Enumerating Predation on Chinook Salmon, Delta Smelt, and Other San Francisco Estuary Fishes Using Genetics

Abstract

The establishment of non-native predator fish is a worldwide phenomenon often having adverse effects on native species. Trophic interactions are complex, and uncertainty is a common theme in discussions of non-native predator management. Several fishes of the San Francisco Estuary have experienced significant declines in recent decades due to multiple factors, including habitat alteration and predation. The role of predation as a direct cause of mortality remains an open question, as does whether habitat conditions play a role in promoting predation on species of concern. Recent studies using visual identification of prey have found little to no evidence of predation on ESA-listed species such as Delta Smelt Hypomesus transpacificus and juvenile Chinook Salmon Oncorhynchus tshawytscha. To increase the likelihood of detecting predation, this study employed a genetic approach. We combined this technique with habitat and water quality data to investigate the role habitat may be playing on incidence of predation. This study focused on detection of predation on Chinook Salmon and Delta Smelt, as well as 6 other native fishes, and 6 non-native fishes by Striped Bass Morone saxatilis, and other piscivores. Unlike previous studies in the region, the proportion of predators with no prey detected in their gut contents was high (47-81%). The study detected Delta Smelt in 1.3% of Striped Bassconsiderably higher than other contemporary predation studies in the Delta. In the month of April 2014, 6.6% of Striped Bass were positive for Chinook Salmon-substantially higher than recent visual diet studies in the Delta. Interestingly, native species comprised a relatively high proportion of Striped Bass prey (60%). Water temperature and conductivity were identified as significant predictors of Chinook Salmon presence in Striped Bass gut contents. This research

Diets of Native and Non-Native Piscivores in the Stanislaus River, California, Under Contrasting Hydrologic Conditions

“…Non-native fish have high relative abundance in the lower San Joaquin River and south Delta (Brown and Michniuk 2007), resulting in a prey base dominated by nonnative fish. In the north Delta, which remains a stronghold for native fish species (Moyle et al 2012), Brandl et al (2021) found that FO of native fish prey was 51% higher than what Michel et al (2018) observed. On the Stanislaus River, native species have higher relative abundance than in the lower San Joaquin River, especially during the juvenile Chinook Salmon migration season when estimates of abundance can range from 127,000 to over 2 million (Pilger et al 2019).…”

“…Nonetheless, we were able to document important predator-prey interactions on the Stanislaus River over 3 years. Although we successfully identified most of the recovered diet items, some rarer, small-bodied (and highly digestible) fishes could have been missed (Brandl et al 2021). In this study we visually identified and genetically validated discrete diet items, which likely yielded precise estimates of consumption for larger prey fishes (i.e., juvenile Chinook Salmon and lamprey), but estimates for smaller (larval) fishes that were more digestible should be considered conservative.…”

“…The high FO of Pacific Lamprey in the diet samples suggested that they are at least seasonally abundant in the Stanislaus River and acted as an important prey resource for piscivores. Other diet studies from the Central Valley have observed predation on lamprey and have ranged from low frequencies (e.g., 0.0 to 0.10 for a variety of predators; FISHBIO 2013; Sabal et al 2016;Weinersmith et al 2019;Brandl et al 2021) to the highest frequency previously reported in Stompe et al (2020) We are not aware of abundance or production estimates for lamprey elsewhere in the Central Valley; however, some information is available on their migration patterns (Goodman et al 2015;Parker 2022) and occupancy in the estuary (Goertler et al 2020). Throughout the year, Lamprey were captured by RSTs in the upper Sacramento River, though the peak period of emigration or downstream movement appeared to be from October to May and associated with rainfall events (Goodman et al 2015).…”

“…In this study we visually identified and genetically validated discrete diet items, which likely yielded precise estimates of consumption for larger prey fishes (i.e., juvenile Chinook Salmon and lamprey), but estimates for smaller (larval) fishes that were more digestible should be considered conservative. In other studies, predators are sacrificed to facilitate collection of complete gastric contents (e.g., Brandl et al 2021;Michel et al 2018). We opted to conduct non-lethal collections because individuals were also being used in a concurrent markrecapture study.…”

“…Later, the decline https://doi.org/10.15447/sfews.2023v21iss4art1 and subsequent listing of some native species led to diet studies identifying predation as a threat to those species (Sabal et al 2016;Weinersmith et al 2019). Documenting predation on increasingly rare, listed species has spurred innovative genetic identification methodologies (e.g., Baerwald et al 2012;Brandl et al 2021). These methods can be used to efficiently characterize the full extent of diets from multiple predators in a fish community.…”