Reducing Uncertainty in Estimating Salmon Mortality at South Delta Fish Salvage Facilities

Tracy, CA (2023) – Water exports from the South San Joaquin Delta have been causing the incidental take of juvenile salmonids, potentially jeopardizing ESA-listed species. The impact of water operations is closely monitored through Federal and State permits, with associated rules for reducing the amount of water diverted from the Delta into canals (export flow) being based on the capture (daily loss density) of “older” juveniles, with “older” serving as a proxy for ESA-listed winter-run Chinook salmon.

Yet, determining which captured individuals are “older” has been challenging due to the ambiguity of the “Delta Model”, a size based model, because fish length does not align with protected status. The failure to accurately identify legally-protected fish creates considerable uncertainty in the estimation of loss density for winter run, a protected stock.

Cramer Fish Sciences – Genidaqs is employing GTSeq high throughput sequencing of single nucleotide polymorphisms (SNPs) to address this challenge. The study focuses on genetic classification of Chinook Salmon captured from the South Delta diversions (i.e., SWP and CVP) fish protection facilities where captured Chinook are counted, subsequently determining the population of origin for each salvaged juvenile. Thus the actual number and distribution of ESA-listed (genetic) winter run is quantified for the Chinook categorized ambiguously by Delta Model length-at-date criteria.

By directly targeting and reducing one source of uncertainty in the estimation of loss for Endangered winter-run Chinook Salmon at South Delta fish protection facilities (i.e., salvage), this study could help mitigate the potential jeopardy of ESA-listed species. Cramer Fish Sciences – Genidaqs also conducts similar activities for other monitoring programs (e.g., Sacramento Trawl, Chipps Island Trawl, Red Bluff Diversion Dam)

Data Repositories

Central Valley Project 2011-2021, edi.1049.2 ( Link )

State Water Project 2011-2021, edi.1056.1 ( Link )