Archaeological evidence across four millennia indicates recent erosion of Chinook salmon age structure in California

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.