Data from: Shell trace elemental fingerprints of the deep-sea methane seep mussel Gigantidas Childressi vary by depth, site, and growth region
Data files
Jan 26, 2026 version files 21.64 MB
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igrace_dsr1_dryad_data_1-23-26.zip
21.57 MB
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README.md
35.64 KB
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README.txt
35.42 KB
Abstract
Larval dispersal is a key driver of population persistence and resilience of marine metapopulations and communities. Determining where and how larvae disperse in the deep sea is one of the most vexing challenges in deep-sea ecology. We used laser ablation inductively coupled plasma mass spectrometry to evaluate the potential role of trace elemental fingerprints (TEFs) of the deep-sea methane seep mussel Gigantidas childressi (n = 92 valves) in discriminating among collection depths, geographic regions (Gulf of Mexico and West Atlantic Margin; GOM and WAM), methane seep sites, and shell growth regions. A priori permutational analyses of variance (PERMANOVA) discriminated among mussel valve TEFs across a depth gradient (650 m to 2206 m), among eight methane seep sites, and among shell growth regions. A priori canonical analyses of principal coordinates (CAP) generally matched PERMANOVA results and additionally discriminated TEFs among geographic regions. Results for post-hoc analyses on individual shell growth regions varied by statistical approach (PERMANOVA VS CAP) and by shell growth region (larval prodissoconch I and prodissoconch II VS settler dissoconch shell). Post-hoc PERMANOVA discriminated only among sites, while post-hoc CAP discriminated among all study factors. Discrimination among depths was mainly driven by the elemental ratio Ba:Ca; discrimination among geographic regions was driven mainly by Ba:Ca and Sr:Ca; discrimination among sites and shell growth regions was driven by all three elemental ratios. Overall, shell TEFs show potential to discern spatial distribution of larval population pools.
This dataset contains files and tools (e.g., MATLAB programs) associated with the raw data, data reduction/pre-proccessing, processing itself, and statistical analysis in PRIMER-e v7 software.
Dataset DOI: 10.5061/dryad.wh70rxx2q
Description of the data and file structure
For improved formatting of this README, open the README.txt file in the main data folder.
Files and variables
File: igrace_dsr1_dryad_data_1-23-26.zip
Description:
File organization structure within the master folder igrace_dsr1_dryad_data folder is described below
Notes
For MATLAB programs, see commented description at the top of each program (or in PDF).
All MATLAB programs can be executed on an external computer; simply point the program to igrace_dsr1_dryad_data folder using the built-in prompt that appears upon running the program
For detailed data reduction and statistical analysis methodology, see Supplemental Material
igrace_dsr1_dryad_data folder
under_described_parameters.txt Text file containing information about under-described parameters found in our datasets. Such parameters may not have units written alongside them in their respective files, or may be deprecated/unused, e.g., due to serving as input files for MATLAB scripts. All other parameters should have units in their respective headers and/or meaning should be clear in context of the file
raw_data folder
individual_samples_and_standards folder
Contains many files; examples below. Units in counts-per-second (CPS)
Example file: 3A1L1a_P2.xls; valve 3A1, growth region L1 (PD1), and arbitrary a_P2 suffix
Example file: 612_1a_P2.xls; NIST 612, arbitrary 1a_P2 suffix
Example file: laser_70a; second ('70a', VS just '70') laser test at 70% fluence
Oct18_sequenceA folder Samples ablated day 1
Oct18_sequenceA_STDs folder Standards ablated day 1
Oct18_SequenceB_only_blank1a folder The blank (blank1a) ablated day 2
Oct18_sequenceB_STDs_and_samples folder Standards and samples ablated day 2, not including blank1a
Oct18_tape folder Tape samples ablated during day 1
Oct18_test1 folder Test ablations ablated day 1
Oct18_test2 folder Test ablations ablated during day 2
Oct19_sequenceA folder Samples ablated day 2
data_grouped_by_session folder
rawdata_session1 Spreadsheet of CPS and ppm data for samples and standards ablated during the first session / day 1; contains samples not statistically analyzed (species other than childressi)
rawdata_session2 Spreadsheet of CPS and ppm data for samples and standards ablated during the first session / day 2; contains samples not statistically analyzed (species other than childressi)
