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Research Shows Snake River Sockeye Broodstock Program
Preserving Population's Genetic Diversity

by Staff
Columbia Basin Bulletin, August 10, 2012

An adult sockeye leaps upstream en route to its natal spawning grounds. A recently published scientific research paper says the ongoing broodstock mixing system, which started with just a handful of fish, has managed quite well to preserve the genetic diversity of a Snake River sockeye salmon population that teetered on the brink of extinction in the late 1980s and early 1990s.

The research article - "Genetic diversity in the Snake River sockeye salmon captive broodstock program as estimated from broodstock records" -- was published online May 9 by the scientific journal, "Conservation Genetics."

Authors are Steven T. Kalinowski of Montana State University, Christine C. Kozfkay of the Idaho Department of Fish and game and Donald M. Van Doornick and Robin S. Waples of National Marine Fisheries Service's Northwest Fisheries Science Center.

The article abstract can be found at:

Analysis of the spawning records of the Redfish Lake sockeye salmon captive broodstock program estimated that "the average inbreeding coefficient among eggs fertilized in 2006, 2007 and 2008 was approximately 0.05," the article says.

"This means that we expect an egg fertilized during these years to have approximately 95 percent of the genetic diversity present in the founders of the breeding program. Given the challenges faced by the early years of the breeding program, this is an unqualified success.

"Predicting the future rate of inbreeding in the population is difficult, but the impact of the initial population bottleneck appears to have been fully experienced, and we expect that inbreeding coefficients in the population will now slowly creep up at a rate proportional to the current effective population size, which appears to be greater than 100," according to the article.

"Individual fitness and population level diversity are two important factors for the persistence of Redfish Lake sockeye salmon, but other factors may ultimately decide the fate of this population. Three potentially serious threats to this population include hatchery selection, existing hydropower development in the Snake and Columbia Rivers, and global climate change.

"The seriousness of these threats to the persistence of Snake River sockeye is highlighted by the fact that the Snake River population almost went extinct in the 1990s and many of the causes for this decline do not seem to have been mitigated," the article says.

"However, the results of this present investigation provide reason for optimism," the article says. "Sockeye salmon in Redfish Lake captive broodstock program appear to have retained approximately 95 percent of the genetic variation of the fish that founded the captive population, and we can hope that this is enough to avoid most of the harmful effects of inbreeding and to provide enough genetic variation for the population to adapt to future challenges."

The Snake River Sockeye Captive Broodstock Program guided by the Idaho Department of Fish and Game began in the spring of 1991, and during the next 7 years, 99 wild-born Oncorhynchus nerka, or sockeye, were captured in central Idaho's Redfish Lake or in Redfish Lake Creek and spawned in captivity.

Project cooperators include NOAA Fisheries, Oregon Department of Fish & Wildlife, Shoshone-Bannock Tribes, and the Bonneville Power Administration.

"These 99 founders included 16 anadromous adults that returned to Redfish Lake from the ocean, 65 juvenile 'outmigrants' that were captured while leaving Redfish Lake on their way to sea, 17 'residual' adult sockeye that lived in the lake, and one fish that was either a residual or an outmigrant," the article says. Residual fish sockeye are those that chose to live their entire life in freshwater rather than swimming to the Pacific to grow to maturity before returning to spawn. Residual fish in some instances do choose to go the ocean.

The sockeye population had sunk to a low ebb with no anadromous spawners returning to the Stanley basin in 1990; a year later, four adults returned and that year Redfish Lake sockeye became the first population of Pacific salmon to be listed as an endangered species under the U.S. Endangered Species Act.

"The population in the wild continued to teeter on the brink of extinction and in 1992, only a single adult returned to Redfish Lake."

The Snake River population is experiencing a bit of a revival in recent years with returns to Idaho high country ranging from 650 to 1,355 from 2008-2011. A large majority of those fish the product of the captive broodstock program.

The researchers used "pedigree analysis to evaluate the effectiveness of the breeding program in retaining genetic variation from 1991 through 2008.

"Results indicate that in 2008, after 5.5 generations of breeding, the average inbreeding coefficient was probably about 0.056," the article says. "We estimated the inbreeding effective population size to be 41 over the entire program and 115 for the most recent generation. This amount of inbreeding is substantially less than has occurred in many high-profile captive breeding programs."

A genetic study highlighted in a "Transactions of the American Fisheries Society" article published a little over a year ago concludes that the remnants of a sockeye population found in the early 1990s were likely native and not the product of introduced kokanee.

Kokanee are fish of the sockeye species confined to freshwater.

"A detailed examination of the O. nerka from lakes in the Sawtooth Valley of Idaho was undertaken to help guide recovery planning for the endangered Redfish Lake population and to help resolve the relationships between the resident and anadromous forms," according to the paper published in June 2011, "Population Genetic Structure and Life History Variability in Oncorhynchus nerka from the Snake River Basin."

Authors were Waples, Paul B. Aeberesold and Gary A. Winansa of the Northwest Fishery Science Center.

"In Redfish Lake, adult sockeye salmon that returned in 1991-1993 were genetically distinct from local kokanee but similar to a small group of 'residual' sockeye salmon discovered in the lake in 1992," the population paper says. "This result is consistent with the hypothesis that the original sockeye salmon population was not extirpated by Sunbeam Dam early in this century."

Construction of the dam on the Salmon River blocked fish passage for more than two decades before being destroyed.

"Populations of O. nerka that appear to be native to the Snake River were also found in Alturas Lake, Stanley Lake, and Warm Lake, although the latter two lakes also showed evidence of nonnative gene pools. Kokanee sampled from Pettit Lake are clearly the result of an introduction of late-spawning kokanee from northern Idaho, and we found evidence of two O. nerka gene pools in Wallowa Lake, both traceable to introductions of nonnative kokanee," the article says.

Research Shows Snake River Sockeye Broodstock Program Preserving Population's Genetic Diversity
Columbia Basin Bulletin, August 10, 2012

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