within Florida Keys National Marine Sanctuary,” said Alexis B. Sturm, first author and a Ph.D. candidate in the Voss Laboratory at FAU Harbor Branch. “These data provide a genomic diversity benchmark that should be considered in coral restoration efforts. In addition, some upper mesophotic communities which are, as of yet, relatively un-impacted by stony coral tissue loss disease outbreaks may serve as important genetic refugia and possible sources of larvae for connected shallow coral populations.”

The researchers stress that further characterization and continued monitoring of these upper mesophotic reefs are needed to better understand the ecosystem services they provide and risks they may face.

“Overall, the genetic results of our study highlight the need to conserve these important mesophotic reef communities and incorporate them into our understanding of coral metapopulation dynamics in the Florida Keys,” said Joshua D. Voss, Ph.D., an associate research professor at FAU Harbor Branch and executive director of the NOAA Cooperative Institute for Ocean Exploration, Research, and Technology (CIOERT) and senior author on the study.  “In addition, quantification of genetic diversity across natural coral populations is critical to informing novel coral management tools currently being developed and employed in the Florida Keys, including coral restoration and reef-wide efforts to preserve species and genetic diversity.”

Study co-authors include Ryan J. Eckert, a Ph.D. student, and Ashley M. Carreiro, an M.S. student, both within the Voss Laboratory at FAU Harbor Branch.

This research was supported by NOAA Office of Ocean Exploration and Research (NA14OAR4320260) awarded to Voss through the CIOERT. Additional funding was awarded to Sturm through a National Science Foundation Graduate Research Fellowship and scholarships from Florida Sea Grant and the Women Divers Hall of Fame. All corals were collected under permit FKNMS-2019-088 from Florida Keys National Marine Sanctuary.

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About Harbor Branch Oceanographic Institute: Founded in 1971, Harbor Branch Oceanographic Institute at Florida Atlantic University is a research community of marine scientists, engineers, educators and other professionals focused on Ocean Science for a Better World. The institute drives innovation in ocean engineering, at-sea operations, drug discovery and biotechnology from the oceans, coastal ecology and conservation, marine mammal research and conservation, aquaculture, ocean observing systems and marine education. For more information, visit www.fau.edu/hboi.

About Florida Atlantic University: Florida Atlantic University, established in 1961, officially opened its doors in 1964 as the fifth public university in Florida. Today, the University serves more than 30,000 undergraduate and graduate students across six campuses located along the southeast Florida coast. In recent years, the University has doubled its research expenditures and outpaced its peers in student achievement rates. Through the coexistence of access and excellence, FAU embodies an innovative model where traditional achievement gaps vanish. FAU is designated a Hispanic-serving institution, ranked as a top public university by U.S. News & World Report and a High Research Activity institution by the Carnegie Foundation for the Advancement of Teaching. For more information, visit www.fau.edu.