Micro-refuges or ecological traps: context-dependent effects of rock pools on intertidal biodiversity across latitudes
Data files
Feb 06, 2026 version files 28.29 MB
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Firth_etal_2026_Functional.Rmd
55.65 KB
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Firth_etal_2026_Richness.R
5.96 KB
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full_dataset_richness.csv
422.34 KB
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README.md
6.46 KB
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rock_pools_tot.csv
13.74 MB
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rockpools_dataset.csv
13.75 MB
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rockpools_functions.csv
67.62 KB
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Singletons.csv
6.24 KB
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Temp_Data.csv
232.50 KB
Abstract
Biodiversity is unevenly distributed across the Earth. At very large spatial scales, the decline in species richness from the tropics to the poles, the Latitudinal Diversity Gradient (LDG), remains one of the most widely recognized patterns in ecology. We investigated how local-scale environmental heterogeneity influences biodiversity patterns across broad biogeographic gradients, using intertidal microhabitats (rock pools and adjacent emergent rock) as a model system within one of the most environmentally stressful ecosystems on Earth. This Dryad dataset compiles standardized biodiversity and microclimate observations from rocky intertidal habitats at 26 locations in 21 countries across six continents, spanning 38°S to 60°N (2019–2022). Across the survey, 675 taxonomic entities were recorded (505 identified to species level), with rock pools containing 618 taxa (274 unique) and emergent rock 401 taxa (57 unique). Data show that microhabitat differences can strongly modify latitudinal biodiversity patterns, with pools generally supporting higher taxonomic and functional diversity than emergent rock, but with context-dependent outcomes under extreme conditions. By mediating exposure to environmental stress, intertidal microhabitats provide insight into how fine-scale variability interacts with latitudinal stress gradients to shape biodiversity distributions. Incorporating microhabitat variability into biogeographic frameworks is important for understanding global biodiversity patterns and predicting ecological responses to climate change.
Dataset DOI: 10.5061/dryad.q2bvq83zx
Description of the data and file structure
This global dataset contains the datasets and R scripts used for analysis in the associated manuscript. Data include taxa abundance and richness, functional grouping information and environmental temperature records (from direct measurements) from intertidal microhabitats in tidepools and emergent rock across sites spawning six continents and three oceans.
The dataset contains the following files: two R scripts with General Aditive Models routine (R and Rmd files, see further methodological details in the main manuscript) and six CSV files used in these analyses:
CODE FILES:
- Firth_etal_2026_Richness.R: R script to reproduce richness-based analyses and figures (GAM framework as described in the manuscript methods).
- Firth_etal_2026_Functional.Rmd: R Markdown workflow to reproduce functional richness analyses, plots, and model outputs
DATA TABLES:
- rockpools_dataset.csv: quadrat-level taxa abundance
- rock_pools_tot.csv: total abundance per sample / summary table
- Singletons.csv: unique taxa counts by treatment/microhabitat (pool vs. emergent rock)
- full_dataset_richness.csv: richness and functional richness per sample
- Temp_Data.csv: in situ microhabitat temperature
- rockpools_functions.csv: functional group assignment for taxa in rockpools_dataset and rock_pools_tot
SOFTWARE: Analyses were conducted in R using GAMs (e.g., mgcv) and post hoc / plotting tools (e.g., emmeans, sjPlot) as described in the manuscript.
DATA TABLES BREAKDOWN
Note: The exact column names are given in the header row of each CSV. Definitions below describe the intended meaning of the key fields.
rockpools_dataset.csv — Sample-level raw biotic data
Description: Quadrat-by-quadrat taxon abundance observations across habitats, sites, and sampling periods.
Key variables:
- Province: Country/Location identifier (one of 26 global locations across 21 countries)
- Location: sampled sites (two per province, ≥500 m separation)
- Sample: Unique identifier per quadrat within site × period × habitat
- Treatment: MicroHabitat: pool or rock (adjacent emergent rock)
- Latitude / Longitude: Coordinates for the location or site (see manuscript Table S1 for details)
- Season: milder or harsher and wet or dry
- Anthropization: level of coastal habitat modification/land based on satellite image observation (subjective)
- Date: sampling date (day-month)
- Benthic cover variables (percent cover)
- TOT_cov: Total biological and substrate cover recorded in the quadrat.
