Diverging carbonate budgets following tropicalisation of temperate reefs

Climate-driven shifts in habitat-forming species abundance and distributions are transforming how ecosystems produce and cycle carbon, nutrients, and energy. Temperate kelp forests are increasingly being replaced by tropical or warm-affinity habitat-forming species like turf seaweeds and corals, i.e., “tropicalised”. These changes can have cascading effects on associated species such as calcifying organisms, which contribute to sediment generation and carbon cycling via the production of calcium carbonate. This study quantified carbonate production and erosion across a temperate kelp forest and three tropicalised reef states following the 2011 marine heat wave: kelp-turf mix, warmer-affinity seaweeds, and coral-turf dominance. Results show gross carbonate production was highest in coral-turf reefs (1.85 ± 0.65 kg m⁻² yr⁻¹), lowest in warmer-affinity seaweed reefs (0.04 ± 0.02 kg m⁻² yr⁻¹), and intermediate in temperate kelp forests (0.60 ± 0.19 kg m⁻² yr⁻¹). These differences were linke..., , # Diverging carbonate budgets following tropicalisation of temperate reefs

Dataset DOI: [10.5061/dryad.83bk3jb68](https://doi.org/10.5061/dryad.83bk3jb68)

## Description of the data and file structure

* This script analyses data from the study:
* \"Diverging carbonate budgets following tropicalisation of temperate reefs\"
* The analysis quantifies changes in benthic community structure, calcification, and bioerosion across a temperate-to-tropical transition.

Analyses and figures correspond to:

* Tropicalisation states (Figure 2)
* Community % cover by organism (Figure 3)
* Carbonate production and bioerosion (Figure 4)

### Files and variables

#### File: Photo_quadrat_data_RSPB-2025-2578.csv

**Description**: Photo-habitat quadrat analyses across sites

* *Site*: Study site
* *Transect*: Replicate transect
* *Functional_Group*: Benthic functional group
* *Count:* Each row = one random point on image

#### File: Calcifier_data_RSPB-2025-2578.csv

**Description**: Percent cover and ca..., , **Changes after Oct 31, 2025:** \
Update Photo_quadrat_data_RSPB-2025-2578.csv. Updating the format of the matrix so it matches the analyses.

Update RSPB-2025-2578_Script.R, added one test that was not in the first version.