drs_settings_and_reference_material_values Spreadsheet of data reduction scheme (DRS) settings and reference material values from GeoREM preferred values; identical for both sessions
processing_tools folder
peak_id folder
order_of_ops_for_peakid_program.pdf Description of the order of operations for the peak ID program
peakid_steps_plainenglish.txt Plain English version of the order_of_ops
peakid_program.m MATLAB program for peak and no-peak identification
peakid_program.pdf PDF of the MATLAB program
driftchecker folder
driftchecker_dryad.mlx MATLAB program that calculates the "slope proportion", a normalized measure of the steepness of the fitted linear trend relative to the mean magnitude of the data, to detect if machine drift occurred
driftchecker_dryad.pdf PDF of the MATLAB program
driftchecker_input.xlsx The information read by the MATLAB program, including but not limited to a placeholder X-axis "Xstep", CPS and ppm for each element, and sample labels. Zero values ("0") indicate values below level of detection (below LOD)
mmolConverter folder
mmolconverter_mk2_dryad.mlx MATLAB program for converting Iolite-output analyte ppm values to X:Ca, elemental:calcium ratios in units of mmol:mol for statistical analysis. Outputs to the matlab_output.xlsx in processed_data folder > data_reduced_and_calibrated folder
mmolconverter_mk2_dryad.pdf PDF of the MATLAB program
matlab_input.xlsx Data (IOLITE-output ppm values) input to the MATLAB program. Study and methodological factors included
boxplotmaker folder
boxplotdata.xlsx Data (natural log-transformed but *not* normalized mmol:mol X:Ca values) called by the MATLAB program
boxplotmaker_dryad.mlx MATLAB program that creates boxplot figures (elemental values on Y axis, study factor levels on X axis)
boxplotmaker_dryad.pdf PDF of the MATLAB program
cap_plot_and_circle_maker folder
cap_plot_replicator_dryad.mlx MATLAB program that produces CAP plots and overlays spearman vector lines with lengths according to correlation strength; only necessary because PRIMER v7 can only overlay Pearson vectors
cap_plot_replicator_dryad.pdf PDF of the MATLAB program
cap_plot_sources.xlsx CAP plot data (coordinates of points) exported directly from CAP plots produced in PRIMER
processed_data folder
data_qaqc_and_outlier_identification folder
all_samples_associated_with_sites_and_notes All samples (including standards, blanks, etc.) processed in Iolite associated with sites and notes; used to remove samples that were i) not G. childressi, ii) associated with laser shoot-through, iii) associated with other problems, such as incomplete data files. Note: #VALUE! errors (e.g., many in CD and CE) indicate values below level of detection, and appear as "BelowLOD" in following datasets
outlier_identification.xlsx Six spreadsheets, each one phase of outlier removal for either the Inclusive or Exclusive dataset. Phases are described at the top of each sheet and in Supplemental Material. Rows highlighted in red indicate samples that were identified as outliers for the reason stated at the top of each sheet.
qaqc_sheets_and_summary.xlsx Five spreadsheets summarizing all quality assurance and control metrics, detailed below
Consistency RSD on 616 sheet Values in ppm for each analyte as measured in NIST 616 for analytical session/day 1 and 2, and resulting % RSD. Blue cells indicate RSD below 15%; yellow below 30%; red above 30%
Drift Summary sheet Scatter plots, fitted linear trend lines and equations, and slope proportion as plotted and calculated by the driftchecker_dryad.mlx MATLAB program at processing_tools_and_files folder > driftchecker folder
session1_recovery sheet Measured and accepted values for analytes (in ppm), % difference (recovery, variation, minimum, and maximum values for our standard reference materials NIST 612 and NIST 614
session2_recovery sheet Same as session1_recovery sheet but for the second analytical session
QAQC_summary sheet Summarizes all information above and additionally provides the proportion of samples (%) below LOD for the calibrated data. At the bottom, checks passed for each analyte are summarized, which identified which elements were best to use in statistical analysis
data_reduced_and_calibrated folder
cps_to_ppm.xlsx Spreadsheet containing IOLITE-output data: CPS ± standard error, ppm ± standard error (and belowLOD and LOD value indicators), and ppm info alone, with all characterizing information (labels, study factors, methodological factors, etc.)
