Dataset DOI: 10.5061/dryad.rfj6q57pb

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Description of the Data and File Structure

This dataset was generated from a multi-year field and laboratory study assessing the influence of contrasting upwelling systems on the physiology, morphology, and survival of two intertidal mollusk species in central-northern Chile.

• Field data: Monthly capture–mark–recapture surveys over 26 months at two sites (semi-permanent vs. seasonal upwelling), environmental variables, and individual morphological traits.
• Laboratory experiments: Conducted under controlled conditions to measure metabolic rate and heart rate.
• Survival analysis: Estimated using Cormack–Jolly–Seber models within a Bayesian framework.
• Physiological & morphological analysis: Linear mixed models.
• Environmental context: Satellite sea surface temperature (SST) data from ERA5 were used to characterize long-term thermal patterns and upwelling intensity.

The compressed file Upwelling_Mollusks_Data.zip contains four main directories, each corresponding to a type of data collected and analyzed. Each folder contains raw data and R scripts.

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Directory and File Descriptions

1. physiology_morphology

Contains individual-level physiological and morphological data, plus R scripts for analysis.

Files:

• cg_data.csv → Raw data for Chiton granosus
• sz_data.csv → Raw data for Scurria zebrina
• cg_analysis.R → R script used to analyze C. granosus data
• sz_analysis.R → R script used to analyze S. zebrina data

Variables in cg_data.csv and sz_data.csv:

• Location: Sampling site (Quintay = seasonal upwelling; Talcaruca = semi-permanent upwelling)
• Date: Sampling date (MM-DD-YYYY)
• Species: Scientific name (Chiton granosus or Scurria zebrina)
• Length: Shell length (mm)
• Width: Shell width (mm)
• Height: Shell height (mm)
• Weight: Buoyant weight (g)
• Met: Oxygen consumption rate (mgO₂ h⁻¹ g⁻¹)
• HR: Heart rate (NA if not measured)

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2. survival

Contains capture–mark–recapture data for both species at both sites, plus model outputs.

Files:

• data_cg_q.csv → Raw data for C. granosus, Quintay site
• data_cg_t.csv → Raw data for C. granosus, Talcaruca site
• data_sz_q.csv → Raw data for S. zebrina, Quintay site
• data_sz_t.csv → Raw data for S. zebrina, Talcaruca site

Variables in survival files:

• Capture_history: Capture–mark–recapture history, with presence (1) or absence (0) of each individual at each sampling occasion (nov_19, dec_19, jan_20, …)

Subfolder: models
Contains survival model analyses (Cormack–Jolly–Seber models). Four models included:

• p(t)phi(.): Apparent survival is constant during the study
• p(t)phi(F): Apparent survival varies with physiological performance
• p(t)phi(L): Apparent survival varies with body length
• p(t)phi(t): Apparent survival varies monthly at each location

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Model: p(t)phi(.)

Files included:

• cg_q_p(t)phi(.).R → R script used to analyze C. granosus, Quintay
• cg_t_p(t)phi(.).R → R script used to analyze C. granosus, Talcaruca
• sz_q_p(t)phi(.).R → R script used to analyze S. zebrina, Quintay
• sz_t_p(t)phi(.).R → R script used to analyze S. zebrina, Talcaruca

Subfolder: graphic

• data.txt → Summary statistics of the model outputs
• graphic_p(t)phi(.).R → R script for generating plots of the effect of locality on survival

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Model: p(t)phi(F)

Files included:

• cg_q_p(t)phi(F).R → R script used to analyze C. granosus, Quintay
• cg_t_p(t)phi(F).R → R script used to analyze C. granosus, Talcaruca
• sz_q_p(t)phi(F).R → R script used to analyze S. zebrina, Quintay
• sz_t_p(t)phi(F).R → R script used to analyze S. zebrina, Talcaruca

