Oncorhynchus tshawytscha

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General Information
Common Name: 
Central Valley fall Chinook salmon

Conservation Status in California: Class 1, Endangered (Moyle et al. 2011).
The Central Valley fall Chinook salmon population is dominated by fish of hatchery origin. Fish of wild ancestry are rare or extirpated.

Life History: 

Life History: Fall Chinook are reasonably well studied because they are the most abundant run in the Central Valley, persisting in large numbers in rivers below dams, and are the principal run raised in hatcheries (Moyle 2002, Williams 2006). They have the classic “ocean type” life history in that adults enter rivers as mature individuals, migrate to spawning grounds and usually spawn in 1-2 months after entry. Peak spawning time is typically in October-November but can continue through December. Juveniles mostly emerge in December through March and rear in natal streams for 1-7 months, usually moving downstream into the main rivers within a few weeks after emerging. They enter the San Francisco Estuary as both fry and smolts. Despite long-term monitoring, causes of apparent high mortality rates of fish as they pass through the estuary are poorly understood. Two general observations suggest that rearing conditions in the estuary are often poor: survival rates seem to be higher in the rivers than in the estuary and highest survival occurs during wet years, when passage through the estuary is likely to be most rapid (Brandes and McClain 2001; Baker and Mohrhardt 2001). Hatchery fry are mostly trucked to be planted below the Delta, on the assumption that their survival is poor when they pass through it naturally. Flooding in wet years also increases rearing habitat in the Delta and Yolo Bypass, which may have a positive effect.
From the estuary, juvenile salmon move through the Golden Gate into the Gulf of the Farallons, which is typically an extremely food-rich region because of upwelling associated with the California current. Immature fish spend 2-5 years at sea where they feed on fish and shrimp, before returning as adults. Most of the fish remain off the California coast between Point Sur and Point Arena during this period, but many move into the coastal waters of Oregon as well. Their movements in the ocean during the rearing period are poorly understood but inshore, offshore and along shore movements are likely in response to changing temperatures and upwelling strength.
Naturally, there are many exceptions to this general life cycle, including fry that spend as much as one year in fresh water. Overall, this life history strategy reflects adaptations that historically allowed these fish to use the productive lower reaches of Central Valley rivers for spawning and rearing, with the fry moving out as water temperatures become increasingly warm in spring and summer. It is likely that many of the fry once reared for several months (or more) in the somewhat cooler Delta and lower estuary after leaving the river. The present-day lower Sacramento River generally has temperatures suitable for rearing all year around in its upstream reaches, thanks to cool-water releases from reservoirs, although levees and diversions have reduced rearing habitat, especially in dry years.
The attributes of fall Chinook salmon that have made them so well adapted to low elevation rivers have also made them ideal for use in hatcheries, because they can be spawned as they arrive and because the fry only have to be reared for a relatively short time before being released. Other aspects of their life history are similar to other Chinook salmon which are covered in more detail in Moyle (2002), Williams (2006), and Moyle et al. (2008).

Habitat Requirements: 

