Human use of small forage fish: Improved ancient DNA species identification techniques reveal long term record of sustainable mass harvesting of smelt fishery in the northeast Pacific Rim

The bulk storage and mass capture of small forage fish has played a primary role in the cultural traditions and subsistence practices of many ancient and modern indigenous communities throughout the world. Archaeologists are improving their recognition of human interaction with these fisheries through the application of fine-mesh screening techniques and ichthyofaunal analysis of fish bone. Because of the differing life histories of many of these fish, determining their species from archaeological contexts can improve our resolution of past harvesting and consumption patterns. This has remained a challenge for many categories of fish, such as salmon and smelt. Here, we present an improved genetic species identification process that utilizes ancient DNA amplification techniques involving a reagent-rich PCR protocol (i.e., “Rescue PCR”) and a PCR Enhancer Cocktail P (i.e., PEC-P) to identify smelt and other forage fish bone from five archaeological sites located along the northern California (United States) Pacific coast dating to the Late Period (after 1300 cal BP). Through the application of these novel techniques, our species identification success rate increased to 71.2% overall, with some sites having a remarkable 100% success rate. We identified the species of 104 of 146 fish vertebrae, and determined that inhabitants at these sites harvested primarily surf smelt with potentially less emphasis on night smelt. Observations of herring, perch, sculpin and rainbow trout/steelhead were also made. Along with these small surf fish, we found evidence of larger fish such as shark and Pacific hake (common predatory fish in the area). The study demonstrates a significant breakthrough in ancient DNA identification techniques that resulted in information that speak to the long term continuity of use of mass harvested forage fish by indigenous peoples. The results of this project help establish a better understanding of subsistence and cultural traditions of northern California indigenous communities, with the potential to provide a more global understanding of fishing technologies, sustainability, and mass harvesting of small fishes.