Mesophotic corals in Hawaii maintain autotrophy to survive low-light conditions: Stable isotope dataset
Data files
Feb 06, 2024 version files 516.78 KB
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Backstrom_ProcB_Biplot_Stats.R
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leptoseris.all.Hotelling.numbers
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leptoseris.all.numbers
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ProcB_Manuscript_Data_CHB_1.15.24.xlsx
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README.md
Abstract
In mesophotic coral ecosystems, reef-building corals and their photosynthetic symbionts can survive with less than 1% of surface irradiance. How depth-specialist corals rely upon autotrophically and heterotrophically-derived energy sources across the mesophotic zone remains unclear. We analyzed the stable carbon (δ13C) and nitrogen (δ15N) isotope values of a Leptoseris community from the ʻAuʻau Channel, Maui, Hawaiʻi (65-125 m) including four coral host species living symbiotically with three algal haplotypes. We characterized the isotope values of hosts and symbionts across species and depth to compare trophic strategies. Symbiont δ13C was consistently 0.5‰ higher than host δ13C at all depths. Mean colony host and symbiont δ15N differed by up to 3.7‰ at shallow depths and converged at deeper depths. These results suggest that both heterotrophy and autotrophy remained integral to colony survival across depth. The increasing similarity between host and symbiont δ15N at deeper depths suggests that nitrogen is more efficiently shared between mesophotic coral hosts and their algal symbionts to sustain autotrophy. Isotopic trends across depth did not generally vary by host species or algal haplotype, suggesting that photosynthesis remains essential to Leptoseris survival and growth despite low light availability in the mesophotic zone.
README: Mesophotic corals in Hawaiʻi maintain autotrophy to survive low-light conditions: Stable Isotope Dataset
https://doi.org/10.5061/dryad.f1vhhmh0z
The complete collection of files used by Backstrom et al. (2024) to organize and analyze all stable isotope data presented in this research article.
Description of the data and file structure
The data are organized into three separate files, accompanied by an R script for processing/analyzing all biplot data:
A Microsoft Excel document (titled "ProcB Manuscript Data CHB 1.15.24") provides a metadata sheet outlining the organized data on all subsequent sheets. These sheets were used to process/analyze all regression data via JMP Pro 14. Outliers as defined and listed in the sheet (and tabulated in Supplementary Table 1) were excluded for analyses pertaining to those data.
A .csv file titled "leptoseris.all.csv," reorganizing the stable isotope data for the whole sample set only by colony fraction (i.e., host vs. symbiont) to plot and run SIBER analyses.
Another .csv file titled "leptoseris.all.Hotelling.csv" reorganizing the same data presented in "leptoseris.all.csv" in a way that allows biplot stats via the Residual Permutation Procedure (RPP) as discussed in the text plus the Hostelling's T2 test, which was not reported but used to validate the RPP stats after checking for data normality.
The R script file, titled "Backstrom_ProcB_Biplot_Stats.R," that outlines the SIBER, RPP, and Hostelling's T2 stats based on the two .csv files of stable isotope data listed above.
Description of data file columns and variables
1. Microsoft Excel Document: ProcB Manuscript Data CHB 1.15.24
The following column labels and corresponding variables are used in the Excel data sheets. Only newly used columns/variables are described for each subsequent sheet:
JMP_Paper_Regressions: Sheet used for linear regressions of stable isotope values by host species, algal haplotype, and collection depth (m):
- ID Number: The original number assigned to each unique coral colony collected by submersible for this study.
- Species: each colony's host species (4 total): L. scabra (green), L. tubulifera (red), Leptoseris sp. 1 (yellow), and L. hawaiiensis (blue). Color coding for clarity and ease of distinction between species.
- Sample ID: The sample ID assigned to each colony fraction for the analyses of this particular study, following the general format of "L_ID Number_Colony Fraction" (ex: "L27 tissue", "L27 algae", etc.). Tissue signifies host fraction, whereas algae signifies symbiont fraction.
- N height (nA): the magnitude of the Elementar Isoprime100 Isotope Ratio Mass Spectrometer Nitrogen signature reading, in nanoAngstroms (nA).
- d15N: The 15-Nitrogen stable isotope signature derived from the N height (nA) and dry mass of the sample.
- N%: The percent composition of Nitrogen found within each sample. Not incorporated in this study.
- C height (nA): the magnitude of the Elementar Isoprime100 Isotope Ratio Mass Spectrometer Carbon signature reading, in nanoAngstroms (nA).
- d13C: The 13-Carbon stable isotope signature derived from the C height (nA) and dry mass of the sample.
- C%: The percent composition of Carbon found within each sample. Not incorporated in this study.
- C:N Ratio: the ratio of Carbon to Nitrogen for each sample, derived from dividing C% by N%. Not incorporated in this study.
- d15N: host-symbiont: the isotopic difference in d15N values between host and symbiont samples, by colony.
- d13C: host-symbiont: the isotopic difference in d13C values between host and symbiont samples, by colony.
- Depth Collected (m): the collection depth of each colony, in meters (m).
- 5-m Depth Zone: the collection depth of each colony, rounded to the nearest 5-meter depth value.
- Collection Depth Bin (m): a copy of the 5-m Depth Zone column, used for all 5-m depth bin analyses.
