Data from: The staircase chart: visualising vertical and cross-shelf movements and dispersal of early-life fish, applied to Japanese jack mackerel
Data files
Apr 08, 2026 version files 671.57 KB
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charts_200m_2.npy
576.13 KB
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ctdtest_st07.csv
1.45 KB
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ctdtest_st22.csv
1.42 KB
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ctdtest_st73.csv
1.81 KB
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ctdtest_st76.csv
1.88 KB
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d18O_data.csv
28.92 KB
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figure_d18O_mid.csv
5.09 KB
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RATOC.csv
7.77 KB
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README.md
3.45 KB
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Schart_submit_2.py
43.66 KB
Abstract
1. Marine fish dispersal during early life stages is a critical process that affects population connectivity and dynamics, yet individual-level field observations remain difficult. This limits our ability to identify the factors controlling the dispersal process, including the active swimming of larvae and pelagic juveniles.
Here, we propose a method to reproduce ontogenetic vertical and horizontal movements of fish on continental shelves. The approach combined high-resolution profiles of oxygen stable isotope values (δ18O) from otoliths, hydrodynamic simulations, and a hidden Markov model. The shelf environment was compressed into a representative cross-section, in which fish movements were predicted by analysing temperature and salinity distributions in relation to otolith δ18O.
Applying the method to Japanese jack mackerel in the East China Sea shelf revealed general ontogenetic vertical migration and variable cross-shelf movements. Twelve fish collected from the southern to northern shelves originated mainly from the southern outer shelf, which is influenced by the northward-flowing Kuroshio current. Fast growers in the first 30 days moved to the inner shelf earlier and stayed south, while others remained in the outer shelf were transported to the northern shelf.
These findings indicate that horizontal movements, potentially influenced by active swimming, play an important role in the retention and dispersal of fish that spawn at shelf edges. This novel method can greatly advance our understanding of marine fish dispersal and improve conservation efforts.
Dataset DOI: 10.5061/dryad.v9s4mw77v
Description of the data and file structure
Files and variables
File: d18O_data.csv
Description: Compiled otolith data
Variables
- Station_original: Station ID in the original survey
- Sta: Renamed station ID for this study
- Original_ID: Fish ID in the original survey
- ID: Renamed Fish ID for this study
- Ind: Individual identifier
- SL: Standard length at catch (mm)
- OR: Otolith radius (um)
- Date_col: Date of collection
- Date_hatch: Estimated hatch date
- Drill_width: Width of micromilled area (um)
- Drill_OR_e: Distance from the core to the outer edge of the milled area (um)
- Drill_OR_m: Distance from the core to the centre of the milled area (um)
- dph: Days post hatch corresponding to the outer edge of the milled area
- dph_m: Median days post hatch of the milled area
- days: Period of milled area formation
- Date_e: Calendar date corresponding to the outer edge of the milled area
- Date_m: Median calendar date of the milled area
- d13C: Stable carbon isotope
- d18O: Stable oxygen isotope
File: charts_200m_2.npy
Description: Likelihood chart for each date of each individual otolith d18O profile in numpy array
File: figure_d18O_mid.csv
Description: Otolith d18O data and corresponding calendar dates for each individual summarised for the generation of staircase charts. The first row is data label, the second row is the estimated hatch dates. The third and lower rows show the combination of dates and otolith d18O.
Variables
- Hatch date (YYYY/MM/DD)
- Median date (YYYY/MM/DD)
- Otolith d18O
File: RATOC.csv
Description: Otolith daily increment width data
Variables
- ID: individual identifier
- Stn: Original station ID
- SL: Standard length (mm)
- Weight: Wet weight (g)
- OR: Otolith radius (um)
- Increments: Number of daily increments
- Age: Days post hatch at catch
- Capture: Date of catch (YYYY/MM/DD)
- Hatch: Date of hatch (YYYY/MM/DD)
- L/R: Left or Right otoliths
- Observer: Observer ID
- IW: Daily increment width at ages (um)
File: ctdtest_st07.csv
Description: CTD results for St. S.
Variables:
- T (degree C): Temperature
- Sal: Salinity
- d18O_oto: The mean otolith edge d18O value.
File: ctdtest_st22.csv
Description: CTD results for St. C.
Variables:
- T (degree C): Temperature
- Sal: Salinity
- d18O_oto: The mean otolith edge d18O value.
File: ctdtest_st73.csv
Description: CTD results for St. N-1.
Variables:
- T (degree C): Temperature
- Sal: Salinity
- d18O_oto: The mean otolith edge d18O value.
File: ctdtest_st76.csv
Description: CTD results for St. N-2.
Variables:
- T (degree C): Temperature
- Sal: Salinity
- d18O_oto: The mean otolith edge d18O value.
File: Schart_submit.py
Description: Analysing Python code.
Code/software
Schart_submit_2.py is developed based on Python 3.9.18 under Anaconda environment.
Required libraries are: numpy, datetime, matplotlib, math, calendar, colorsys, scipy, os, string, pandas, pylab.
The code was used to visualise otolith d18O profiles, compare fractionation equations, perform the staircase chart analysis and visualise the results.
Juvenile T. japonicus were collected during a bottom trawl survey in the East China Sea conducted by the Japan Fisheries and Education Agency from May to June 2014. We analysed geographic differences in transport and migration by selecting otoliths from 12 juveniles at four stations with relatively large catches: Sts. S and C on the southern shelf and Sts. N-1 and N-2 on the northern shelf. Station St. N-2, near N-1, served to confirm regional movement differences.
The extracted otoliths (sagittae) were cleaned, air-dried, and embedded in epoxy resin. To facilitate the observation of daily increments and subsequent micromilling, the otoliths were ground with sandpaper to expose the core, polished with an alumina polishing suspension (BAIKOWSKI International Corporation), and coated with nail polish. The daily increment widths were quantified from the core to edge using an otolith measurement system (RATOC System Engineering Co., Ltd.). As an indicator of the early life growth rate, the SL at 30 dph was estimated from the otolith radius at 30 dph, based on the reported linear relationship between the otolith and body sizes (Xie et al., 2005):
SL30 = 2.65 + 0.0425* OR30
where SL30 and OR30 are the SL and otolith radius at 30 dph, respectively.
Before micromilling, the polished nail surface was removed using acetone. Otolith portions were formed over an average of 5 days (18 days at the core, 7 days at the edge, and 4 days for the remaining sections on average). These portions were sequentially milled from the core to edge using a high-precision milling system (Geomill 326, Izumo-web). The milling depth was set to 50 μm from the surface. Following each milling, the extracted otolith powder was collected in a small reaction tube for isotope analysis, and the otoliths were cleaned with an air duster to prevent cross-contamination. The δ18O was measured using a microscale stable isotope analytical system (MICAL3c with IsoPrime 100, Ishimura et al., 2004; 2008). The otolith powders reacted with 104% phosphoric acid at 25 °C, resulting in the release of CO2 gas, which was purified and introduced into the mass spectrometer. The δ18O values were expressed in δ-notation relative to the Vienna Pee Dee Belemnite (VPDB) reference standard, reported as ‰ values, with an analytical precision better than ± 0.10 ‰. These procedures yielded otolith δ18O profiles with corresponding calendar date ranges for each value.
