DOI: 10.5061/dryad.z08kprrn4
title: Habitat heterogeneity over multiple scales supports dense and diverse megafaunal communities on a NE Pacific ridge

description: Marine environments are highly heterogeneous, varying across scales of a
 few meters to entire ocean basins. Understanding the relationship between
 environmental variability and species distribution is essential for
 area-based management and conservation. However, this requires a precise
 alignment of seabed mapping, environmental and biological sampling, which
 is often difficult to achieve in the deep sea. There is thus an urgent
 need to tackle this challenge to effectively manage high-diversity
 habitats such as deep-sea coral and sponge (DSCS) aggregations. Relying on
 multiple subsea platforms, seafloor mapping and imaging techniques, we
 mapped the distribution of megafaunal communities at Sur Ridge (800-1250 m
 depth; off Central California) across multiple spatial scales. First,
 remotely operated vehicle (ROV) video transects were conducted to
 characterize community distribution along the ridge, in relation to
 substratum type, environmental conditions and 1-m scale bathymetry. Five
 distinct communities, located in specific areas of the ridge were
 identified. These communities were primarily structured by depth,
 availability of hard substratum and terrain complexity (slope and
 rugosity). Indicator taxa were identified for each community and their
 distribution was characterized at the cm scale from co-registered 5-mm
 resolution photomosaic and 5-cm lateral resolution bathymetry produced
 during low altitude ROV surveys. High-resolution mapping allowed the
 identification of associations between DSCS and other benthic taxa and
 showed that, even at these small scales, different taxa associate with
 distinct microhabitats. These results highlight the importance of
 accounting for habitat heterogeneity, and its role in supporting
 biodiversity, when designing management and conservation strategies.
description: All data were collected at Sur Ridge, a high-relief topographic
 feature ~35 km west of Point Sur, California. Data on
 megafaunal densities and seafloor substratum type were collected from
 remotely operated vehicle (ROV) video transects conducted throughout Sur
 Ridge between July 2014 and December 2021 (ROV <em>Doc
 Ricketts</em> deployed from the R/V <em>Western
 Flyer</em>). The ROV was equipped with two parallel laser beams (29
 cm apart) to estimate the width of the field of view during transects. A
 total of 58 video transects (each 50 m long) were annotated using MBARI’s
 video annotation and reference system (VARS; Schlining and Stout 2006).
 All species were identified to the lowest taxonomic level possible based
 on morphology and sorted into morphotypes. Megafaunal densities were then
 estimated based on transect area. Substratum types were estimated from 40
 frame grabs per video transect, which were captured at regular intervals
 using GOM player (version 2.3.80.5345). Frame grabs were analyzed with
 PAPARA(ZZ)I v. 2.8 software application (Marcon and Purser, 2017): One
 point was randomly generated on each image and classified in one of 11
 substratum categories based on Wentworth (1922) and MBARI’s Deep-Sea Guide
 (Jacobsen Stout et al. 2016): bedrock, rocky outcrop, boulder, eroded
 surface, cobble, pebble, gravel, biogenic, coarse sand, sand and mud. The
 proportion composition of each substratum type was then calculated for all
 transects and included in a substratum composition matrix.
 Different physical and environmental variables were considered to
 understand the distribution of megafaunal communities on Sur
 Ridge: -          Pressure (depth), salinity
 (conductivity), temperature and dissolved oxygen were recorded by sensors
 mounted on the ROV while transecting. These environmental variables were
 averaged for each transect. -          The first and
 second Principal Component scores obtained from the principal component
 analysis performed on the Hellinger-transformed substratum composition
 matrix were used to evaluate the effect of substratum type on megafauna
 diversity patterns. -          Terrain variables,
 including rugosity, slope, curvature, eastness, northness, broad- and
 fine-scale standardized benthic position indexes were extracted from the
 20-m resolution bathymetry of Sur Ridge using the BTM ArcGIS toolbox
 (Walbridge et al. 2018). Note: While Sur Ridge was mapped comprehensively
 at a 1-m resolution using MBARI Dorado class Autonomous Underwater
 Vehicles, the bathymetry was subsequently downscaled to 20 m to account
 for ROV navigation uncertainties associated with the use of USBL
 positioning during transects. High-resolution (cm
 resolution) data on megafauna distribution in relation to terrain were
 collected using MBARI’s Low Altitude Survey System (LASS). An area of ~
 100 x 100 m on the northern slope of Sur Ridge was mapped on October 13,
 2020 using the LASS operated from the ROV <em>Doc
 Ricketts</em>. The LASS toolsled combined color stereo still cameras
 illuminated by strobe lights, and multibeam sonar for producing
 co-registered 5-mm resolution photomosaic and 5-cm resolution bathymetry,
 respectively. Megafauna visible on the georeferenced photomosaic produced
 with the LASS were annotated as point shapefiles in ArcMap V10.8.2.
 Spatial coordinates of all observations were recorded. Terrain parameters
 including slope, curvature, rugosity, northness, eastness, fine- and
 broad-scale standardized benthic position indexes were extracted from the
 5-cm resolution bathymetry using the BTM ArcGIS toolbox. Terrain parameter
 values associated with each megafauna annotation were extracted and used
 in the analyses. Nearest-neighbor analysis was
 performed in ArcMap to measure the distance between megafauna (other than
 deep-sea corals and sponges) and the closest coral and sponge.
 References: Jacobsen Stout,
 N., L. Kuhnz, L. Lundsten, B. Schlining, K. Schlining, and S. von Thun.