Subfolder: graphic

• data_1-6_months.txt → Summary statistics for the first 6 months of capture–recapture
• graphic_met.R → R script for generating plots of the relationship between physiological yield and survival probability

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Model: p(t)phi(L)

Files included:

• cg_q_p(t)phi(L).R → R script used to analyze C. granosus, Quintay
• cg_t_p(t)phi(L).R → R script used to analyze C. granosus, Talcaruca
• sz_q_p(t)phi(L).R → R script used to analyze S. zebrina, Quintay
• sz_t_p(t)phi(L).R → R script used to analyze S. zebrina, Talcaruca

Subfolder: graphic

• data_1-6_months.txt → Summary statistics for the first 6 months of capture–recapture
• graphic_large.R → R script for generating plots of relationship between body length and survival probability

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Model: p(t)phi(t)

This model assumes both capture probability and survival vary over time.

Files included:

• cg_q_p(t)phi(t).R → R script used to analyze C. granosus, Quintay
• cg_t_p(t)phi(t).R → R script used to analyze C. granosus, Talcaruca
• sz_q_p(t)phi(t).R → R script used to analyze S. zebrina, Quintay
• sz_t_p(t)phi(t).R → R script used to analyze S. zebrina, Talcaruca

Subfolder: graphic

• cg_q.csv → Summary statistics for C. granosus, Quintay
• cg_t.csv → Summary statistics for C. granosus, Talcaruca
• sv_q.csv → Summary statistics for S. zebrina, Quintay
• sv_t.csv → Summary statistics for S. zebrina, Talcaruca
• graphic_time.R → R script for generating plots of monthly survival probability

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Variables contained in graphic data files (for all models)

• meanPhi: Estimated mean survival probability (appears in models where ϕ varies with time)
• mean: Posterior mean of the parameter
• sd: Standard deviation of the posterior distribution
• min: Minimum value of the posterior distribution
• 25%: First quartile (25th percentile)
• 50%: Median (50th percentile)
• 75%: Third quartile (75th percentile)
• max: Maximum value of the posterior distribution
• Rhat: Gelman-Rubin convergence diagnostic
• n.eff: Effective sample size
• overlap0: Proportion of posterior distribution overlapping zero
• f: Factor/indicator variable

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3. temperature_pH

Contains in situ environmental monitoring data and analysis scripts.

Files:

• tem_pH_q.csv → Temperature and pH data from Quintay
• tem_pH_t.csv → Temperature and pH data from Talcaruca
• tem_pH_boxplot.R → R script for generating boxplots
• tem_vs_pH.R → R script analyzing temperature–pH relationship

Variables:

• Date: Sampling date (MM-DD-YYYY)
• Temperature: Seawater temperature (°C)
• pH: Seawater pH
• Season: Sampling season (Summer, Winter, …)

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4. satellite_SST

Contains satellite-derived sea surface temperature data (ERA5) and processing scripts.

Files:

• quintay_sst_2019_2021.nc → NetCDF SST for Quintay
• talcaruca_sst_2019_2021.nc → NetCDF SST for Talcaruca
• sst_netcdf.R → R script for reading, processing, and plotting SST

Usage notes for .nc files:

The .nc files can be accessed using Panoply, a free NASA application that allows inspection and plotting of NetCDF data without coding. The files can also be read and processed in R using the ncdf4 package.

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Abbreviations Used

• cg: Chiton granosus
• sz: Scurria zebrina
• t: Talcaruca
• q: Quintay
• sst: Sea surface temperature (°C)
• met: Metabolism
• tem: Temperature (°C)
• phi (ϕ): Apparent survival probability
• p: Encounter probability
• F: Physiological performance, covariate included in some models
• L: Body length, covariate included in some models
• t: Full temporal variation of survival
• . (dot in model notation) : Constancy over time of survival

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Code/software

• All analyses were conducted in R version 4.2.3
• Survival models were fitted in a Bayesian framework using JAGS through the R package jagsUI
• NetCDF files were processed using the ncdf4 R package