Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) north of the San Francisco Estuary

Abstract

Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (the SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the estuary at the southern edge of their distribution. However, populations also exist in other estuaries along the coast, which are far less described despite their potential importance in a meta-population. We surveyed Longfin Smelt populations along the northern California coast for larval recruitment. We conducted surveys in 2019 and 2020 to (1) identify estuaries north of the SFE where spawning occurs, and (2) evaluate how habitat features (e.g., salinity, temperature, dissolved oxygen, turbidity) influenced Longfin Smelt larvae abundance. We detected larvae in four of 16 estuaries we surveyed, and all were large estuaries north of Cape Mendocino. No larvae were detected in eight coastal estuaries in closer proximity to the SFE. Larvae catch probability increased with turbidity and decreased with salinity with no significant influence of temperature and dissolved oxygen. In the wet winter of 2019, we observed lower densities of larvae in Humboldt Bay and the Eel River, and detected no Longfin Smelt in the Klamath and Mad Rivers; in the dry winter of 2020, we detected larvae in two additional estuaries. Possibly elevated freshwater outflow in 2019 increased transport rates to the sea, resulting in the observed low larval recruitment. Our results suggest that, while populations of Longfin Smelt exist in large estuaries north of Cape Mendocino, coastal estuaries in proximity to the SFE were either under-sampled or are not permanently inhabited by Longfin Smelt. This suggests that the threatened estuary Longfin Smelt population may lack the resiliency afforded by meta-populations and advocates for increased monitoring over a range of hydrologic conditions and improving detection probabilities for future assessments of gene flow between populations.