 2016. The Deep-Sea Guide (DSG). Monterey Bay Aquarium Research Institute
 (MBARI), Moss Landing, California, USA. Marcon, Y., and
 A. Purser. 2017. PAPARA(ZZ)I: An open-source software interface for
 annotating photographs of the deep-sea. SoftwareX
 <strong>6</strong>: 69–80.
 doi:10.1016/j.softx.2017.02.002 Schlining, B. M., and
 N. J. Stout. 2006. MBARI’s Video Annotation and Reference System.
 <em>OCEANS 2006</em>. 1–5. Walbridge, S.,
 N. Slocum, M. Pobuda, and D. J. Wright. 2018. Unified Geomorphological
 Analysis Workflows with Benthic Terrain Modeler. Geosciences (Basel)
 <strong>8</strong>:94.
 doi:10.3390/geosciences8030094 Wentworth, C. K. 1922. A
 Scale of Grade and Class Terms for Clastic Sediments. J Geol
 <strong>30</strong>: 377–392. doi:10.1086/622910
description: # Habitat heterogeneity over multiple scales supports dense and diverse
 megafaunal communities on a NE Pacific ridge
 [https://doi.org/10.5061/dryad.z08kprrn4](https://doi.org/10.5061/dryad.z08kprrn4) ## Description of the data and file structure ### Files and variables #### File: FGirard\_SurRidge\_substratum\_matrix.xlsx **Description:** Substratum composition matrix containing the estimated proportions of each substratum type per transect. ##### Variables * The first column contains transect numbers. * The remaining columns show the estimated proportions per transect for all substratum types. #### File: FGirard\_SurRidge\_distances\_to\_DSCS\_LASS.xlsx **Description:** Distances between megafaunal taxa (other than deep-sea corals and sponges) observed on the LASS mosaic and nearest coral and sponge. ##### Variables * Taxon: Name of observed taxa (megafauna other than coral or sponge). * Distance to nearest coral: Unit: m. * Nearest coral taxon: name of nearest coral taxon. * Distance to nearest sponge: Unit: m. * Nearest sponge taxon: name of nearest sponge taxon. #### File: FGirard\_SurRidge\_environmental\_matrix.xlsx **Description:** Matrix of environmental and terrain variables used in the analyses. ##### Variables The first column contains transect numbers. The remaining columns show the estimated values per transect for all environment or terrain variables: * Depth: average depth measured by the ROV during the transect. Unit: m. * Oxygen: Average dissolved oxygen concentration measured by the ROV during the transect. Unit: ml/l. * Salinity: Average salinity measured by the ROV during the transect. Unit: psu. * Temperature: Average temperature measured by the ROV during the transect. Unit: degrees Celsius. * SubPC1: First principal component scores obtained from the principal component analysis performed on the Hellinger-transformed substratum composition matrix. Dimensionless. * SubPC2: Second principal component scores obtained from the principal component analysis performed on the Hellinger-transformed substratum composition matrix. Dimensionless. * Rugosity: Average roughness values extracted from Sur Ridge bathymetry at ROV locations during the transect. Dimensionless. * sBPI broad: Average broad-scale standardized bathymetric position index values extracted from Sur Ridge bathymetry at ROV locations during the transect. Dimensionless. * sBPIfine: Average fine-scale standardized bathymetric position index values extracted from Sur Ridge bathymetry at ROV locations during the transect. Dimensionless. * Northness: Average northness values extracted from Sur Ridge bathymetry at ROV locations during the transect. Dimensionless. * Eastness: Average eastness values extracted from Sur Ridge bathymetry at ROV locations during the transect. Dimensionless. * SD depth: Standard deviation of the depth measured by the ROV during the transect. Unit: m. * Depth range: Depth range covered by the ROV during the transect. Unit: m. * Slope: Average slope values extracted from Sur Ridge bathymetry at ROV locations during the transect. Unit: degrees. * Curvature: Average curvature values extracted from Sur Ridge bathymetry at ROV locations during the transect. Dimensionless. * SD slope: Standard deviation of slope values extracted from Sur Ridge bathymetry at ROV locations during the transect. Unit: degrees. #### File: FGirard\_SurRidge\_fauna\_matrix.xlsx **Description:** Megafauna density matrix used in the community analysis. ##### Variables * The first column contains transect numbers. * The remaining columns show estimated densities (number of individuals/ transect area in m^2) per transect for all observed taxa. #### File: FGirard\_SurRidge\_terrain\_variables\_associated\_with\_fauna\_LASS.xlsx **Description:** Terrain variables associated with megafaunal annotations on the LASS photomosaic. ##### Variables * Taxon: Name of observed taxa. * Phylum: Phylum of each observed taxon. * sBPI fine: Fine-scale standardized bathymetric position index value extracted from the LASS bathymetry at megafaunal observation location. Dimensionless. * sBPI broad: Broad-scale standardized bathymetric position index value extracted from the LASS bathymetry at megafaunal observation location. Dimensionless. * Slope: Slope value extracted from the LASS bathymetry at megafaunal observation location. Unit: degrees. * Northness: Northness value extracted from the LASS bathymetry at megafaunal observation location. Dimensionless. * Eastness: Eastness value extracted from the LASS bathymetry at megafaunal observation location. Dimensionless. * Curvature: Curvature value extracted from the LASS bathymetry at megafaunal observation location. Dimensionless. * Rugosity: Roughness value extracted from the LASS bathymetry at megafaunal observation location. Dimensionless. Missing values are indicated by NA. ## Code/software All data can be viewed and analyzed in R V4.3.1 software environment (R Core Team 2023) or other data processing software programs (e.g., Microsoft Excel).