DOI: 10.5061/dryad.wh70rxx2q
title: Data from: Shell trace elemental fingerprints of the deep-sea methane seep mussel <em>Gigantidas Childressi</em> vary by depth, site, and growth region

description: 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.
description: # Data from: Shell trace elemental fingerprints of the deep-sea methane
 seep mussel *Gigantidas Childressi* vary by depth, site, and growth region
 Dataset DOI:
 [10.5061/dryad.wh70rxx2q](https://doi.org/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 &gt;
 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 &gt; 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 &gt; 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.