Diversity and population structure of Pacific herring (Clupea pallasi) along the Northwest coast: an interdisciplinary investigation using high-throughput sequencing and ancient DNA

Abstract

Forage fish are key trophic links in coastal ecosystems, transferring energy from lower to higher trophic levels. In the Pacific Northwest, herring are one of the most abundant forage fish species and are prey for a wide variety or organisms. Additionally, human inhabitants of the region have used herring as a food resource for millennia, and archaeological research has demonstrated that herring bones are among the most abundant fish remains unearthed from ancient village sites. Given the importance of herring to the coastal ecosystem and human livelihoods, there is considerable interest in sustainably managing the fisheries which target this species. However, management is complicated by limited knowledge of herring population structure and a lack of long-term temporal data on population diversity. In this dissertation, I (i) develop a laboratory protocol to remove intraspecific contamination from tissues that is compatible with restriction site-associated sequencing, (ii) investigate the mechanisms driving genetic differentiation between herring populations, using genomic data collected from wild spawning aggregations, and (iii) quantify the relative contributions of genetically distinct herring populations to food supplies over the last millennium, using ancient DNA extracted from herring bones.