Research ArticleMarine Ecology

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

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Science Advances  15 Feb 2017:
Vol. 3, no. 2, e1602373
DOI: 10.1126/sciadv.1602373
  • 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 FST values. In the scatterplots, colors indicate the outlier category, and frequency distributions of overall FST estimates are plotted along the y axis. The dashed line indicates the minimum FST 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).

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/2/e1602373/DC1

    fig. S1. Genotype frequencies of SNP outliers for A. fragilis.

    fig. S2. Genome-wide pairwise differentiation (FST) of populations.

    fig. S3. Genetic structuring of S. intersepta populations based on most divergent SNPs.

    table S1. Details of the sampled A. fragilis and S. intersepta populations.

    table S2. Estimators of the number of STRUCTURE clusters for A. fragilis and S. intersepta.

    table S3. Genome-wide pairwise differentiation (FST) of populations.

  • Supplementary Materials

    This PDF file includes:

    • fig. S1. Genotype frequencies of SNP outliers for A. fragilis.
    • fig. S2. Genome-wide pairwise differentiation (FST) of populations.
    • fig. S3. Genetic structuring of S. intersepta populations based on most divergent SNPs.
    • table S1. Details of the sampled A. fragilis and S. intersepta populations.
    • table S2. Estimators of the number of STRUCTURE clusters for A. fragilis and S. intersepta.
    • table S3. Genome-wide pairwise differentiation (FST) of populations.

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