Data from: Temporal shifts in ovulation between laboratory and semi-natural environments in the model fish medaka
Data files
Feb 16, 2026 version files 15.22 KB
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RawData.csv
10.53 KB
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README.md
4.70 KB
Abstract
Research on model organisms in controlled laboratory settings has enabled fundamental biological discoveries. However, the ecological validity of these findings remains uncertain when natural ecology is poorly understood. Medaka (Oryzias latipes) has served as a model fish for over a century. Recent studies on medaka have shown that the timing of daily mating behaviour differs by 3–4 h between laboratory and natural conditions; however, the underlying physiological timing of reproduction remains unclear. This study compared daily ovulation timing in medaka that spawn under standard laboratory conditions (artificial photoperiod, constant water temperature) and semi-natural conditions (natural light, daily temperature fluctuations) by dissecting ovaries sampled hourly to assess ovulation status. The time when 50% of individuals had ovulated was 4.2 h before sunrise in semi-natural conditions and 0.7 h before lights-on in laboratory conditions, indicating a 3.5 h (2.6–4.3 h) shift. These quantitative results revealed the significant physiological differences between laboratory and natural conditions despite the controlled conditions typical of laboratory reproductive studies. These findings have important implications for studies on circadian rhythms and reproductive physiology. They also emphasise the necessity of incorporating ecological context into an experimental design to ensure the biological relevance and reproducibility of model organism research.
Dataset DOI: 10.5061/dryad.n8pk0p37n
Description of the data and file structure
This study collected data to compare the timing of ovulation in medaka fish (Oryzias latipes) between standard laboratory conditions and semi-natural environments. The experimental efforts involved:
Experimental Design: Two parallel experiments using the same medaka strain (himedaka) - one under controlled laboratory conditions (artificial 14L:10D photoperiod, constant 26°C) and another under semi-natural conditions (natural light cycles, fluctuating temperatures 16-27°C) during the breeding season.
Data Collection Method: Hourly sampling of female medaka over 4-day periods, with 3 females collected per time point (144 females per condition, 288 total). Females were housed with males in divided tanks to maintain social cues while preventing spawning.
Measurements: Each sampled female was euthanized and dissected to examine ovary morphology and determine ovulation status based on oocyte characteristics. Fish were classified as "ovulated" when >90% of mature oocytes had completed ovulation.
Temporal Scope: Laboratory experiments conducted February 2025 (sampling midnight to 11 AM), semi-natural experiments conducted May-June 2025 (sampling 9 PM to 8 AM).
The data were collected to quantify temporal differences in this fundamental reproductive process between laboratory and natural conditions, addressing questions about the ecological validity of model organism research and circadian rhythm regulation.
Files and variables
File: RawData.csv
Description: Complete raw dataset from the medaka ovulation timing experiment comparing laboratory and semi-natural environmental conditions. Contains individual-level measurements for all 288 female medaka sampled across both experimental conditions.
Variables:
- No: Sequential observation identifier/row number for each individual fish sampled (integer, range: 1-288)
- Experiment day: Experimental session number indicating which of the 4 replicate days each observation came from (integer, range: 1-4)
- Laboratory experiments: February 11-12, 12-13, 13-14, and 16-17, 2025
- Semi-natural experiments: May 31-June 1, June 1-2, June 2-3, and June 3-4, 2025
- Sampling time: Hour when the individual was sampled (integer)
- Laboratory condition: 0-11 (representing 00:00 to 11:00, 12 hourly time points)
- Semi-natural condition: 21-8 (representing 21:00 to 08:00, 12 hourly time points)
- Standard length of female (mm): Body length measurement from snout to end of caudal peduncle, measured to 1 mm precision using digital calipers (integer values representing measurements in mm)
- Body mass of female (g): Total body weight measured to 0.001 g precision using electronic balance (float)
- Ovulation (1 = yes, 0 = no): Binary outcome variable indicating ovulation status based on ovarian dissection (integer)
- 1 = Ovulated (>90% of mature oocytes had completed ovulation)
- 0 = Non-ovulated (only partial or no ovulation observed)
- Treatment: Experimental condition (string)
- Expected values: "Laboratory" or "Semi-natural" (or abbreviated versions)
- Time after sumset: Laboratory conditions: time elapsed from 10 p.m., when the lights were turned off. Semi-natural conditions: time elapsed from 7 p.m., when the sun set.
Sample Size: 288 observations total (144 per treatment condition, 3 individuals × 12 time points × 4 experimental days per condition)
Code/software
Based on the manuscript, the following free/open software is needed to reproduce the data analysis:
Primary Software:
- R version 4.5.1 (R Core Team 2025) - Used for all statistical analyses
Required R Functionality:
- Base R statistical functions for:
- Logistic regression analysis (
glm()function with binomial family and logit link) - Likelihood ratio tests for model selection (
anova()function) - Model comparison and parameter estimation
- Logistic regression analysis (
Access information
Supplementary Environmental Data Sources:
- Sunrise/sunset times: National Astronomical Observatory of Japan website (https://eco.mtk.nao.ac.jp/koyomi/dni/2023/dni22.html)
- Temperature records: Japan Meteorological Agency website (https://www.data.jma.go.jp/obd/stats/etrn/view/nml_sfc_ym.php?prec_no=52&block_no=47632&year=&month=&day=&view=)
