Homogenization of Fall‐Run Chinook Salmon Gene Pools in the Central Valley of California, USA

Abstract

We assessed the population genetic structure and temporal stability of genetic diversity from 1999 to 2001 in collections of fall-run Chinook salmon Oncorhynchus tshawytscha in California's Central Valley. Tests for genotypic differentiation at seven microsatellite loci revealed few significant pairwise comparisons between samples from five hatchery populations and eight naturally spawning populations throughout the Central Valley that were separated by 50-350 km. All collections were genetically homogeneous and failed to cluster with their nearest geographic neighbors. Likewise, evaluation of temporal change in genetic diversity revealed few changes over the 3 years of the study. Our results suggest that fall-run Chinook salmon throughout the Central Valley comprise a genetically homogeneous population that has lower among-population genetic diversity than fall-run Chinook salmon populations examined elsewhere over similar geographic scales. The lack of genetic distinction and the lack of temporal differences in allele frequencies between hatchery and naturally spawning fish indicate that considerable gene flow occurs between fall-run Chinook salmon throughout the Central Valley. Due to the prevalence of off-site release of hatchery-reared juveniles and the history of interbasin hatchery transfers and stocking within the Central Valley, homogenization of Central Valley fall-run populations is most likely the result of hatchery practices for the past 140 years.

Isotopes and genes reveal freshwater origins of Chinook salmon Oncorhynchus tshawytscha aggregations in California’s coastal ocean

“…Therefore, identifying the relative contributions of populations from these rivers to the various salmon runs is important for recovery efforts. Otolith microstructure and 87 Sr/ 86 Sr data allowed for this finer-scale identification of natal origin in CV fall-run salmon, which cannot be discriminated with GSI, due to hatchery practices (Williamson & May 2005). Spatial structure was found in 2 (MOH and NIH) out of 8 natal populations.…”

“…87 Sr/ 86 Sr ratios in otoliths vary among rivers across the geographic range of the CV fall-run due to differences in watershed geology and can be used to assign adult fish to individual hatchery or river of origin, which is unachievable using genetic stock identification (Williamson & May 2005, Barnett-Johnson et al 2008, Hobson et al 2010Fig. 1b).…”

Weakening portfolio effect strength in a hatchery-supplemented Chinook salmon population complex

“…To mitigate for these effects, five hatcheries were established to propagate fall-run Chinook salmon, which naturally breed in low-elevation reaches of large rivers (Moyle 2002). Recent work suggests that the fall-run populations breeding in the different river systems are now genetically indistinguishable (e.g., Williamson and May 2005), likely due to a long history of movement of individuals (gametes) among hatcheries as well as considerable and ongoing straying of hatchery-produced fish as adults (CDFG-NOAA 2001). Chinook salmon mature at a range of ages, with CVC most often returning to spawn at age-3, with lesser contributions of age-2 and age-4 spawners and negligible contributions from older age classes .…”

“…In stark contrast with Bristol Bay's diverse and productive salmon fishery and other high latitude stocks with limited anthropogenic impact to freshwater habitat is California's Central Valley fall-run Chinook (CVC) salmon (Oncorhynchus tshawytscha) stock complex (Griffiths et al 2014). The Central Valley freshwater habitat is highly regulated and modified, and recent work suggests that the fall-run populations breeding in the different river systems are now genetically indistinguishable (Williamson and May 2005), in contrast with other studied salmon complexes that exhibit geographic structuring (e.g., Habicht et al 2007), and that hatchery-produced fish contribute the majority of total production (Barnett- Johnson et al 2007; Kormos et al 2012;Mohr and Satterthwaite 2013;Palmer-Zwahlen and Kormos 2013). …”

An Evaluation of Otolith Thermal Marking at the Feather River Hatchery, California

“…Though genetic stock identification techniques based on allele frequencies would not be sufficient to accurately identify the run type and origin of individuals at the FRH (Banks et al 2000;Williamson and May 2005;Garza and Pearse 2008), recent work with single nucleotide polymorphisms (SNPs) has demonstrated the possibility of using a genetics-based method to determine the origin and run type of FRH-produced fish (Clemento et al 2011). Parentage-based tagging using SNPs is a method that requires not only genotyping of the parent broodstock, but also the genotyping and parentage analysis of returning offspring (Anderson and Garza 2006).…”