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

description: 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).
description: 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, <em>relative
 abundance</em> 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.
description: # 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.