DOI: 10.5061/dryad.wh70rxww9
title: Shelled Pteropod individual-based model output for the publication: The impact of aragonite saturation variability on shelled pteropods: An attribution study in the California current system

description: Observations from the California Current System (CalCS) indicate that the
 long-term trend in ocean acidification (OA) and the naturally occurring
 corrosive conditions for the CaCO3 mineral aragonite (saturation
 state Ω &lt; 1) have a damaging effect on shelled pteropods, a
 keystone group of calcifying organisms in the CalCS. Concern is heightened
 by recent findings suggesting that shell formation and developmental
 progress are already impacted when Ω falls below 1.5. Here, we quantify
 the impact of low Ω conditions on pteropods using an individual-based
 model (IBM) with life-stage-specific mortality, growth, and behaviour in a
 high-resolution regional hindcast simulation of the CalCS between 1984 and
 2019. Special attention is paid to attributing this impact to different
 processes that lead to such low Ω conditions, namely natural variability,
 long-term trend, and extreme events. We find that much of the observed
 damage in the CalCS, and specifically &gt;70% of the shell
 CaCO3 loss, is due to the pteropods’ exposure to naturally
 occurring low Ω conditions as a result of their diel vertical migration
 (DVM). Over the hindcast period, their exposure to damaging waters (Ω
 &lt; 1.5) increases from 9% to 49%, doubling their shell CaCO3 loss,
 and increasing their mortality by ∼40%. Most of this increased exposure is
 due to the shoaling of low Ω waters driven by the long-term trend in OA.
 Extreme OA events amplify this increase by ∼40%. Our approach can quantify
 the health of pteropod populations under shifting environmental
 conditions, and attribute changes in fitness or population structure to
 changes in the stressor landscape across hierarchical time scales.
description: This dataset contains the modelled trajectories of shelled
 pteropod in the California Current System for each year in the period
 between 1984 and 2019. The population dynamics were modelled using an
 extended version of the shelled pteropod Individual-Based Model (spIBM). The environmental conditions experienced by the modelled pteropods and their movement were calculated using the Lagrangian tool OceanParcelsv2.1.3 and the biogeochemical-physical forcing taken from the high-resolution hindcast simulation of the Northeast Pacific taken from Desmet et al. (2022). The spIBM is parameterized based on members of the <em>Limacinidae</em> family, and calibrated to capture the observed pteropod abundance signal, life-stage duration, and succession sequence for the temperate region. It simulates the pteropod life-cycle using four life-stages (eggs, larvae, juveniles, and adults) across two generations per year (spring and overwintering generation). The pteropod population is simulated from January 1st to December 31st at a daily resolution based on the environmental conditions individuals experience during their current-driven drift and diurnal vertical migrations with an one-hour timestep. The model and post-processing were done using Python 3.7.1.
description: # Shelled Pteropod Individual-Based Model output for the publication
 "The impact of aragonite saturation variability on shelled pteropods:
 An attribution study in the California Current System"
 [https://doi.org/10.5061/dryad.wh70rxww9](https://doi.org/10.5061/dryad.wh70rxww9) This dataset contains the simulated shelled pteropod trajectories for the period between 1984-2019 in the California Current System used for the publication "The impact of aragonite saturation variability on shelled pteropods: An attribution study in the California Current System". The trajectories were simulated using an improved version of the shelled pteropod Individual-Based Model [spIBM](https://doi.org/10.5281/zenodo.11096564). This version of the spIBM simulates the response of individuals to damaging conditions in two scenarios, which allowed us to distinguish between responses caused by the natural variability in aragonite saturation state (Ω), the long-term ocean acidification trend, and extreme events using the following scenarios: | Scenario | Abbreviation | Modes of variability | Description | | :---------------------------- | :----------- | :-------------------------------------------------------------- | :----------------------------------------------------------------------------------------------------------------- | | Full simulation | NTE | Natural variability, long-term trend, extreme events | Pteropods are affected by all components that result in damaging conditions. | | Extreme events set to Ω = 1.5 | NT | Natural variability, long-term trend | Pteropods are affected by all components except extreme events. | | Constant CO2 | NE | Natural variability, extreme events without the long-term trend | Pteropods affected by the natural variability and extreme events, but without the influence of the long-term trend | | Constant CO2 without extremes | N | Natural variability | Pteropods are affected by the natural variability only. | ## Description of the data and file structure Each compressed directory (.tar.gz) contains the daily NetCDF files with the simulated trajectories for a year from the 1st of January to the 31st of December. The name of the directory indicates which scenario in the table above was compared to the Null-scenario. For each simulation year in the period between 1984 and 2019, there are four compressed directories (.tar.gz) containing