matlab_output.xlsx Spreadsheet containing the X:Ca, elemental:calcium ratios in units of mmol:mol as output by the mmolconverter_mk2_dryad.mlx MATLAB program at processing_tools_and_files folder > mmolConverter folder
primer_data_analysis
cap_results folder
growth_region_controlled_results folder
exc_folder
d_shell folder
depth folder
exc_d_depth_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Depth factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_D_Depth_Spearman.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Depth factor; contains the results of calculation of Spearman correlations
exc_d_depth_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Depth factor; primary CAP output (p-values, classification success, etc.)
site folder
exc_d_site_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Site factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_D_Site_Spearman.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Site factor; contains the results of calculation of Spearman correlations
exc_d_site_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Site factor; primary CAP output (p-values, classification success, etc.)
geographic_region folder
exc_d_geographicregion_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Geographic Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_D_Ge_Spearman.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Geographic Region factor; contains the results of calculation of Spearman correlations
exc_d_geographicregion_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for dissoconch shell for the Geographic Region factor; primary CAP output (p-values, classification success, etc.)
pd2_shell folder
depth folder
exc_pd2_depth_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Depth factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_PD2_Depth_Spearman.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Depth factor; contains the results of calculation of Spearman correlations
exc_pd2_depth_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Depth factor; primary CAP output (p-values, classification success, etc.)
site folder
exc_pd2_site_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Site factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_PD2_Site_Spearman.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Site factor; contains the results of calculation of Spearman correlations
exc_pd2_site_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Site factor; primary CAP output (p-values, classification success, etc.)
geographic_region folder
exc_pd2_geographicregion_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Geographic Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_PD2_Ge_Spearman.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Geographic Region factor; contains the results of calculation of Spearman correlations
exc_pd2_geographicregion_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch II shell for the Geographic Region factor; primary CAP output (p-values, classification success, etc.)
pd1_shell folder
depth folder
exc_pd1_depth_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Depth factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_PD1_Depth_Spearman.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Depth factor; contains the results of calculation of Spearman correlations
exc_pd1_depth_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Depth factor; primary CAP output (p-values, classification success, etc.)
site folder
exc_pd1_site_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Site factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_PD1_Site_Spearman.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Site factor; contains the results of calculation of Spearman correlations
exc_pd1_site_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Site factor; primary CAP output (p-values, classification success, etc.)
geographic_region folder
exc_pd1_geographicregion_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Geographic Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_PD1_Ge_Spearman.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Geographic Region factor; contains the results of calculation of Spearman correlations
exc_pd1_geographicregion_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for prodissoconch I shell for the Geographic Region factor; primary CAP output (p-values, classification success, etc.)
inc_folder
d_shell folder
depth folder
inc_d_depth_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Depth factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_D_Depth_Spearman.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Depth factor; contains the results of calculation of Spearman correlations
inc_d_depth_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Depth factor; primary CAP output (p-values, classification success, etc.)
site folder
inc_d_site_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Site factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_D_Site_Spearman.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Site factor; contains the results of calculation of Spearman correlations
inc_d_site_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Site factor; primary CAP output (p-values, classification success, etc.)
geographic_region folder
inc_d_geographicregion_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Geographic Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_D_Ge_Spearman.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Geographic Region factor; contains the results of calculation of Spearman correlations
inc_d_geographicregion_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for dissoconch shell for the Geographic Region factor; primary CAP output (p-values, classification success, etc.)
pd2_shell folder
depth folder
inc_pd2_depth_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Depth factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_PD2_Depth_Spearman.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Depth factor; contains the results of calculation of Spearman correlations
inc_pd2_depth_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Depth factor; primary CAP output (p-values, classification success, etc.)
site folder
inc_pd2_site_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Site factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_PD2_Site_Spearman.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Site factor; contains the results of calculation of Spearman correlations
inc_pd2_site_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Site factor; primary CAP output (p-values, classification success, etc.)
geographic_region folder
inc_pd2_geographicregion_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Geographic Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_PD2_Ge_Spearman.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Geographic Region factor; contains the results of calculation of Spearman correlations
inc_pd2_geographicregion_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch II shell for the Geographic Region factor; primary CAP output (p-values, classification success, etc.)
pd1_shell folder
depth folder
inc_pd1_depth_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Depth factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_PD1_Depth_Spearman.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Depth factor; contains the results of calculation of Spearman correlations
inc_pd1_depth_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Depth factor; primary CAP output (p-values, classification success, etc.)