- Coral % Cover: an observational variable from previous studies of these Leptoseris colonies (e.g., Padilla-Gamiño et al. (2019); see reference list) providing environmental context of the percent coral cover found around the site of each colony's collection, relative to the rest of the benthos surrounding the colony. Not used in this study.
- Symbiodinium COI mtDNA: Coenosarc #1: The COI algal haplotype of each coral colony, based on mitochondrial DNA of symbionts recovered from the coenosarc tissue in Pochon et al. (2015) (see reference list).
- Symb. COI mtDNA: Calyx: The COI algal haplotype analyzed for a subset of colonies by Pochon et al. (2015) to confirm homogenous COI-type of algae across tissues of a single colony. N/A = not measured for that colony.
- Symb. COI mtDNA: Coenosarc #2: Same as (18) above, but for a second sample of the coenosarc instead of the calyx material of each colony.
- Notes: Additional notes on each sample. Duplicate averages were calculated on the "Duplicate_%diff" page.
- d13C, Residual: Residual values of each d13C measurement, divided by colony fraction (tissue vs. algae) only, to detect and confirm outliers as identified by JMP histogram analyses.
- d13C, Cook's D Influence: Cook's Distance values relative to the mean d13C values for tissue and algae samples, respectively.
- d15N, Residual: Residual values of each d15N measurement, divided by colony fraction (tissue vs. algae) only, to detect and confirm outliers as identified by JMP histogram analyses.
- d15N, Cook's D Influence: Cook's Distance values relative to the mean d15N values for tissue and algae samples, respectively.
- Outlier Issues: Exclude From: Outlier assignment based on the residual, Cook's D, and histogram analyses. Outliers are labeled by variable (with commas separating outlier values in lists if multiple per sample). N/A signifies that the sample was not an outlier for any variables.
JMP_Paper_Iso_Diff: Sheet used for linear regressions of differences in stable isotope values between host species and algal haplotype and collection depth (m). The only notable difference between this sheet and "JMP_Paper_Regressions" is that each colony has been condensed into a single row to list differences in isotopic values (d13C, d15N) between host and symbiont components (i.e., tissue and algae) as single-row values.
JMP_Paper_Multi_Linear: Sheet used for multivariate linear regression analyses in JMP, with each row representing all variable for both fractions (host and symbiont) for a single colony:
- N%, H: the sample percent composition of Nitrogen, for the host fraction (H).
- N%, S: the sample percent composition of Nitrogen, for the symbiont fraction (S).
- d15N, H: the sample d15N stable isotope value, for the host fraction (H).
- d15N, S: the sample d15N stable isotope value, for the symbiont fraction (S).
- Mean d15N: the averaged value of both host and symbiont-fraction d15N signatures for the coral colony.
- C%, H: the sample percent composition of Carbon, for the host fraction (H).
- C%, S: the sample percent composition of Carbon, for the symbiont fraction (S).
- d13C, H: the sample d13C stable isotope value, for the host fraction (H).
- d13C, S: the sample d13C stable isotope value, for the symbiont fraction (S).
- Mean d13C: the averaged value of both host and symbiont-fraction d13C signatures for the coral colony.
- C:N Ratio, H: The Carbon-to-Nitrogen percent ratio for the host fraction (H). Not incorporated in this study.
- C:N Ratio, S: The Carbon-to-Nitrogen percent ratio for the symbiont fraction (S). Not incorporated in this study.
Sample_Summary: Sheet providing many of the parameters listed above but containing additional information about the sampling procedure.
- Date: The date that the samples were analyzed by Isotope Ratio Mass Spectrometer.
- Tray: the 96-well plate tray number containing the specific sample.
- Genus: the Leptoseris genus specifier (distinguished from other genera potentially run on the same tray).
- Sample Dry Weight (mg): the dry weight of the sample analyzed for stable isotopes, in milligrams (mg).
Duplicate_%diff: Sheet providing percent difference calculations for all samples run in duplicate for quality control.
- Sample ID: now includes rows for relative percent difference between both replicates listed above ("Rel. % Difference") and an average value provided as the final measurement for that duplicate sample ("Average [Sample ID] to report").
2. .csv File: leptoseris.all.csv
The following column labels and corresponding variables are used in this .csv file, with each row representing either a host or symbiont sample of a given colony:
- iso1: the d13C value assigned to the specific sample (by row).
- iso2: the d15N value assigned to the specific sample (by row).
- group: the colony fraction ID (1 = host, 2 = symbiont).
- community: the genus-level community ID for the specific sample ( = 1 for all colonies, which belong to the same genus, Leptoseris).
3. .csv File: leptoseris.all.Hotelling.csv
The following column labels and corresponding variables are used in this .csv file, with each row representing either a host or symbiont sample of a given colony:
- gp: the "group", i.e., the colony fraction ID (1 = host, 2 = symbiont).
- d13C: the d13C value assigned to the specific sample (by row).
- d15N: the d15N value assigned to the specific sample (by row).
Code/Software
R Script contains code derived from Conti-Jerpe et al. (2020) and Turner et al. (2010), as cited in the article. The R script is annotated to explain the format of all .csv files used in the code. All histogram and regression analyses were conducted in JMP Pro 14.