Archaeological evidence across four millennia indicates recent erosion of Chinook salmon age structure in California
Data files
Dec 03, 2025 version files 153.55 KB
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meps14972.zip
150.44 KB
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README.md
3.11 KB
Abstract
Chinook salmon (Oncorhynchus tshawytscha) provide crucial ecosystem services, but their populations are in steep decline throughout most of their native range. These anadromous fish express a complex age structure, increasing resilience to disturbances. Recent decades have seen widespread diversity loss, but the lack of long-term baselines makes it difficult to assess this change. In this study, we collaborate with the Estom Yumeka Maidu Tribe of Enterprise Rancheria and use fish otoliths (ear stones) to reconstruct changes in age structure for California Central Valley Chinook salmon covering the last 4 millennia. Specifically, we compare the returner age structure of present-day hatchery and natural populations in the Feather and Yuba River (2002-2020) with archaeological data from the same watershed, spanning the Middle-Holocene (1800-1000 BCE) to the Late-Holocene (500-1770 CE) and Post-European-Contact (1770-1870 CE) time periods. We observe a shift to younger ages, from dominantly age-4 returners in the archaeological samples to age-3 fish in both hatchery and wild populations today. The recent time period also shows reduced variance and diversity in return ages compared to the Post-European-Contact time period, which has the most robust sample size of the archaeological collection. The shift to younger ages in returning fish may have caused losses in productivity, while the reduction in variance and diversity may have reduced their resilience to environmental stochasticity. The erosion of age structure since European Contact suggests anthropogenic factors, such as loss of freshwater and estuarine habitats, industrialized ocean fishing, and hatcheries, as potential contributors. Incorporating archaeological data into ecological assessments can help guard against hidden shifting baselines and inform restoration targets for more resilient populations. This dataset contains the ancient and modern otolith age data as well as associated metadata, including site location and time period. Furthermore, the scripts include all data processing and statistical analyses carried out in the manuscript.
Dataset DOI: 10.5061/dryad.rxwdbrvng
Description of the data and file structure
This dataset contains the data and scripts for the analyses performed in “Archeological evidence across four millennia indicates recent erosion of Chinook salmon age structure in California.”
Files and variables
Files are in a single file 'meps14972.zip' and need to be extracted. There is an R project file included and several subfolders that are referenced in the script. The data folder contains the data used for the analyses, the scripts folder contains the R scripts, and the outputs folder contains all figures and tables generated from this R project. Files in the outputs folder will get overwritten with subsequent runs of the scripts and should thus not be edited manually.
Scripts
01_data_analysis: Data preparation, homogenization of variable types and names, data analysis, and creation of output plots and tables
Data files
ages.csv: Fish age data for all samples in this study. Column descriptions are as follows:
- lab_id: unique ID
- age: estimated age based on otoliths
- location: Feather River or Yuba River
- site_id: Feather River, Yuba River, Archaeological sites
- class: Modern or Ancient
- year: Survey year
- time_period: Designated time period as described in the manuscript
- run: spring-run, fall-run, NA
- adipose_fin: Adipose fin present, absent, or unknown
- FL_mm: Fork length in mm
- sex: Male or Female
hvn.csv: Table designating hatchery vs natural origin for Chinook salmon based on published data (Willmes et al., 2024)
Willmes et al., 2024, Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population, Journal of Fish Biology, 10.1111/jfb.15847.
Outputs
- age_comp.png: Plot of the proportions of age classes by river and time horizon.
- age_comp_interval.png: Plot of the proportions of age classes for the Feather River by time interval. Figure 2 in the manuscript (as this figure is already included in the primary article, it was not archived at Dryad to avoid duplication and copyright issues)
- age_metrics.png: Plot of the changes in Mean return age, Age variance, and Age Diversity (H’) of returning Chinook salmon through time. Figure 3 in the manuscript (as this figure is already included in the primary article, it was not archived at Dryad to avoid duplication and copyright issues)
- age_summary.csv: Summary table of the number of fish by river and time interval.
- pairwise_combined.csv: Summary table of pairwise comparisons for return age for each time period using a Fisher’s exact and a Levene’s test for homogeneity of variances. Table 3 in the manuscript.
- summary_age_structure_metrics.csv: Summary table of the age structure metrics used to create Figure 3 in the manuscript.
Code/software
All scripts were written in R using R Studio, and all packages are cited in the text and script files.