DOI: 10.5061/dryad.n8pk0p37n
title: Data from: Temporal shifts in ovulation between laboratory and semi-natural environments in the model fish medaka

description: 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.
description: # Data from: Temporal shifts in ovulation between laboratory and
 semi-natural environments in the model fish medaka Dataset DOI:
 [10.5061/dryad.n8pk0p37n](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 &gt;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 (&gt;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
 ## 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](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=](https://www.data.jma.go.jp/obd/stats/etrn/view/nml_sfc_ym.php?prec_no=52&block_no=47632&year=&month=&day=&view=))