DOI: 10.5061/dryad.ghx3ffc2p
title: Differing temperature regimes have no impact on the heat stress response of shallow and upper mesophotic populations of a temperate calcareous sponge

description: Marine heatwaves (MHWs) are increasing in intensity and frequency globally
 due to anthropogenic climate change. Temperate mesophotic ecosystems
 (TMEs) are light-dependent habitats found at depths of approximately
 30–150m, between shallow euphotic zones and the deep sea. TMEs typically
 experience lower, more stable temperatures than adjacent shallow
 ecosystems, which may result in intraspecific differences in thermal
 tolerance between populations. Sponges, often the dominant benthic
 organisms in TMEs, display varied responses to thermal stress. We
 hypothesised that shallow-water sponges may be more resilient to heat
 stress than those from adjacent upper-mesophotic zones. Here we have
 deposited all data and code used in the analysis for this study.
description: # Differing temperature regimes have no impact on the heat stress response
 of shallow and upper mesophotic populations of a temperate calcareous
 sponge ## Overview This repository contains all datasets and code used in
 the analyses for the manuscript *"*Differing temperature regimes have
 no impact on the heat stress response of shallow and upper mesophotic
 populations of a temperate calcareous sponge" (DOI:
 10.1098/rspb.2025.1103). The study examines how shallow (10 m) and
 upper–mesophotic (30–50 m) populations of a temperate calcareous sponge
 respond to marine heatwaves (MHWs) - extreme thermal events that are
 becoming more frequent and intense due to anthropogenic climate change.
 Temperate mesophotic ecosystems (TMEs), typically experiencing cooler and
 more stable thermal regimes, may host populations with different thermal
 tolerances than their shallow-water counterparts. This repository provides
 full transparency and reproducibility for all analyses, figures, and
 microbial community assessments presented in the manuscript. Below is a
 detailed description of the dataset structure, contents, and associated
 analytical scripts. Repository Contents #### 1. Raw and Processed Data
 #### **01_RawData.zip: raw FASTQ sequencing reads** * Contains all raw 16S
 rRNA amplicon sequencing reads used for microbial community analyses. *
 These reads were processed into an OTU table using the pipeline described
 in `MHW_microbial_sequences.R`. #### **all.data.xlsx** A multi-sheet Excel
 file containing all environmental, physiological, and microbial datasets.
 Sheets include: * **fiord.temp.10** – Temperature (degree C) logger data
 collected at 10 m depth. * **fiord.temp.30** – Temperature logger data
 collected at 30 m depth. * **fiord.temp.50** – Temperature logger data
 collected at 50 m depth. * **regression** – Buoyant weight and ash-free
 dry weight (AFDW) measurements used to calculate respiration rates (per
 gram AFDW) and construct regression models. * **schedule** – Temperature
 data from experimental heatwave simulations, used to generate temperature
 schedule plots. * **resp_bw** – Buoyant weight measurements and
 respiration rates for each sponge under each thermal treatment across
 experimental time points. * **survival** – Survival data used for
 Kaplan–Meier survival analyses. * **OTU** – Operational Taxonomic Unit
 (OTU) table generated from 16S sequences and used for microbial community
 composition analyses. Each sheet includes raw data in the format used
 directly for statistical and graphical workflows. #### 2. **Code and
 Scripts** **MHW_final_complete_stats_and_plots_ProcB.R** * Main script
 used for all statistical analyses and figure generation. * Includes: *
 Data wrangling and transformation * Temperature time-series analyses *
 Survival modelling (Kaplan–Meier) * Linear mixed-effects models *
 Respiration analyses * Community composition analyses (ordination,
 PERMANOVA, etc.) * All plotting code used in the manuscript (ggplot2) *
 Packages and functions referenced throughout correspond to those described
 in the Methods section of the manuscript. **MHW_microbial_sequences.R** *
 Full pipeline for processing raw 16S amplicon data. * Steps include: *
 Quality filtering and trimming * Error modelling * Generation of OTU table
 * Taxonomic assignment * Export of processed community data for downstream
 analyses. * Ensures reproducibility from raw sequences through to the
 final OTU table. #### 3. **Study Context** Marine heatwaves (MHWs) are
 increasing globally due to climate change and pose a particular threat to
 TMEs - light-dependent ecosystems found between ~30–150 m depth. These
 habitats typically experience stable, cooler temperatures that may
 influence the thermal tolerance of resident species, including sponges,
 which are often dominant benthic organisms. This study compares
 physiological and microbial responses to heat stress between shallow and
 upper–mesophotic sponge populations to test the hypothesis that
 shallow-water individuals possess greater thermal resilience. All data and
 code used to evaluate this hypothesis are provided here. #### 4. **How to
 Use These Files** **Reproducibility** 1. Begin by downloading all data
 files, including `01_RawData.zip` if microbial analyses are desired. 2.
 Use `MHW_microbial_sequences.R` to reproduce the OTU table from raw reads.
 3. Load `all.data.xlsx` into R using `readxl`, `openxlsx`, or similar
 packages. 4. Run `MHW_final_complete_stats_and_plots_ProcB.R` to reproduce
 all figures and statistical outputs from the manuscript. **Dependencies**
 All required R packages are listed and loaded in the scripts themselves
 #### 5. **Contact** For further clarification, please refer to the Methods
 section of the manuscript or contact the corresponding author. #### 6.
 **Data Availability** This README accompanies the Dryad submission and
 provides all relevant details required for reuse, interpretation, and
 replication.