Seismic disturbance, productivity and depth shape hadal benthic habitats and biodiversity in the Japan, Ryukyu and Izu-Ogasawara trenches (northwest Pacific Ocean)
Data files
Feb 13, 2026 version files 172.92 KB
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0._Dive_overview.R
7.39 KB
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1._Ordination_analysis.R
5.31 KB
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2._Indicator_species_analysis.R
3.43 KB
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3._Abundance__Richness_and_Diversity_assessment.R
5.58 KB
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Dive_RelativeAbundance_long.csv
20.08 KB
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Habitat_subperiod.csv
6.46 KB
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README.md
3.04 KB
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SubperiodCounts_long.csv
95.14 KB
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SubperiodCounts_wide.csv
26.49 KB
Abstract
This dataset contains biological annotations from six hadal submersible dives conducted in Japan, Ryukyu, and Izu-Ogasawara (Izu-Bonin) subduction trenches in the Northwest Pacific Ocean during August–September 2022. Video footage spanned depths of 6939 m to 9775 m and allowed for observations of benthic biodiversity and habitat characteristics across trenches differing in seismic activity and productivity regimes. The dataset contains nearly 30,000 organism observations, representing 70 morphotaxa across 11 phyla and eight habitat categories. The dataset supports the associated publication, investigating the effects of multiscale environmental drivers on benthic community structure and habitat characteristics in hadal environments. Accompanying R code is provided for generating dive-level visual summaries, as well as basic community analysis and visualisation (ordination, indicator species, and assessments of community composition).
Dataset DOI: 10.5061/dryad.k0p2ngfj6
Description of the data and file structure
This dataset contains biological annotations of six hadal submersible dives in Japan, Ryukyu, and Izu-Ogasawara trenches. Datasets and scripts are supporting information for the manuscript titled "Seismic activity, productivity and depth shape hadal benthic habitats and biodiversity in the Japan, Ryukyu and Izu-Ogasawara trenches (Northwest Pacific Ocean)".
Files and variables
File: Dive_RelativeAbundance_long.csv
Description: This file lists the total counts, relative abundance (ind/min), and feeding and mobility traits of morphotaxa observed in each of the six dives. OpCode refers to the Dive, and ID indicates morphotaxa sorted by phylum
Variables
- OpCode: Dive ID
- Phylum: Morphotaxa Phylum
- ID: Morphotaxa ID
- Total_Count: Total number of individuals of each morphotaxon observed
- Dive.Analysis.Time: Total dive time analysed
- Relative.Abundance: Relative abundance of each morphotaxon (ind/min)
- Feeding: Feeding trait of morphotaxon
- Mobility: Mobility trait of morphotaxon
File: Habitat_subperiod.csv
Description: This dataset lists the majority habitat type observed during each sampling unit
Variables
- OpCode: Dive ID
- Subperiod: 3 min subperiod per dive, which functioned as a sampling unit
- Habitat: one of eight habitat classes defined using a combination of substrate type and slope angle
File: SubperiodCounts_wide.csv
Description: morphotaxon abundance per time-standardised sampling unit, in wide format
Variables
- Subperiod: 3 min subperiod per dive, which functioned as a sampling unit
- Morphotaxa: ID under consideration
File: SubperiodCounts_long.csv
Description: Morphotaxon abundance per time-standardised sampling unit, in long format
Variables
- subperiod: sampling unit
- ID: morphotaxon
- Number: Total number of times each morphotaxon was observed per sampling unit
- OpCode: Dive ID
File: 0._Dive_overview.R
Description: Script to generate basic summary visualisations of the biological characteristics of each dive
File: 1._Ordination_analysis.R
Description: Script to conduct multivariate analysis (nMDS) and generate associated visualisations, based on sampling units
File: 2._Indicator_species_analysis.R
Description: Script to conduct indicator species analysis per trench, depth zone, and habitat, based on sampling units.
File: 3._Abundance__Richness_and_Diversity_assessment.R
Description: Script to calculate community characteristics from 3-min subperiods and visualise by dive and habitat
Code/software
Datasets are in .csv format and can be viewed using Microsoft Office Excel. Scripts are produced for R/RStudio. Packages required are listed in each script.
Video data were collected during six crewed hadal submersible dives in Japan, Ryukyu, and Izu-Ogasawara (Izu-Bonin) trenches in August–September 2022. Dives followed transect-style surveys at depths of 6939–9775 m, with high-definition forward- and downward-facing video recorded throughout.
Megafauna (benthic, demersal, and benthopelagic organisms visible in the video) were annotated using EventMeasure software. Only footage with good visibility, even lighting (~1 m above seafloor), and steady submersible movement was included. Organisms were identified to the lowest possible taxonomic level; unidentified forms were grouped into morphologically distinct morphotaxa and assigned feeding and mobility traits.
Annotation sare given for each dive ("Dive_xx"). To account for differences in dive duration and usable video footage, relative abundance was also calculated as the number of individuals per minute of analysed video.
In addition, each dive was segmented into three minute non-overlapping sampling units ("Subperiod_xx"). Each sampling unit was assigned a dominant habitat category using a majority-rule approach. Eight habitat categories were defined across the dataset based on substrate type and slope gradient.