Biochemical Identification and Assessment of Population Subdivision in Morphologically Similar Native and Invading Smelt Species (Hypomesus) in the Sacramento–San Joaquin Estuary, California

Abstract
The invasion of the Sacramento–San Joaquin estuary by the wakasagi Hypomesus nipponensis poses threats of competition and hybridization with the endemic delta smelt Hypomesus transpacificus, a species listed as threatened by federal and state agencies. Small individuals of these species are difficult to distinguish morphologically, but correct identification is extremely important to avoid mistaking delta smelt for wakasagi under the limited take provisions of the federal endangered species act. Allozyme markers were used to identify 280 individual fish from several sites across the range of H. transpacificus. We used these results to document the current level of invasion by H. nipponensis, quantify levels of misidentification based on morphological characters, identify hybrid individuals, and estimate levels of gene flow in H. transpacificus. Wakasagi have spread throughout the Sacramento–San Joaquin estuary, and further monitoring will be necessary to determine the long-term consequences of th...