Dataset for "Oxygen limitation is not a major physiological mechanism restricting early life development in zebrafish"

This repository contains the raw and processed data underlying the study:

“Oxygen limitation is not a major physiological mechanism restricting early life development in zebrafish.”

The dataset includes morphometric, physiological, and survival measurements collected across two independent experiments (Experiment 1 and Experiment 2) designed to test the effects of oxygen availability (12.5, 25, 50, 100, and 200% air saturation) and temperature (15.7 to 39.3°C) on embryonic, larval, and juvenile zebrafish performance.

All files are provided in .csv format and can be opened with standard spreadsheet software or statistical programming environments (R, Python, MATLAB, etc.). Each row corresponds to an individual or experimental unit (holding beaker), and columns contain measured traits and associated metadata (e.g., Oxygen treatment, Temperature treatment, developmental stage in hours post fertilizaton).

File overview

Embryo traits

• Yolk sac area – Experiment 1 (.csv)
  Quantified yolk sac area measurements from embryos (mm^2), used as a proxy for energy reserves and developmental progression.

• Yolk sac area – Experiment 2 (.csv)
  Same measurements as above for the independent replicate experiment.

• Heart rate – Experiment 2 (.csv)
  Embryonic heart rate measurements (Hertz, Hz), used as an indicator of metabolic and physiological performance.

Larval traits

• Larval length – Experiment 1 (.csv)
  Standard body length measurements (mm) of larvae at the specified developmental stage.

• Larval length – Experiment 2 (.csv)
  Replicate dataset of larval body length measurements.

• Hatching rate and survival to first feeding – Experiment 1 (.csv)
  Hatching success and survival metrics quantified from embryo to first-feeding stage (e.g., see Larvae_count_cummulative, SurvivalToFeed).

• Hatching rate and survival to first feeding – Experiment 2 (.csv)
  Replicate measurements of hatching success and early survival.

Juvenile traits

• Body size and CTmax – Experiments 1 & 2 (.csv)
  Juvenile body size measurements and critical thermal maximum (CTmax) values (in °C), used to assess growth and upper thermal tolerance. See columns Beaker_ID and Experiment to track fish individuals rearing origin.

Experimental design notes

• Data originate from two independent experiments (Exp 1 and Exp 2) performed under controlled oxygen treatments.

• Traits span multiple life stages: embryo, larva, and juvenile.

• Measurements include:

  • Morphology (yolk sac area, length, body size)

  • Physiology (heart rate, CTmax)

  • Performance and fitness proxies (hatching success, survival)

Data structure

Across files, columns typically include:

• Beaker or clutch ID

• Treatment (e.g., oxygen and temperature condition)

• Photo or video ID

• Developmental stage or time point

• Measured trait value(s)

Exact variable names are specified within each file header.

Code of paper plots and statistical analyses

Code was developed in R studio (R software v4.4.1; R Core Team, 2024) and include two script files:

• Code used to produce paper plots (see Paper_Plots.R)

• Code used for statistical models (see Paper_Models.R)