Seismic disturbance, productivity and depth shape hadal benthic habitats and biodiversity in the Japan, Ryukyu and Izu-Ogasawara trenches (northwest Pacific Ocean)

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).

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.

# Seismic disturbance, productivity and depth shape hadal benthic habitats
and biodiversity in the Japan, Ryukyu and Izu-Ogasawara trenches
(northwest Pacific Ocean) Dataset DOI:
[10.5061/dryad.k0p2ngfj6](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.