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 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.

Keywords: Coral reefs; RADseq; deep reef refuge hypothesis; divergent selection; endosymbiont contamination; mesophotic coral ecosystems; vertical connectivity.

Fig. 1. Sampling locations, skeletal morphology, and endosymbiont associations.

(A) Map showing sampled populations on the Bermuda reef platform. Symbols with lighter shading indicate shallow populations, and symbols with darker shading indicate deep populations. GS, “Gurnet Rock” shallow; GD, “Gurnet Rock” deep; JS, “John Smith’s Bay” shallow; JD, “John Smith’s Bay” deep; PS, “Princess Beach” shallow; PD, “Princess Beach” deep; WD, “Western Blue Cut” deep. (B) Skeletal signature of the different populations of A. fragilis (green) and S. intersepta (blue). Symbol shape corresponds to sampling locations (A), and hue indicates sampling depth [shallow (light) and deep (dark)]. (C) Endosymbiont (Symbiodinium) haplotypes associated with A. fragilis (only a single haplotype identified). (D) Endosymbiont (Symbiodinium) haplotypes associated with S. intersepta. Images of species modified from photographs by the Florida Fish and Wildlife Conservation Commission (with permission).

Fig. 2. Pairwise genetic distances between individuals of A. fragilis and S. intersepta.

Darker intensity in heat maps corresponds to greater genetic distance. Highly similar pairs are indicated in red (94 to 98% similarity, indicating potential clonemates), and the diagonal (that is, self-comparisons) is replaced with a black line. Individuals are grouped by population, and for S. intersepta, two out-group individuals from Curaçao are included. Bar graphs indicate the number of genotyped SNPs for each individual.

Fig. 3. Genetic differentiation and outlier SNPs.

(A) Genetic differentiation versus expected heterozygosity of all SNPs genotyped for A. fragilis. (B) Genotype frequencies of all 12 depth-associated outliers (showing one representative SNP per RAD locus). (C) Genetic differentiation versus expected heterozygosity of all SNPs genotyped for S. intersepta. (D) Genotype frequencies of all four consensus outliers (BayeScan and Fdist, indicated by a black dot) and eight additional outliers (Fdist) with the highest F_ST values. In the scatterplots, colors indicate the outlier category, and frequency distributions of overall F_ST estimates are plotted along the y axis. The dashed line indicates the minimum F_ST at which consensus outliers were identified (for S. intersepta). Genotype frequencies are given for shallow and deep populations, with the hue of stacks indicating genotype (ref/ref, homozygote for the reference allele; ref/alt, heterozygote; alt/alt, homozygote for the alternative allele).

Fig. 4. Genetic structuring across depths and locations.

(A) STRUCTURE diagram (K = 3) for A. fragilis as inferred from the overall (top) and neutral (bottom) data set. (B) PCA for A. fragilis as inferred from the overall data set. (C) STRUCTURE diagram (K = 2) for S. intersepta as inferred from the overall data set (top) and discriminant analysis of principal components (DAPC) for the overall data set (bottom). (D) PCA for S. intersepta as inferred from the overall data set. STRUCTURE and DAPC bar graphs indicate ancestry proportions for individuals in each population. In the PCA, sampling depth of individuals is indicated by hue [shallow (light) and deep (dark)], and location is denoted by symbol shape (following Fig. 1A).

Fig. 5. Admixture between shallow and deep populations in A. fragilis.

SNP genotypes for the 25 outlier SNPs (indicated in red hues) (left) and 108 additional highly divergent SNPs (indicated in grayscale) (middle) for all shallow and deep individuals (eastern populations only) sorted by depth and overall ancestry assignment (right). Hues indicate genotype [following Fig. 3 (B and D)] with a white color indicating missing data. In the overall ancestry assignment, light green refers to the “shallow” cluster, and dark green corresponds to the “deep” cluster, with the horizontal solid line separating individuals originating from shallow and deep reefs. Highly divergent SNPs were selected as those with an allele frequency difference (Δp) of ≥0.5 between shallow and deep individuals with >0.98 ancestry assignment (threshold indicated by the dashed lines).

Fig. 6. Depth-generalist species abundances and overlap in community structure.

(A) Species densities of the four depth-generalist coral species common to shallow (left) and deep (right) reefs in Bermuda. (B) Proportion of the four depth-generalist species of the overall coral community on shallow and deep reefs in Bermuda (with the proportion of other species indicated in white). Shading behind pie graphs indicates the proportion of species with vertical connectivity potential: M. cavernosa (25), S. intersepta (this study), and O. franksi (based on reproductive mode and depth distribution).