Long-term decline in egg size of Japanese hatchery chum salmon links to declines in return rate and abundance
Data files
Sep 17, 2026 version files 842.77 KB
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egg_chum.zip
838.38 KB
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README.md
4.39 KB
Abstract
Variation in life-history traits contributes to fitness and population productivity in salmonids. To investigate long-term changes in egg size and body size of Japanese hatchery chum salmon and their links to declines in return rate and abundance, I analyzed egg size and female fork length (FL) of approximately 21,000 age-4 and age-5 fish from 13 hatchery-enhanced rivers in Japan during 1999–2019. River-specific generalized additive models (GAMs) identified synchronous declines in egg size across most rivers. Hierarchical GAMs adjusting for female FL, age, and river effects revealed a nationwide decline in egg size, whereas adjusted FL showed pronounced interannual variation without a long-term decline. Mean age at return also declined after approximately 2010 because of shifts in age composition. Standardized exponential decay rates were remarkably similar for egg size, return rate, and chum salmon abundance, suggesting common underlying environmental and evolutionary processes. These findings suggest that long-term declines in maternal investment may have contributed to declining return rates and abundance, underscoring the importance of life-history traits in evaluating the long-term consequences of hatchery enhancement programs.
Kitada, S. 2026. Long-term decline in egg size of Japanese hatchery chum salmon links to declines in return rate and abundance. Canadian Journal of Fisheries and Aquatic Sciences.
2026-09-06
Description
This repository contains the data and R scripts used in the article above.
The scripts were developed and tested using R version 4.5.2.
Scripts and data
01_trait_box_plot.R
Generates annual boxplots of female fork length and egg size for age-4 and age-5 chum salmon across 13 hatchery-enhanced rivers, retaining all observed values.
Data:
chum_trait_dat.csv
02_trait_summary.R
Calculate river-specific means, standard deviations (SDs), and sample sizes for female fork length and egg size, and visualize their geographic distributions.
Data:
chum_trait_dat_exc_outliers.csv
13rivers_lon_lat.csv
03_river_specific_gam.R
Fit river-specific generalized additive models (GAMs) for female fork length and egg size using individual-level data.
Data:
chum_trait_dat_exc_outliers.csv
04_nationwide_gam.R
Fit nationwide generalized additive models (GAMs) for female fork length and egg size using individual-level data.
Data:
chum_trait_dat_exc_outliers.csv
05_age_comp.R
Calculate annual age composition and mean age at return for Japanese chum salmon, and visualize temporal changes.
Data:
age_comp_dat.csv
06_japan_chum_decline.R
Visualize long-term declines in return rate, abundance, and egg size.
Data:
chum_catch_num_country.csv
return_rate_egg_size_exc_outliers.csv
07_trait_relationships.R
Plot relationships among egg size, return rate, and female fork length.
Data
The data folder contains the six CSV files listed above. The variables in each data file are described below.
## chum_trait_dat.csv
Individual-level data on female chum salmon traits. This file contains all observed values.
year: Year of return.
prefecture: Japanese prefecture in which the river is located.
region: Geographic region.
river: Name of the river.
FL: Female fork length (cm).
age: Age.
gonad: Gonad weight (g).
fec: Fecundity (number of eggs).
eggW: Mean egg weight (g).
## chum_trait_dat_exc_outliers.csv
Individual-level data on female chum salmon traits after exclusion of observations identified as outliers.
year: Year of return.
prefecture: Japanese prefecture in which the river is located.
region: Geographic region.
river: Name of the river.
FL: Female fork length (cm).
age: Age.
gonad: Gonad weight (g).
fec: Fecundity (number of eggs).
eggW: Mean egg weight (g).
## 13rivers_lon_lat.csv
Geographic coordinates of the 13 rivers included in the river-specific analyses.
river: Name of the river.
lon: Longitude (decimal degrees).
lat: Latitude (decimal degrees).
## age_comp_dat.csv
Annual age composition of Japanese chum salmon by survey sampling .
year: Year of return.
area: Geographic area of Japan.
Age2: Percentage of age-2 fish (%).
Age3: Percentage of age-3 fish (%).
Age4: Percentage of age-4 fish (%).
Age5: Percentage of age-5 fish (%).
Age6: Percentage of age-6 fish (%).
Age7: Percentage of age-7 fish (%).
Age8: Percentage of age-8 fish (%).
sample_size: Number of fish sampled.
## chum_catch_num_country.csv
Annual commercial catch of chum salmon by country (1000 fish).
Year: Year.
Canada: Commercial catch in Canada.
Japan: Commercial catch in Japan.
Korea: Commercial catch in Korea.
Russia: Commercial catch in Russia.
USA: Commercial catch in the USA.
## return_rate_egg_size_exc_outliers.csv
Japanese chum salmon return rate and annual mean female traits for age-4 and age-5 fish after exclusion of observations identified as outliers.
Year: Year. For RR, this is the year of fry release; for Egg4, FL4, Egg5, and FL5, this is the year of return.
RR: Return rate, calculated as the total number of fish returning at ages 2–5 from fry released in the corresponding year divided by the number of fry released in that year.
Egg4: Mean egg weight of age-4 females (g) returning in the year.
FL4: Mean fork length of age-4 females (cm) returning in the year.
Egg5: Mean egg weight of age-5 females (g) returning in the year.
FL5: Mean fork length of age-5 females (cm) returning in the year.
How to use
Download the egg_chum.zip folder.
Set the working directory to the egg_chum folder.
Run the scripts in numerical order.