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Holding on to Individuality

The two large salmon-bearing watersheds in California, the Klamath-Trinity and the Sacramento-San Joaquin basins, drive the production of the recreational, commercial, and tribal harvest of Chinook salmon in the state. Differences in the timing of freshwater return and spawning create a temporal separation between the salmon runs in both systems: the Central Valley has four runs of Chinook salmon (spring-, fall-, late fall- and winter-run), while the Klamath-Trinity system is home to only spring- and fall-run stocks. High homing fidelity of Chinook salmon limits interbreeding among populations separated by location and run-timing, which results in unique genetic signatures and, presumably, localized adaptations of different salmon runs.  


However, in these major watersheds and elsewhere, large-scale infrastructure developments and fisheries management practices have presented great obstacles to the maintenance of distinct genetic structure, or patterns of genetic diversity, among Chinook salmon populations. For example, the construction of large dams -- such as Lewiston Dam on the Trinity River -- prevents the historical geographic separation of temporally distinct runs within a river. Spring-run Chinook salmon, which used to ascend and reproduce in cool headwater reaches, are now forced to share downstream spawning habitat with their fall-run counterparts, resulting in hybridization between the two stocks (Kinziger et al. 2008). Further, large-scale artificial propagation of Chinook salmon and associated stocking practices can contribute to the erosion of distinct population genetic structure, even though these practices are often intended to mitigate the loss of natural production resulting from dam construction. The reasons for this include the high tendency for hatchery-reared Chinook salmon to stray, particularly individuals that are released at locations far from their natal hatchery (CDFG & NMFS 2001). Furthermore, transfers of fertilized eggs among watersheds were exceedingly common in the past, which eroded genetic differences among salmon populations. In California's Central Valley, these practices have resulted in the loss of genetic structure, effectively homogenizing fall-run Chinook salmon populations and raising concerns regarding the fish's ability to retain the adaptive potential required to persist under ever- changing environmental conditions (Williamson and May 2005).


In contrast, fall-run stocks from different tributaries in the Klamath-Trinity system continue to exhibit significant genetic structuring, despite being subjected to large-scale hatchery influences, finds a recent paper in the journal Transactions of the American Fisheries Society (Kinziger et al. 2013). The study authors, which include FISHBIO biologist Michael Hellmair, evaluated genetic variation in all major populations of Chinook salmon in the basin and were able to resolve three distinct genetic lineages. The first is a lower basin group (downstream of the Klamath-Trinity confluence), which is more closely related to coastal Chinook stocks from northern California and southern Oregon than to other Chinook populations in the Klamath-Trinity watershed (Gall et al. 1992). The second is a Klamath group, which encompasses the Iron Gate Hatchery population and fish from tributaries to the mainstem Klamath River upstream of and including the Scott River. The third is a Trinity group, which includes spring- and fall-run populations from the Salmon and Trinity rivers and those stocks propagated in the Trinity River hatchery.


Within the Klamath-Trinity groups, the largest level of genetic differentiation is observed between populations from the Iron Gate and Trinity River hatcheries, located at the final points of anadromous migration on the Klamath and Trinity rivers, respectively. Though the results also indicate genetic mixing between hatchery stocks and wild populations in the Klamath-Trinity basin, most of the straying and genetic mixing appears to happen among geographically adjacent populations in a stepping-stone fashion. This suggests that some semblance of natural population structuring is retained in the Klamath-Trinity system, wherein geography maintains the majority of Chinook salmon genetic structuring within the basin, despite the influence of hatchery practices.

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No fish left behind 

These two fishery biologists are checking every last hiding spot for fishes that are being temporarily deprived of water. We recently monitored conditions in a small section of Mormon Slough and relocated fish that become stranded when a small section of the river was temporarily blocked by water-filled dams and the channel was pumped dry. Downstream flow was diverted around the project site through neighboring stream channels. FISHBIO has conducted a number of fish rescues over the years (see Expect the unexpected, A muddy situation), and this particular effort is part of a fish passage improvement project on the Calaveras River.


The fish passage problem is due to a low-flow road crossing that consists of three 3-foot diameter corrugated metal culverts in a concrete road prism. The road crossings are a substantial barrier to upstream migration of adult salmonids because water velocities often exceed those that salmon require for effective passage through the culverts, over the downstream apron, and over the riprap. The old crossing is being removed and replaced by three large, bottomless box culverts with a concrete overlay. Old, jagged concrete riprap will be removed from the channel bottom and replaced with rounded cobble and gravel. The new road crossing and reshaped channel bottom should provide easier passage for migrating salmonids.


Many anadromous streams in the western United States have been highly altered from their historic conditions. During the 19th and 20th centuries, thousands of barriers to fish passage were erected as roads, bridges, and dams were built... Read more >
IN THE NEWS: Recent stories you might have missed...

Stinky Butte Creek means good year for spring-run fish

Chico ER 

The remains of a very good chinook salmon spring run can be viewed, and in many cases smelled, along Butte Creek this week. The final numbers won't be known for a while, and the fish are still spawning, but Fish and Wildlife biologist Clint Garman said the threatened species had a good year. This week a crew has been walking creekside and wielding machetes. After salmon spawn, they die... Read more > 

Parasite Found in Local Salmon
Two Rivers Tribune
Chinook salmon caught in the Klamath River were found infested with a white and egg-shaped parasite named Henneguya embedded in their muscle tissues. The parasite was first found in Sweden and Canada. It can be transferred from fish to fish. While at sea, the fish are subjected to sea lice that attach themselves. The sea lice eat the skin and blood of the fish, breaking their first layer of outer protection, which allows the parasite to enter the body... Read more >
Local tribes, environmental groups discuss dam removal

The fight over water in the Klamath Basin will be discussed by a panel of tribal representatives and environmental advocates tonight as a part of Humboldt State University's Biodiversity Conference. "I would argue that the Klamath River Dam is one of the most important issues on the North Coast," Karuk Tribe Klamath River coordinator Craig Tucker said. Tucker, along with speakers from the Yurok, Hoopa Valley and Klamath tribes, will answer questions on environmental,.. Read more > 

Whisky feed for Scottish salmon

World Fishing & Aquaculture

Over 500 million litres of whisky are produced in the UK each year and for every litre, up to 15 litres of co-products can be generated. Chemical engineers from Heriot-Watt University in Scotland are looking to convert some of the co-products into fish feed, which they say could provide a sustainable and economic supply of feedstock for the growing Scottish fish farming industry... Read more >

Scientists warn of mass extinctions in world's oceans


A team of marine scientists issued a dire warning Oct. 3 on the state of the world's oceans. They say that mass extinctions may already be inevitable. A report issued by the International Programme on the State of the Ocean and the International Union for Conservation of Nature states that the world's oceans are experiencing decreasing oxygen levels, warming and acidification as a result of several stressors, including climate change, pollution and overfishing. Read more >