Dataset DOI: 10.5061/dryad.gmsbcc335

Description of the data and file structure

This submission contains two compressed archives. The primary archive (otolithPaper_data.zip) contains three complementary analytical workflows, while the second archive (reviewerComments_addressed_aoteaoraNZ_kingfish_otolithShape.zip) contains supplementary analyses generated in response to peer review.

• otolithPaper_data.zip – the primary dataset used to reproduce all analyses presented in the manuscript. The dataset is organized into three main directories. Each directory contains:
  • an otolithImages/ folder containing subfolders named AW, BP, CE, CH, and SO, corresponding to sampling regions used by ShapeR;
  • a CSV file containing specimen metadata, morphometric measurements, and shape descriptors;
  • an R script used to reproduce the analyses for that dataset.
• reviewerComments_addressed_aoteaoraNZ_kingfish_otolithShape.zip – additional scripts and analyses produced in response to peer-review comments that are supplementary to the primary dataset.

For the otolithPaper_data.zip, the three directories/analyses are;

populationLevelDifferences/

• Contains 112 otolith images from five sampling regions (AKW, CEW, CHA, SOU, BPLE)
• Used for stock-level discrimination analysis across all five populations
• Data file: populationLevelDifferences_std_indicesContours.csv
• Analysis script: populationLevelDifferences_script.r

priorTest1/

• Contains 58 otolith images (paired left and right otoliths) from 29 individuals
• Used for left–right bilateral asymmetry analysis
• Data file: priorTest1_right_left_pairs_std_indices.csv
• Analysis script: priorTest1_script.r

priorTest2/

• Contains the original temporal comparison dataset for AKW (2014 vs 2019) used in the manuscript. Expanded temporal analyses for CHA and CEW are provided separately in the reviewerComments_addressed archive.
• Used for temporal comparison of otolith shape variation within populations
• Data file: priorTest2_std_indicesContours.csv

• Analysis script: priorTest2_script.r

The reviewerComments_addressed_aoteaoraNZ_kingfish_otolithShape.zip archive contains the following supplementary scripts:

• priorTest2_2.1_2.2_2.3_script.r - Extended temporal comparison script that expands Prior Test 2 to include analyses across three populations: Prior Test 2.1: Temporal comparison of AKW samples (2014 vs 2019); Prior Test 2.2: Temporal comparison of CHA samples (2019 vs 2023); Prior Test 2.3: Temporal comparison of CEW samples (2019 vs 2021)

• powerAnalysis.r - Simulation-based power analysis for the population-level PERMANOVA using standardised wavelet coefficients. This script performs Monte Carlo simulations to estimate statistical power across a range of sample sizes per group, helping to assess the robustness of the stock discrimination findings.

Image Naming Convention

Otolith images follow a standardized naming convention:

• [sample]_d.jpg = right (distal) sagittal otolith
• [sample]_ld.jpg = left (distal) sagittal otolith

The picname column in each CSV file corresponds to the image filename without the .jpg extension. For example, a picname value of "388827_03_d" refers to the image file "388827_03_d.jpg" located in the appropriate regional subfolder.

Data and Sample Summary

All otolith images have been converted to black-and-white for shape analysis. Complete metadata for each specimen is provided in the corresponding CSV file, including fish body length, sampling year, and microscope settings used during image acquisition.

Files and variables

The following standardized regional codes are used throughout the dataset to designate population origin:

• AKW – Auckland West
• CEW – Central West
• CHA – Challenger Plateau
• SOU – Southland
• BPLE – Bay of Plenty

Common Metadata Columns (All CSV Files)

All CSV files contain the following metadata columns:

Otolith Morphometric Measurements

The following columns contain direct measurements of otolith size and shape (present in all CSV files):

Standardised Shape Indices (priorTest1 and priorTest2 data only)

Present in priorTest1 and priorTest2 datasets.

Columns ending in _std represent values standardised for fish length using the allometric correction described in the manuscript.

The following indices are included:

• Circularity
• Rectangularity
• Roundness
• Aspect_Ratio
• Form_Factor
• Ellipticity
• Squareness

Wavelet Coefficients (populationLevelDifferences and priorTest2 data only)

Present in the populationLevelDifferences and priorTest2 datasets.

Wavelet coefficient columns follow the naming convention:

Ws{n}c{m}

where:

• n = wavelet decomposition level (scale)
• m = coefficient number within that scale.

Fourier Descriptors (populationLevelDifferences and priorTest2 data only)

Present in the populationLevelDifferences and priorTest2 datasets.

Fourier descriptor columns follow the naming convention:

FD{n}{x}

where:

• n = harmonic number
• x = coefficient (a, b, c or d).

File: otolithPaper_data.zip

Otolith Data Directory Tree

Generated on: 2025-12-10 12:38:10.065404

Root directory: otolith_data

Total files: 205

File: reviewerComments_addressed_aoteaoraNZ_kingfish_otolithShape.zip

The archive reviewerComments_addressed_aoteaoraNZ_kingfish_otolithShape.zip contains supplementary analyses produced in response to peer-review comments. These files provide additional statistical support.

Code/software

All data processing, image-based otolith shape extraction, morphometric analyses, and statistical testing were conducted using the R statistical computing environment (R Foundation for Statistical Computing). All analyses rely exclusively on free and open-source software. The workflows were implemented as reproducible R scripts and are organised to mirror the directory structure of the data repository.

The exact versions of all R packages used in the analytical workflows are provided in the file software_package_versions.csv. The software environment used for this study included the following package versions: