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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.

During California’s Gold Rush of 1849–1855, thousands of miners rushed to San Francisco, Sacramento, and elsewhere throughout northern California, creating a significant demand for food. Here we investigate the role of Atlantic cod (Gadus morhua) and Pacific cod (G. macrocephalus) during the Gold Rush era using historical records, ancient DNA, and vertebral morphology in the cod assemblage recovered from Thompson’s Cove (CA-SFR-186H), a Gold Rush–era site in San Francisco. From the 18 cod bones recovered from Thompson’s Cove, our analysis of five specimens for ancient DNA indicates that Atlantic cod were imported during the 1850s, likely as a (largely) deboned, dried and salted product from the East Coast of the United States. Curiously, while locally available in very deep waters off the California coast, Pacific cod were minimally fished during the 1850s and became abundantly available in the 1860s after an Alaska-based fishery developed.

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 anthropomorphic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Using ichthyofaunal analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara circa 1781-1834 CE, 86 salmonid vertebrae were identified. Ancient DNA sequencing identified three of these as from Chinook salmon and the remainder from steelhead trout. These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their historic range to include San Francisco Bay’s southernmost watershed.One Sentence SummaryFirst application of ancient DNA to extend a species’ historic range finds Chinook salmon native to San Jose, California.