DOI: 10.5061/dryad.rxwdbrvng
title: Archaeological evidence across four millennia indicates recent erosion of Chinook salmon age structure in California

description: 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.
description: # Archaeological evidence across four millennia indicates recent erosion
 of Chinook salmon age structure in California Dataset DOI:
 [10.5061/dryad.rxwdbrvng](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.