site folder
inc_pd1_site_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Site factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_PD1_Site_Spearman.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Site factor; contains the results of calculation of Spearman correlations
inc_pd1_site_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Site factor; primary CAP output (p-values, classification success, etc.)
geographic_region folder
inc_pd1_geographicregion_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Geographic Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_PD1_Ge_Spearman.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Geographic Region factor; contains the results of calculation of Spearman correlations
inc_pd1_geographicregion_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for prodissoconch I shell for the Geographic Region factor; primary CAP output (p-values, classification success, etc.)
inc_and_exc_results folder
exc folder
depth folder
exc_depth_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for the Depth factor; primary CAP output (p-values, classification success, etc.)
exc_depth_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for the Depth factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_Depth_Spearman.xlsx Spreadsheet of Exclusive data CAP results for the Depth factor; contains the results of calculation of Spearman correlations
geographic_region folder
exc_geographicregion_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for the Geographic Region factor; primary CAP output (p-values, classification success, etc.)
exc_geographicregion_score_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for the Geographic Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_Geograph_Spearman.xlsx Spreadsheet of Exclusive data CAP results for the Geographic Region factor; contains the results of calculation of Spearman correlations
growth_region folder
exc_growthregion_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for the Growth Region factor; primary CAP output (p-values, classification success, etc.)
exc_growthregion_scores_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for the Growth Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_GrowthRegion_Spearman.xlsx Spreadsheet of Exclusive data CAP results for the Growth Region factor; contains the results of calculation of Spearman correlations
site folder
exc_site_cap_main_output.xlsx Spreadsheet of Exclusive data CAP results for the Site factor; primary CAP output (p-values, classification success, etc.)
exc_site_score_elements_merged.xlsx Spreadsheet of Exclusive data CAP results for the Site factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
exc_Site_Spearman.xlsx Spreadsheet of Exclusive data CAP results for the Site factor; contains the results of calculation of Spearman correlations
inc folder
depth folder
inc_depth_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for the Depth factor; primary CAP output (p-values, classification success, etc.)
inc_depth_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for the Depth factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_Depth_Spearman.xlsx Spreadsheet of Inclusive data CAP results for the Depth factor; contains the results of calculation of Spearman correlations
geographic_region folder
inc_geographicregion_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for the Geographic Region factor; primary CAP output (p-values, classification success, etc.)
inc_geographicregion_score_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for the Geographic Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_Geograph_Spearman.xlsx Spreadsheet of Inclusive data CAP results for the Geographic Region factor; contains the results of calculation of Spearman correlations
growth_region folder
inc_growthregion_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for the Growth Region factor; primary CAP output (p-values, classification success, etc.)
inc_growthregion_scores_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for the Growth Region factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_GrowthRegion_Spearman.xlsx Spreadsheet of Inclusive data CAP results for the Growth Region factor; contains the results of calculation of Spearman correlations
site folder
inc_site_cap_main_output.xlsx Spreadsheet of Inclusive data CAP results for the Site factor; primary CAP output (p-values, classification success, etc.)
