DOI: 10.5061/dryad.7m0cfxq9b
title: Depth-structured sponge assemblages offer limited evidence for mesophotic refuge potential under the deep reef refuge hypothesis

description: Temperate mesophotic ecosystems (TMEs) have the potential to act as
 climate refugia for shallower benthic species impacted by environmental
 change. However, the extent to which mesophotic ecosystems might provide
 an ecological refuge, particularly for key functional groups like sponges,
 remains poorly known in temperate systems. Our study investigates sponge
 assemblage structure across a depth gradient at the Poor Knights Islands
 Marine Reserve, New Zealand, to assess the potential for mesophotic depths
 to act as ecological refuges for species inhabiting shallow water in the
 scenarios where mesophotic depths avoid shallower disturbances. Using ROV
 and SCUBA-based image surveys across three sites, sponge abundance data
 were collected from depths spanning 5 to 65 meters. Assemblage
 composition, species richness, and depth-dependent abundance patterns were
 analysed using nMDS, PERMANOVA, and linear regression. Results revealed
 high beta diversity across depths, with sponge assemblages strongly
 structured by depth. The majority of sponge operational taxonomic units
 (OTUs) were restricted to either shallow (&lt;30 m) or mesophotic
 (&gt;30 m) zones, with between 26.4% and 32.7% of OTUs shared between
 both, and a total of 18 sponge OTUs found in multiple depths in each zone
 across all three sites. Depth related abundance patterns tended to be
 species specific, meaning the potential for any refuge effect will likely
 also vary between species depending on their local abundance. Our findings
 highlight the vertical structuring of sponge assemblages and suggest that,
 while TMEs may offer some refuge potential to specific species in
 scenarios where mesophotic habitats avoid disturbances experienced by
 shallow species, the benefits won’t apply to entire sponge assemblages.
description: # Depth-structured sponge assemblages offer limited evidence for
 mesophotic refuge potential under the deep reef refuge hypothesis Dataset
 DOI: [10.5061/dryad.7m0cfxq9b](https://doi.org/10.5061/dryad.7m0cfxq9b) ##
 Description of the data and file structure This repository contains the
 data and R code used to analyse sponge assemblage structure across depth
 gradients at the Poor Knights Islands Marine Reserve, New Zealand. The
 analyses assess sponge assemblage composition, diversity, and
 depth-related abundance patterns in shallow and mesophotic reef zones,
 with the aim of evaluating the potential for mesophotic ecosystems to act
 as ecological refuges for shallow sponge species. The dataset accompanies
 the manuscript: *Depth-structured sponge assemblages offer limited
 evidence for mesophotic refuge potential under the deep reef refuge
 hypothesis* ### Files and variables #### File: PK_all_sites_sponges.xlsx
 **Description:** Excel file containing sponge percentage cover data
 derived from benthic image analysis. **Sheets:**  * `NAW` – Northern Arch
 West * `NAE` – Northern Arch East * `IP` – Imagination Point #####
 Variables: * `Sample` – Unique identifier for each image/quadrat * `Site`
 – Sampling site * `Depth` – Sampling depth (m) * `Zone` – Depth zone
 (`Shallow` &lt;30 m, `Mesophotic` &gt;30 m) * Columns 5 onward – Sponge
 species or operational taxonomic units (OTUs), expressed as percentage
 cover per image **Notes:** * Percentage cover values represent
 proportional cover of the benthos per image. * OTUs include both
 identified species and morphospecies where taxonomic resolution was not
 possible from imagery. #### File:
 Sponge_assemblage_stats_and_plots_ecography.R **Description:** R script
 containing all data processing, statistical analyses, and figure
 generation used in the manuscript. **Main analyses include:** * Data
 import and formatting * Non-metric multidimensional scaling (nMDS) using
 Bray–Curtis dissimilarities * PERMANOVA and PERMDISP analyses testing for
 differences among depths and zones * Beta diversity partitioning (turnover
 vs. nestedness) using Jaccard dissimilarity * Linear regression analyses
 of total sponge cover and depth-generalist sponge abundance * Figure
 generation for assemblage ordinations, dispersion plots, and diversity
 summaries * Export of PERMANOVA and PERMDISP results to Excel files
 **Reproducibility notes:** * A fixed random seed (`set.seed(123)`) is used
 for permutation-based analyses. * All analyses were conducted in R version
 4.4.0. * File paths in the script may need to be updated to match the
 user’s local directory structure. ## Code/software ### **Key R packages
 used:**\ `tidyverse`, `vegan`, `pairwiseAdonis`, `betapart`, `ggplot2`,
 `patchwork`, `lme4`, `emmeans`, among others. ### Relationship Between
 Data, Code, and Manuscript * The Excel file (`PK_all_sites_sponges.xlsx`)
 contains the raw percentage cover data used for all analyses. * The R
 script (`sponge assemblage stats and plots ecography.R`) imports these
 data and performs all statistical analyses reported in the manuscript. *
 Figures and statistical outputs generated by the script correspond to
 figures and tables in the main text and supplementary materials. --- ###
 How to Run the Analyses 1. Download all files to a single working
 directory. 2. Open `sponge assemblage stats and plots ecography.R` in R or
 RStudio. 3. Update the `setwd()` paths if necessary. 4. Ensure all
 required R packages are installed. 5. Run the script sequentially from top
 to bottom. 
 
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