a directory containing the daily trajectories (**trajectories**) and another one which contains the environmental conditions experienced by each pteropod throughout each day (**environmental**). Within the **trajectories** directory, one finds files named **PPC_JitPtero_Day_DDD_reduced.nc**, were *DDD* depicts the day in the simulation. These files ending in **_reduced.nc** have the daily average values of environmental conditions experienced during one day, and the current state of each simulated individual. Within the **environmental** directory, one finds files named **PPC_JitPtero_Day_DDD_env.nc**, were *DDD* depicts the day in the simulation. These files ending in **_env.nc** have the environmental conditions experienced throughout the day in a 1 hour timestep. ### Contents and structure of the PPC\_JitPtero\_Day\_DDD\_reduced.nc files These files are named as **PPC_JitPtero_Day_DDD_reduced.nc**, indicating that the file was compressed using NCO's Precision Preserving Compression (*PPC*), the trajectories were calculated using a Just-In-Time (*Jit*) particle tracking for pteropods, for the day *DDD*, and was reduced to the daily averages. These files contain the following variables for all simulated pteropod (X) with the dimension (traj=X, obs=1): | Variable name | type | Description | | :-------------------- | :----- | :------------------------------------------------------------------------- | | trajectory | int | Unique identifier for each particle in Parcels | | time | double | Seconds since 1984-01-01T12:00:00 | | lat | float | Latitude in degrees North | | lon | float | Longitude in degrees East | | z | float | Depth in meters | | distance | float | Distance from the coast in km | | temp | float | Last temperature experienced in °C | | temp\_sum | float | Sum of temperatures experienced in a day in °C | | food | float | Last chlorophyll-a concentration experienced in mg m-3 | | food\_sum | float | Sum of food experienced in a day in mg m-3 | | oxygen | float | Last oxygen concentration experienced in mmol m-3 | | arag | float | Last Ω experienced in the Null-scenario | | arag\_sum | float | Sum of Ω below 1.5 experienced in the Null-scenario in a day | | step\_counter | float | Number of timesteps in a day | | step\_counter\_arag | float | Number of timesteps with aragonite saturation state below 1.5 | | damage | float | Accumulated shell CaCO3 damage in the Null scenario in mg | | extreme\_damage | float | Accumulated shell CaCO3 damage in the alternative scenario in mg | | arag\_hind | float | Aragonite saturation state of the NTE-scenario | | generation | float | Generation of the pteropod | | stage | float | Life-stage of the pteropod | | survive | float | Flag depicting if the pteropod is alive or not in the Null-scenario | | flag\_would\_die | float | Flag depicting if the pteropod is alive or not in the alternative scenario | | num\_spawning\_events | float | Counter of the number of spawning events | | shell\_size | float | Size of the pteropod in the Null-scenario | | extreme\_shell\_size | float | Size of the pteropod in the alternative scenario | | shell\_thickness | float | Empty field that could be used to store the shell thickness | | days\_of\_growth | float | Age of the pteropod | | ERR | float | Egg Release Readiness index | | spawned | float | Flag depicting if a pteropod has spawned eggs | | MyID | float | ID used to keep track of particles across days | | Parent\_ID | float | MyID of the pteropod that spawned the current pteropod | | Parent\_shell\_size | float | Size of the parent pteropod at spawning | | extreme\_arag\_flag | float | Flag depicting if an extreme event was experienced in the last step | | extreme\_arag | float | Last Ω experienced in the alternative scenario | | extreme\_arag\_sum | float | Sum of Ω below 1.5 experienced in the alternative scenario | | reseed\_area | float | Flag depicting if the pteropod is still in the region of interest | ### Contents and structure of the PPC\_JitPtero\_Day\_DDD\_env.nc files These files are named as **PPC_JitPtero_Day_DDD_env.nc**, indicating that the file was compressed using NCO's Precision Preserving Compression (*PPC*), the trajectories were calculated using a Just-In-Time (*Jit*) particle tracking for pteropods, for the day DDD, and was reduced to only include the environmental conditions from Desmet et al. along the simulated pteropod trajectories in a 24 hour timestep (traj=X, obs=24). The field 'arag' represents the aragonite saturation state in the NULL-scenario. The field 'extreme_arag' represents the aragonite saturation state in the alternative scenario, where the NTE-scenario is the hindcast simulation from [Desmet et al. (2022)](https://doi.org/10.1029/2021JC018159), and the NE-scenario corresponds to the aragonite saturation state under constant atmospheric CO2 from [Desmet et al. (2023)](https://doi.org/10.5194/bg-20-5151-2023). The remaining scenarios were derived from the NTE- and NE-scenarios. | Variable name | Description | | :------------------ | :---------------------------------------------------------- | | lat | Latitude in degrees North | | lon | Longitude in degrees East | | z | Depth in meters | | temp | Temperature simulated in Desmet et al. 2022 | | food | Chlorophyll-a concentration simulated in Desmet et al. 2022 | | oxygen | Oxygen concentration simulated in Desmet et al., 2022 | | arag | Aragonite saturation state of the NULL-scenario | | extreme\_arag\_flag | Flag depicting if an extreme event was encountered | | extreme\_arag | Aragonite saturation state of the alternative scenario |