Kelp forests as nursery and foundational habitat for reef fishes

### Description for Paper to be Published in ECOLOGY

**Title:** Kelp Forests as Nursery and Foundational Habitat for Reef Fishes

**Abstract:**

The conservation of marine biodiversity necessitates an understanding of habitats that support and replenish species of interest, along with knowledge about the abundance and diversity of multi-species assemblages. Kelp forests, among the most productive marine coastal habitats globally, significantly influence reef fishes – a group with considerable ecological and socio-economic importance. With the widespread and escalating loss of kelp forests, it is urgent to quantify these effects to assess and project cascading impacts on biodiversity. This study evaluates relationships between kelp forests and associated reef fish populations through a global meta-analysis of experimental kelp removals and comparative surveys of kelp and adjacent non-kelp habitats. Our analyses show that kelp forests increase the abundance of reef fishes, with the significance of this effect varying based on the structural complexity of the kelp forests. Experimental studies demonstrate that kelp forests have a significant positive effect on fish species richness, indicating that kelp act as true foundation species by supporting the diversity of associated multi-species assemblages. Importantly, kelp forests enhance the recruitment of early life history stages, suggesting they serve as nursery habitats for many reef fish taxa. Furthermore, kelp forests differentially affect species with varying functional traits; both small-bodied fishes from lower trophic levels (e.g., herbivores and detritivores, micropredators, and mesopredators) and large-bodied fishes from higher trophic levels (e.g., piscivores, general carnivores) are facilitated by kelp forests. These results suggest that the loss of kelp forests, especially those with complex morphology, can reduce total abundance and diversity of fish, potentially causing cascading consequences for coastal ecosystem function.

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### Description of Files and Datasets

**Metadata File:**

- **README.xlsx:** Contains metadata for columns in each raw data file, providing detailed descriptions and definitions.

**Derived Data Files:**

- **biomass_clean.csv:** Cleaned data on fish biomass, processed from raw data for analysis.

- **masterFish_clean.csv:** Comprehensive dataset on various fish species, cleaned and ready for analysis.

- **single_sp_abund_clean.csv:** Cleaned data on the abundance of individual fish species.

- **sp_rich_clean.csv:** Data on species richness, cleaned for analysis.

- **total_abund_clean.csv:** Cleaned data on total fish abundance across different habitats.

**R Code Files:**

- **0_Clean_data.R:** Script for cleaning raw data and preparing derived datasets.

- **1_maps.R:** Script for creating maps, including modifications for saving figures (`ggsave`).

- **2_paper_info.R:** Script for cleaning unnecessary information and preparing data for publication.

- **3_total_analysis_figures.R:** Script for generating figures related to total abundance analysis.

- **4_richness_analysis_figures.R:** Script for generating figures related to species richness analysis.

- **5_scale_analysis.R:** Script for creating figures related to scale analysis.

- **6_adult_trophic_bodysize_analysis.R:** Script for analyzing slopes for individual trophic groups based on body size.

- **7_juvenile_analysis.R:** Script for updating and analyzing juvenile fish data.

- **Final_FishKelpStats.R:** Script for final statistical analyses and updates for readability.

- **make_three_panel_plot.R:** Script for creating three-panel plots, updated for panel type.

- **open_all_data_for_analysis.R:** Script to open and prepare all data for comprehensive analysis.

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This study provides critical insights into the role of kelp forests as foundational habitats and nurseries for reef fishes, highlighting the ecological importance of preserving these complex marine ecosystems. The datasets and scripts included facilitate a thorough understanding and replication of our analyses, ensuring transparency and aiding future research in marine conservation.