Dataset DOI: 10.5061/dryad.rjdfn2zqz

Description of the data and file structure

This dataset includes the raw experimental data from individual squid, comprising routine metabolic rate (RMR), ammonia excretion, behavioral analysis results, and electroretinogram (ERG) recordings. Additionally, the R scripts for data analysis and visualization are also provided here. 

There were three groups in this dataset: control (normal seawater, pH 8.2) and two ocean acidification (OA) groups (pH 7.8) exposed for 7 days (acute) or 90 days (chronic).

Files and variables

File: Carbonate_calibration.csv

Description: This file, to be used together with Squid_Hemolymph.csv, provides the calculation procedures for deriving hemolymph pCO₂ and [HCO₃-]_. The calculations use a hemolymph-specific pKa1 of 6.10 (Truchot, 1976) to better reflect the buffering properties of cephalopod blood, and αCO2 values appropriate for 32 ppt salinity at 25°C. Carbonate chemistry calculations also incorporate the carbonic acid dissociation constants of Mehrbach et al. (1973), refitted by Dickson and Millero (1987).

File: Squid_Behavioral_assessment.csv

Description: We provide the results of the novel tank test for three groups of squid: a control group (pH 8.1) and two ocean acidification (OA, pH 7.8) groups exposed for different durations, 7 days (acute) and 90 days (chronic). The Group column labels these as acute-OA and chronic-OA. 

Variables

• Duration in Upper zone (%): The percentage of total observation time that each squid spent in the upper zone.
• Duration in Left zone (%): The percentage of total observation time that each squid spent in the left zone.
• Duration in Front zone (%): The percentage of total observation time that each squid spent in the front zone.
• Group: include three groups: control (pH 8.2),  acute-OA (pH 7.8, 7 days), and chronic-OA (pH 7.8, 90 days).

File: Squid_CFF.csv

Description: Here is presented the critical flicker fusion calculated from the Electroretinogram (ERG) recording. CFF was determined by averaging the peak response amplitudes at different stimulus frequencies. The CFF threshold, defined as the maximum frequency with a response ≥ 0.9, served as a measure of temporal resolution.

Variables

• CFF (critical flicker fusion): The critical flicker fusion value from each group.
• Group:  include three groups: control (pH 8.2),  acute-OA (pH 7.8, 7 days), and chronic-OA (pH 7.8, 90 days).

File: Squid_ERG.csv

Description: Here, provide the ERG recording data in the unit as maximum response frequency/ Stimulus frequency. 

Variables

• Frequency: This means the Stimulus frequency (Hz).
• Group: control (pH 8.2),  acute-OA (pH 7.8, 7 days), and chronic-OA (pH 7.8, 90 days).
• mean_value: The mean of the ratio between the maximum response frequency and the stimulus frequency for each stimulus frequency (Hz).
• sd_value: The standard deviation of the ratio between the maximum response frequency and the stimulus frequency for each stimulus frequency (Hz).

File: Squid_Hemolymph.csv

Description: This file contained three parameters from squid's hemolymph.

Variables

• Hemolymph pH: The pH of the hemolymph was measured using an In-Lab Micro pH probe (Mettler-Toledo, Columbus, Ohio, USA) connected to a WTW 340i meter (Xylem Analytics).
• Hemolymph PCO2 (atm): The systemic partial pressure of CO₂ in hemolymph, calculated by combining the measured hemolymph pH and total carbon using the Henderson-Hasselbalch equation.
• Hemolymph [HCO3-] (mmol l-1): The bicarbonate concentration in hemolymph, derived mathematically from the measured pH and total carbon using the Henderson-Hasselbalch equation.
• Group: control (pH 8.2),  acute-OA (pH 7.8, 7 days), and chronic-OA (pH 7.8, 90 days).

File: Squid_normalized_total_distance.csv

Description: Normalized total distance traveled by squid during the novel tank test.

Variables

• normalized total distance (Body lengths moved in total): The total distance moved by each squid during the novel tank test, expressed in body lengths and normalized across individuals.
• Group: control (pH 8.2),  acute-OA (pH 7.8, 7 days), and chronic-OA (pH 7.8, 90 days).

File: Squid_Prey_Capture.csv

Description: In the prey capture experiments, individuals that successfully captured prey are marked as "1", while those that did not are marked as "0". For individuals with successful captures, the dataset also includes the time taken to capture the prey and the number of attempted attacks.

Variables

• Prey Capture (1 = Success: individuals that successfully captured prey are marked as "1", while those that did not are marked as "0".
• 0 = fail): individuals that successfully captured prey are marked as "1", while those that did not are marked as "0".
• Group: control (pH 8.2),  acute-OA (pH 7.8, 7 days), and chronic-OA (pH 7.8, 90 days).
• Hunt duration (sec): The time (in seconds) each squid took to successfully capture the prey.
• The number of attempted attacks: The total number of attacks each squid attempted during the prey capture trial.

File: Squid_RMR.csv

Description: This file contains the routine metabolic rate (RMR) of individual squid.

Variables

• Routine metabolic rate (umol O2 g-1 h-1): The routine metabolic rate normalized to body weight (g) and measurement duration (hours), expressed in µmol O₂ g⁻¹ h⁻¹.
• Group: control (pH 8.2),  acute-OA (pH 7.8, 7 days), and chronic-OA (pH 7.8, 90 days).

File: Squid_Ammonia.csv

Description: This file contains the ammonia excretion rate of individual squid.

Variables

• Ammonia excretion rates (umol NH4 g-1 h-1): The ammonia excretion rate normalized to body weight (g) and measurement duration (hours), expressed in µmol NH₄⁺ g⁻¹ h⁻¹.
• Group: control (pH 8.2),  acute-OA (pH 7.8, 7 days), and chronic-OA (pH 7.8, 90 days).

File: Squid_normalized_velocities.csv

Description: Normalized swimming velocities of squid during the novel tank test.

Variables

• normalized velocities (Body lengths per second): The instantaneous swimming speed of each squid, expressed in body lengths per second and normalized across individuals.

• Group: control (pH 8.2),  acute-OA (pH 7.8, 7 days, and chronic-OA (pH 7.8, 90 days).

File: squid.zip

Description: This zip file contains all R scripts for data analysis and visualization, including the full workflow for the transcriptome analysis. All details are provided in the README.md file.

Code/software

The R version: 4.4.1

Access information

Other publicly accessible locations of the data:

• None

Data was derived from the following sources:

• None