Ancient DNA analysis of archaeological specimens extends Chinook salmon's known historic range to San Francisco Bay's tributaries and southernmost watershed

PLoS One. 2021 Apr 15;16(4):e0244470. doi: 10.1371/journal.pone.0244470. eCollection 2021.

Abstract

Understanding a species' historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropogenic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Through the morphology-based analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara (CA-SCL-30H), Santa Clara County, circa 1781-1834 CE, 88 salmonid vertebrae were identified. Ancient DNA sequencing identified three separate individuals as Chinook salmon and the remainder as steelhead/rainbow trout (Oncorhynchus mykiss). These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their documented historic range to include San Francisco Bay's southernmost tributary watershed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animal Migration / physiology*
  • Animals
  • DNA, Ancient / analysis*
  • Ecosystem
  • Fossils / pathology
  • Oncorhynchus mykiss / genetics
  • Pacific Ocean
  • Rivers
  • Salmon / genetics*
  • San Francisco

Substances

  • DNA, Ancient

Grants and funding

The ancient DNA sequencing analysis was funded by a grant from the Guadalupe Coyote Resource Conservation District (GCRCD), a non-profit California State Agency to BMK. Stephanie A. Moreno is Executive Director and Richard B. Lanman is President of the Board of Directors of the GCRCD and were co-authors involved in study design, data analysis, decision to publish and preparation of the manuscript. The funder provided support in the form of salary for author SAM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.