Habitat Requirements: The general habitat requirements are similar to that of other Chinook salmon that minimize their time in fresh water (Healey 1991; Moyle 2002). For a more specific summary of Central Valley Chinook salmon requirements see Stillwater Sciences (2006).
Temperature is an important factor in Chinook salmon survival and growth and tolerances vary with life history stage (Table 1). Likewise, they are sensitive to dissolved oxygen levels, water clarity and other factors that indicate high water quality.
Spawning Chinook use the largest substrate of any California salmonid for spawning, a mixture of small cobble and large gravel. Such coarse material allows sufficient water flow through the substrate to provide oxygen for developing embryos and remove their metabolites. As a result, the selection of redd sites is often a function of gravel permeability and subsurface water flow. Typically, redds are observed at depths from a few centimeters to several meters and at water velocities of 15-190 cm/sec. Preferred spawning habitat seems to be at depths of 30-100 cm and at water velocities of 40 -60 cm/sec. Redds are typically constructed over 2-15 m2, where the loosened gravels permit steady access of oxygen-containing water (Healey 1991). However, because females dig the redds, redd size is a function of female size as well as looseness of the substrate. For maximum embryo survival, water temperatures must be between 5º and 13º C and oxygen levels must be close to saturation. With optimal conditions, embryos hatch after 40-60 days and remain in the gravel as alevins for another 4-6 weeks, usually until the yolk sac is fully absorbed.
Once alevins emerge with their yolk-sac absorbed, they become fry, which tend to aggregate along stream edges, seeking cover in bushes, swirling water, and dark backgrounds. As they grow larger and become increasingly vulnerable to avian predators, especially herons and kingfishers, they move into deeper (>50 cm) water. Larger juveniles may wind up in the tails of pools or other moderately fast-flowing habitats where food is abundant and there is some protection from predators. As they move downstream, they use more open waters at night, while seeking protected pools during the day. Pools that are cooler than the main river, from upwelling or tributary inflow, may be sought out by the migrating juveniles as daytime refuges.
The habitat use of Central Valley fall Chinook salmon that may differ most from Chinook salmon elsewhere in California is the use of off-channel habitats by fry, including floodplains, where they grow faster because of warmer temperatures and abundant food (Sommer et al. 2001; Limm and Marchetti 2006; Jeffres et al. 2008). Historically, this habitat was extremely abundant along the valley reaches of the rivers and was probably a major reason for the large numbers of salmon produced by Central Valley rivers. Off-channel habitat (e.g., tidal marshes) may also have been important at one time in the San Francisco Estuary, but it is largely unavailable at the present time. In the ocean, habitats for the first few months are poorly documented, but it is assumed that the fish stay in coastal waters where the cold California Current creates rich food supplies, especially small shrimp, by upwelling. During the day, they avoid surface waters. Subadult Chinook salmon swim about in pursuit of anchovies, herring, and other small fish, typically at depths of 20-40 m, moving offshore and into deeper waters in response to temperature, food availability, and predators, such as orcas and sea lions.


Distribution: Central Valley fall run Chinook historically spawned in all major rivers of the Central Valley, migrating as far as the Kings River to the south and the Upper Sacramento, McCloud, and Pit Rivers to the north. There were also small, presumably intermittent runs, in smaller streams such as Putah and Cache creeks. Today they spawn upstream as far as the first impassible dam (e.g., Keswick Dam on the Sacramento River) although on the San Joaquin side of the Central Valley they are only allowed as high up as the Merced River because Friant Dam has cut off all natural flows to the lower San Joaquin River. Today, further upstream movement is blocked by the CDFG-operated weir at Hills Ferry. Overall, about 70% of Chinook salmon spawning habitat has been cut off by dams (less for fall run by itself), although cold-water releases from some dams may allow some spawning where it did not formally exist, such as in lower Putah Creek (Yoshiyama et al. 1998).

Abundance Trends: 

