Biodiversity science of ancient fisheries: Archaeological indicators of eelgrass meadow health and indigenous (Wiyot) aquaculture, Humboldt Bay, CA

Humboldt Bay, California, mirrors many coastal estuaries impacted by historical development and climate change, leading to biodiversity loss. Disintegrating habitats also affect local Indigenous communities, whose deep-rooted histories include stewardship of these biologically and culturally essential places. Understanding human-fisheries dynamics is crucial for biocultural restoration. We present a snapshot of fisheries use at Digawututklh (CA-HUM-23), a Late Holocene ethnographic Wiyot village on the north spit of Wigi (Humboldt Bay), an area experiencing the highest rate of level rise in California that it is exacerbated by the high rate of subsidence where the Juan de Fuca Plate dives under the North American Plate. To expand knowledge of species use, we employ complementary faunal and genetic analyses and test the capabilities of ancient DNA (aDNA) barcoding methods. We employ a broad-spectrum sampling approach to identify previously unidentifiable elements and confirm aDNA identification of fish bone is feasible on a wide range of non-vertebral elements and tiny, fragile fragments. Our findings highlight the potential of this methodology and the need for further sequencing of modern fish bones to refine aDNA species identification. This biodiversity-centered approach provides a more comprehensive picture of historical fisheries in this endangered northern California estuary. Contrary to a salmon-focal economy assumed in prominent developmental models, results reveal complex interactions with multiple fish species, employing diverse capture methods and technologies, such as tidal weirs, nets, and spears. Identified fish species, along with shellfish, crab, waterfowl, and mammals recovered at the site, indicate significant record of human connectivity with eelgrass ( Zostera marina ) meadows. The eelgrass biome of Humboldt Bay —a highly productive habitat that supplies nutrients, shelter, and nursery grounds for diverse species—was a key target for early indigenous aquaculture, practiced by the some of the earliest sedentary plank house villagers in coastal northwest California. The study provides insight into Wiyot sustainable practices, informed by traditional ecological knowledge of food webs and seasonal spawning and migratory patterns. • Documents Indigenous Wiyot interactions with estuarine fish at a 1175 cal BP village in Humboldt Bay, California. • Employs a biodiversity framework, analyzing archaeological fish bone with complementary morphological zooarchaeology and aDNA methods, revealing diverse fishing practices. • Evaluates broad-spectrum sampling and aDNA analysis of non-vertebral fish bone elements, and previously unidentified small and fragmentary “miscellaneous fish.” • Demonstrates ancient eelgrass meadow health and human connection to this vital biome, suggesting sustainable resource use. • Informs contemporary conservation by applying archaeological data to understand past human-environment dynamics.