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Supplemental Information

Table 1: Analysis of Molecular Variance (AMOVA) Fixation index (FST) values.

Analysis of Molecular Variance (AMOVA) Fixation index (FST) values showing no genetic differentiation among Orbicella faveolata and Orbicella franksi, among Orbicella faveolata within the two geographic locations or among Orbicella franksi within the two geographic locations.

DOI: 10.7287/peerj.preprints.246v1/supp-1

Table 2: The sequencing coverage and mapping efficiency by geographic location and species.

Summary of sequence coverage ITS-2 amplicon sequencing of Flower Garden Banks, Gulf of Mexico. Individuals are sorted by geographic location and species using the 454 GS FLX platform.

DOI: 10.7287/peerj.preprints.246v1/supp-2

Table 3: The significant Markov Chain Monte Carlo Generalized Linear Model results.

Only showing significant results from Poisson-lognormal Generalized Linear Models (GLMs). Haplotypes IV and V are significantly diminished at the west bank compared to the east bank (PMCMC<0.001). Haplotype V is also significantly more diminished in Orbicella faveolata than in Orbicella franksi (PMCMC=0.002).

DOI: 10.7287/peerj.preprints.246v1/supp-3

Figure 1: The general location of the Flower Garden Banks and pictures of coral species.

A. Location of Flower Garden Banks National Marine Sanctuary, Gulf of Mexico (27°54’ N, 93°35’W for east Flower Garden Banks and 27°53’N, 93°49’W west Flower Garden Banks) Credit: USGS (http://pubs.usgs.gov/of/2003/of03-002/html/FGB_figs.htm) B. Orbicella faveolata from Panama, Credit: Mónica Medina C. Orbicella franksi from Panama, Credit: Mónica Medina

DOI: 10.7287/peerj.preprints.246v1/supp-4

Figure 2: DISTRUCT plots of all STRUCTURE analyses.

DISTRUCT plots from STRUCTURE for K=2 except where noted A. All samples from Orbicella faveolata and Orbicella franksi in east and west Flower Garden Banks National Marine Sanctuary, Gulf of Mexico, n=193 B. Same as A but potential hybrids removed (n=174) C. Orbicella faveolata only with potential hybrids removed (n=73, K=3) and D. Orbicella franksi only with potential hybrids removed (n=101) E. The selected 60 Orbicella faveolata (n=30) and Orbicella franksi (n=30)

DOI: 10.7287/peerj.preprints.246v1/supp-5

Figure 3: The percentage of reads for the four minor haplotypes by geographic location and species.

Percentage of minor Symbiodinium B1 haplotypes by geographic location and coral species. Only haplotypes I, III, IV, V are shown. The dominant Symbiodinium B1 haplotype II, used 93.26% across all individuals, is not shown. (East: Orbicella faveolata = 27,121 sequences, East: Orbicella franksi = 40,078 sequences, West: Orbicella faveolata = 26,143 sequences, West: Orbicella franksi = 27,376 sequences)

DOI: 10.7287/peerj.preprints.246v1/supp-6

Figure 4: Distribution of abundance of two haplotypes significant by site.

Distribution of abundance (log2 transformed) of Symbiodinium type B1 haplotypes IV and V in east and west Flower Garden Banks, Gulf of Mexico from the Poisson-lognormal model. Circles indicate Orbicella faveolata. Triangles indicate Orbicella franksi. Haplotypes I, II and III did not have significant effects, not shown.

DOI: 10.7287/peerj.preprints.246v1/supp-7

Figure 5: Principle Components Analysis (PCA) showing the first two principle components.

PCA plot of variance stabilized transformed (VST) data from a count data set showing partitioning of samples by geographic location. Principle component 1 (PC1) explains 40.83% of the variation and principle component 2 (PC2) explains 22.63% of the variation (n=56).

DOI: 10.7287/peerj.preprints.246v1/supp-8

Supplementary Data 1: The R script and input file used for MCMC GLMs and two Perl scripts used to trim and clean sequences in bioinformatics analysis.

Custom perl scripts used to remove 454 Rapid adaptors and barcodes (454trim.pl) and short reads (noshorts.pl) and R script (FGB_Symbiodinium_OTU.R).

DOI: 10.7287/peerj.preprints.246v1/supp-9

Supplementary Figure 1: The primer design to uniquely barcode individuals.

Rapid-barcode primer design annealed in second PCR to uniquely identify individuals and pool.

DOI: 10.7287/peerj.preprints.246v1/supp-10

Supplementary Figure 2: The delta K figures from STRUCTURE HARVESTER.

Delta K figures from STRUCTURE HARVESTER from STRUCTURE analysis for all collected individuals (n=193), with potential hybrids removed (n=174), the selected 60 individuals, Orbicella faveolata (n=73) and Orbicella franksi (n=101).

DOI: 10.7287/peerj.preprints.246v1/supp-11

Supplementary Figure 3: The Clustal alignment of five Flower Garden Bank Symbiodinium haplotypes and previously published Symbiodinium B1.

Clustal Omega alignment of five reference haplotypes displayed in SeaView and the previously published Symbiodinium B1 (JN 558059.1).

DOI: 10.7287/peerj.preprints.246v1/supp-12

Additional Information

Competing Interests

We have no competing interests.

Author Contributions

Elizabeth Green conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Sarah W. Davies conceived and designed the experiments, performed the experiments, wrote the paper, reviewed drafts of the paper.

Mikhail V. Matz conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Mónica Medina conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Field Study Permissions

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

Flower Garden Banks National Marine Sanctuary permit FGBNMS-2009-005-A2, A3

Funding

Research was funded by the National Science Foundation grant DEB-1054766 to MVM and IOW 0644438 and IOS 0926906 to Mónica Medina, and the PADI Foundation Award to SWD. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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