Trends in Abundance: The historic abundance of fall Chinook is hard to ascertain because populations were severely impacted before good records were kept. For instance, massive hydraulic mining operations during the Gold Rush buried major spawning and rearing areas under mining debris and Chinook were heavily fished during the 19th century. The best estimates of historic numbers suggest that fall run Chinook were likely the most abundant of the four Central Valley runs or tied for that honor with spring Chinook salmon, at about a million spawners per year, plus or minus a couple of hundred thousand fish (Yoshiyama et al. 1998). In the 1960s-90s, average production (the total of in-river escapement plus catch in the fisheries) was estimated to be about 374,000 fish per year (Figure 1), although the number of spawners usually varied somewhere between 200,000 and 300,000 fish, occasionally dropping to 100,000 or so. In 1992-2005, production averaged about 450,000 fish per year, although it dropped to less than 200,000 fish in 2006 and to about 90,000 spawners in 2007, despite virtual cessation of fisheries. These numbers include both fish of hatchery origin and those which spawn naturally, with hatchery fish comprising up to 90% of the total, depending on river, year, and who was counting (Barnett-Johnson et al. 2007). Escapements vary tremendously among rivers in the Central Valley as well, with perhaps the greatest variation in the Stanislaus, Tuolumne, and Merced Rivers, tributaries to the lower San Joaquin River (Figure 2). The exact cause of the variation in abundance in these three rivers is not well understood but largest returns follow years with high outflows and high smolt survival. High discharge may be of special value during smolt outmigration through a dewatered southern delta.
Following overexploitation by early fisheries and the alteration of California rivers during the Gold Rush, fall Chinook salmon abundance had declined to about 10% of original numbers by the 1940s (Yoshiyama et al. 1998?). The construction of large dams throughout the Central Valley in the 1940s-60 further reduced wild chinook numbers but to what extent is uncertain because large hatcheries began mass production of hatchery fish at this time. The hatcheries were built for mitigation, more or less as an afterthought, and to mollify commercial fishermen concerned with dam construction causing collapse of the salmon runs. For decades hatcheries maintained salmon numbers at approximately 375,000 fish (escapement + catch) returning to the Central Valley each year. Because only a small proportion of hatchery fish were marked, visual segregation of wild from hatchery fish was impossible so the proportion of hatchery to “wild” fish spawning in streams has always been uncertain. Also, the impact of hatchery fish on wild salmon populations is poorly documented. Recent evidence demonstrates that Central Valley fall Chinook salmon populations are genetically uniform, suggesting that straying hatchery fish have been hybridizing with “wild” fish for generations (Lindley et al. 2009), blurring the distinction between wild and hatchery fish. Today all CV fall Chinook are primarily of hatchery origin. If we define wild fish in the strictest sense, as fish with no hatchery ancestry, then the CV fall run Chinook salmon may already be extinct.
Recent data estimates that 90% of adults in the ocean fishery were hatchery raised (Barnett-Johnson et al. 2007). Consequently, natural reproduction (spawning in the wild without consideration of origin of the spawners) produced only 10,000 CV fall run Chinook in 2008 or about 1% of historic numbers. However, the number of truly locally adapted wild fish is likely lower than this estimate because fish produced naturally carry hatchery genes from past introgression for generations (Araki et al. 2009). Despite court rulings that ban hatchery fish from being considered under the Endangered Species Act (NMFS 2005) there has been little effort to assess the status and abundance of “wild” fall run Chinook in California. The difficulty in segregating hatchery salmon from “wild” salmon has contributed to this situation, but even if we ignore genetics and count all naturally reproduced fish as “wild”, abundances are so low as to warrant federal listing as an endangered species.


Description: Members of the Central Valley fall Chinook salmon Evolutionary Significant Unit (ESU), like other Chinook salmon, have numerous small black spots on the back, dorsal fin, and both lobes of the tail in both sexes. This spotting on the caudal fin and the black coloration of their lower jaw make them distinguishable from other sympatric salmonid species. They have 10-14 major dorsal fin rays, 14-19 anal fin rays, 14-19 pectoral fins rays, and 10-11 pelvic fin rays. There are 130-165 scales along the lateral line. Branchiostegal rays number 13-19. They possess more than 100 pyloric caeca and have rough and widely spaced gill rakers, 6-10 on the lower half of the first gill arch.
Spawning Chinook adults are the largest Pacific salmonid, often 75-80 cm SL, but lengths may exceed 140 cm. California Chinook are usually smaller, typically 45-60 cm SL. The average weight is 9-10 kilograms, although the largest Chinook taken in California was 38.6 kg. Spawning adults are olive brown to dark maroon without streaking or blotches on the side. Males are often darker than females and develop a hooked jaw and slightly humped back during spawning. Juvenile Chinook have 6-12 parr marks, which often extend below the lateral line, and the marks are typically equal to or wider than the spaces between them. Parr can also be distinguished from other salmon species by the adipose fin, which is pigmented on the upper edge, but clear at the base and center. Some parr begin to show spots on the dorsal fin, but most fins are clear. There are no morphological features to separate this Evolutionary Significant Unit (ESU) from other Chinook salmon ESUs, so separation is based on genetic data and life history characteristics.