inc_site_score_elements_merged.xlsx Spreadsheet of Inclusive data CAP results for the Site factor; contains the scores for the CAP axes and elements, merged into one dataset in PRIMER, for calculating Spearman correlations
inc_Site_Spearman.xlsx Spreadsheet ofInclusive data CAP results for the Site factor; contains the results of calculation of Spearman correlations
datasets folder
distance_matrices folder
growth_region_controlled_matrices folder
exc folder
exc_d_euclidean_resemblance_matrix.xlsx Euclidean distance/resemblance matrix for Exclusive data for dissoconch shell
exc_pd1_euclidean_resemblance_matrix.xlsx Euclidean distance/resemblance matrix for Exclusive data for prodissoconch I shell
exc_pd2_euclidean_resemblance_matrix.xlsx Euclidean distance/resemblance matrix for Exclusive data for prodissoconch II shell
inc folder
inc_d_euclidean_resemblance_matrix.xlsx Euclidean distance/resemblance matrix for Inclusive data for dissoconch shell
inc_pd1_euclidean_resemblance_matrix.xlsx Euclidean distance/resemblance matrix for Inclusive data for prodissoconch I shell
inc_pd2_euclidean_resemblance_matrix.xlsx Euclidean distance/resemblance matrix for Inclusive data for prodissoconch II shell
inc_and_exc_overall_matrices folder
exc_euclidean_resemblance_matrix.xlsx Euclidean distance/resemblance matrix for Exclusive data
inc_euclidean_resemblance_matrix.xlsx Euclidean distance/resemblance matrix for Inclusive data
input_raw_multiplied_and_transformed_data folder
growth_region_controlled_datasets folder
exc folder
exc_mult_trans_log_d.xlsx Original ratios for Exclusive dissoconch data multiplied by 100,000 and natural log-transformed
exc_mult_trans_log_pd1.xlsx Original ratios for Exclusive prodissoconch I data multiplied by 100,000 and natural log-transformed
exc_mult_trans_log_pd2.xlsx Original ratios for Exclusive prodissoconch II data multiplied by 100,000 and natural log-transformed
inc folder
inc_mult_trans_log_d.xlsx Original ratios for Inclusive dissoconch data multiplied by 100,000 and natural log-transformed
inc_mult_trans_log_pd1.xlsx Original ratios for Inclusive prodissoconch I data multiplied by 100,000 and natural log-transformed
inc_mult_trans_log_pd2.xlsx Original ratios for Inclusive prodissoconch II data multiplied by 100,000 and natural log-transformed
inc_and_exc_overall_datasets folder
exc_100k.xlsx Exclusive dataset multiplied by 100,000
exc_log.xlsx Exclusive dataset natural log-transformed post-multiplication
inc_100k.xlsx Inclusive dataset multiplied by 100,000
inc_log.xlsx Inclusive dataset natural log-transformed post-multiplication
raw_exc.xlsx Original Exclusive dataset (in units of mmol:mol X:Ca)
raw_inc.xlsx Original Inclusive dataset (in units of mmol:mol X:Ca)
normalised_data folder
growth_region_controlled_norm_data folder
exc folder
exc_norm_d.xlsx Exclusive dissoconch dataset (previously multiplied by 100,000 and natural log-transformed) normalized to homogenize trace elemental ratio magnitude across trace elements
exc_norm_pd1.xlsx Exclusive prodissoconch I dataset (previously multiplied by 100,000 and natural log-transformed) normalized to homogenize trace elemental ratio magnitude across trace elements
exc_norm_pd2.xlsx Exclusive prodissoconch II dataset (previously multiplied by 100,000 and natural log-transformed) normalized to homogenize trace elemental ratio magnitude across trace elements
inc folder
inc_norm_d.xlsx Inclusive dissoconch dataset (previously multiplied by 100,000 and natural log-transformed) normalized to homogenize trace elemental ratio magnitude across trace elements
inc_norm_pd1.xlsx Inclusive prodissoconch I dataset (previously multiplied by 100,000 and natural log-transformed) normalized to homogenize trace elemental ratio magnitude across trace elements
inc_norm_pd2.xlsx Inclusive prodissoconch II dataset (previously multiplied by 100,000 and natural log-transformed) normalized to homogenize trace elemental ratio magnitude across trace elements
inc_and_exc_overall_norm_data folder
exc_norm.xlsx Normalized Exclusive dataset
exc_norm_draftsman_plot.tif Draftsman plot of the normalised Exclusive dataset
exc_norm_histogram.tif Histogram of the normalised Exclusive dataset
inc_norm.xlsx Normalised Inclusive dataset
inc_norm_draftsman_plot.tif Draftsman plot of the normalised Inclusive dataset
inc_norm_histogram.tif Histogram of the normalised Inclusive dataset
permanova_designs folder
iterative_model_development_process.xlsx Spreadsheet with detailed workflow of the iterative PERMANOVA model development process, referencing models 1a-1e and models 2-4. Note that Model 3 was the primary analytical model used. Very similar models were used for Inclusive and Exclusive datasets.
initial_omnibus_design_nocontrasts_models1a-1d.txt PERMANOVA models 1a-1d: terms, nesting structure, and fixed/random identifiers. See iterative development process spreadsheet for details. Note that continuous covariates are present in the model, as seen in individual PERMANOVA results.