- Bare_space: Percentage of uncovered substrate
- Sediment: Percentage covered by loose or settled sediment
- Bleached/Burnt_algae: Percentage of algae that are bleached, stressed, or dead
- Dead_Saccostrea-Mytilus_shells; Percentage of cover made up of dead shells
- Filamentous_algae: Percentage covered by thin, hair-like algae, often fast-growing and disturbance-tolerant.
- Biofilm_Periphyton: Percentage covered by microbial films
- Non-calcareous_crusts: Crusting organisms without calcium carbonate skeletons
- Crusts: Percentage covered by calcareous crusts
- Taxa names: Lowest possible morpho-taxonomic identification. Numbers indicate abundance: Percent cover for sessile taxa (0–100), and counts for mobile taxa
rock_pools_tot.csv — Sample-level totals / summaries
Description: Same as rockpools_dataset.csv but with aggregated biotic summaries per sampling unit (total cover per quadrat).
Key variables (described above): Province, Location, atitude, Longitude, Treatment, Season, Anthropization
- Bare_space: percent cover of uncolonized (exposed) rock
Singletons.csv — Unique taxa per microhabitat
Description: Counts of taxa that occur exclusively in rock pools or exclusively on emergent rock within a defined grouping level (season x site). This corresponds to the “unique taxa” metric described in the manuscript.
Key variables (described above): Province, Location, Treatment, Season
- Pool: number of taxa found only in pools
- Rock: number of taxa found only on emergent rock
full_dataset_richness.csv — Richness and functional richness table
Description: The analysis-ready dataset used for functional richness models (number of functions per quadrat).
Key variables (described above): Province, Location, atitude, Longitude, Treatment, Season, Anthropization
rich: mean number of functions per quadrat (alpha diversity)
rockpools_functions.csv — Functional group assignments
Description: Lookup table mapping each taxon to a functional group category.
Key variables:
- Taxonomical variables: Phyllum.Division, Class, Order, Family, Genus and Sample (name given by samplers = lowest available identification)
Functional grouping variables:
- Heterotrophs (Metazoans): herbivores (H.Veg), omnivores (H.Omn), carnivores (H.Car), detritivores (H.Det), scavengers (H.Scav)
- Autotrophs: morpho-functional groups: encrusting (A.Enc), turf (A.Turf), sub-canopy (A.SubC), canopy (A.Canop), with calcification subgroups: Crustose Coralline Algae (A.CrusC) and Articulated Coralline Algae (A.ArtC)
Temp_Data.csv — In situ microhabitat and temperature data
Description: Point measurements of substratum temperature (° C) collected using temperature loggers or thermocouples during sampling, for both pools and emergent rock. Due to limited access to this equipment by some researchers, temperature data for both habitats and sampling periods were collected for 17 out of the 26 locations (two sites at each location); there was no latitudinal bias in this subset.
Key variables (described above): Province, Location, Treatment, Season, Date
- Pool_depth: average pool depth from pool's water surface to bottom during low tide
- major_diameter: larger diameter measurement for the pool during low tide
- minor_diameter: shorter diameter measurement for the pool during low tide
- Temp: Temperature (º C) collected during sampling
- direction: temperature difference between pool and emergent rock: hotter = pool measurement was higher than that for its nearby emergent rock (pool>rock º C); cooler = pool measurement was lower than that for its nearby emergent rock (pool<rock º C)
This Dryad dataset compiles standardized biodiversity and microclimate observations from rocky intertidal habitats at 26 locations in 21 countries across six continents, spanning 38°S to 60°N (2019–2022). At each location, two rocky shore sites (≥500 m apart) were sampled during locally defined “milder” and “harsher” periods. During each sampling event, 20 quadrats (10 × 10 cm) were placed at mid-shore height in (i) shallow rock pools (<12 cm; avoiding sediment) and (ii) adjacent emergent rock (~20 cm away). Sessile taxa were recorded as percent cover (nearest 5%) and mobile/solitary taxa as counts, identified to the lowest possible taxonomic level. The dataset also includes functional-group assignments and in situ substrate temperature measurements (°C) where available (temperature data were collected for 17 of 26 locations), alongside R scripts used in the associated analyses.