secondary_omnibus_design_model1e.txt PERMANOVA model 1e: terms, nesting structure, and fixed/random identifiers. See iterative development process spreadsheet for details. Note that continuous covariates are present in the model, as seen in individual PERMANOVA results.
tertiary_omnibus_design_models2-4.txt PERMANOVA models 2-4: terms, nesting structure, and fixed/random identifiers. See iterative development process spreadsheet for details. Note that continuous covariates are present in the model, as seen in individual PERMANOVA results.
gr_isolated_omnibus_design.txt PERMANOVA model for testing terms when controlling shell growth regions (prodissoconch I, II, and dissoconch): terms, nesting structure, and fixed/random identifiers. See iterative development process spreadsheet for details. Note that continuous covariates are present in the model, as seen in individual PERMANOVA results.
permanova_results folder
growth_region_controlled_models folder
exc folder
exc_d_permanova.xlsx PERMANOVA results and supplemental information for the Exclusive dissoconch (D-shell) dataset
exc_pd1_permanova.xlsx PERMANOVA results and supplemental information for the Exclusive prodissoconch I (PD1) dataset
exc_pd2_permanova.xlsx PERMANOVA results and supplemental information for the Exclusive prodissoconch II (PD2) dataset
inc folder
inc_d_permanova.xlsx PERMANOVA results and supplemental information for the Inclusive dissoconch (D-shell) dataset
inc_pd1_permanova.xlsx PERMANOVA results and supplemental information for the Inclusive prodissoconch I (PD1) dataset
inc_pd2_permanova.xlsx PERMANOVA results and supplemental information for the Inclusive prodissoconch II (PD2) dataset
inc_and_exc_models folder
effect_size_inc_and_exc.xlsx Effect size calculations and results for Model 3 for both Inclusive and Exclusive estimates of components of variation, sourced from PERMANOVA results. Effect size was set to 0 if the estimate was negative.
exc_models_permanova.xlsx PERMANOVA results and supplemental information for Exclusive dataset models that did not control for shell growth region: models1a-1e, model 2, model 3, and model 4. This manuscript focuses on Model 3 results.
inc_models_permanova.xlsx PERMANOVA results and supplemental information for Inclusive dataset models that did not control for shell growth region: models1a-1e, model 2, model 3, and model 4. This manuscript focuses on Model 3 results.
permdisp_results folder
exc folder
exc_growthregion_permdisp.xlsx Permutational dispersion results based on Exclusive data for the shell growth region term to contextualize PERMANOVA results for that term
exc_samplenumber_permdisp.xlsx Permutational dispersion results based on Exclusive data for the sample number (individual variability) term to contextualize PERMANOVA results for that term
exc_site_nodac_permdisp.xlsx Permutational dispersion results based on Exclusive data for the site term to contextualize PERMANOVA results for that term
exc_site_on_samplenumber_dac_permdisp.xlsx Permutational dispersion results based on Exclusive data for the site term based on the distance-among-centroids resemblance matrix of sample numbers, to account for individual variability before considering site dispersion, to contextualize PERMANOVA results for the site term
inc folder
inc_growthregion_permdisp.xlsx Permutational dispersion results based on Inclusive data for the shell growth region term to contextualize PERMANOVA results for that term
inc_samplenumber_permdisp.xlsx Permutational dispersion results based on Inclusive for the sample number (individual variability) term to contextualize PERMANOVA results for that term
inc_site_nodac_permdisp.xlsx Permutational dispersion results based on Inclusive for the site term to contextualize PERMANOVA results for that term
inc_site_on_samplenumber_dac_permdisp.xlsx Permutational dispersion results based on Inclusive for the site term based on the distance-among-centroids resemblance matrix of sample numbers, to account for individual variability before considering site dispersion, to contextualize PERMANOVA results for the site term
benjamini_hochberg_adjusted_p_values.xlsx Spreadsheet with description of process of Benjamini-Hochberg adjustment for multiple comparisons, and identification of significant/insignificant p-values for PERMANOVA and CAP results
igrace_dryad_primer_workspace_dryad.pwk Full PRIMER workspace accessible for users of PRIMER-e v7. Does not contain any files critical for analysis that are not already present in this Dryad repository.
primer_workspace_visualized.pdf Document containing screenshots of the PRIMER workspace for visualization of workflow and file organization
[End of README]
Code/software
See description for .mat and .mlx files in the README.
