Genetic diversity in the Snake River sockeye salmon captive broodstock program as estimated from broodstock records

Abstract

Snake River sockeye salmon spawning in Redfish Lake, Idaho are one of the most endangered taxa of Pacific salmon. The wild population nearly went extinct in the 1990s, and all surviving fish were incorporated into a captive broodstock program at that time. We used pedigree analysis to evaluate the effectiveness of the breeding program in retaining genetic variation from 1991 through 2008. Broodstock records document which males were crossed with which females, but fish from multiple crosses were frequently raised in the same tank so the exact pedigree of the population is unknown. Therefore, a simulation-based approach was used to estimate how much genetic diversity was retained by this breeding program. Results indicate that in 2008, after 5.5 generations of breeding, the average inbreeding coefficient was probably about 0.056. 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. Our results depend on several assumptions regarding the relatedness of fish in the breeding program, but simulations suggest our main results are relatively insensitive to these assumptions.

Genomic signatures among Oncorhynchus nerka ecotypes to inform conservation and management of endangered Sockeye Salmon

“…As the Redfish Lake population likely experienced a population bottleneck in the early 1990s, this may have increased levels of divergence of this population relative to others due to founder effects, although current estimates of effective population size indicate that the population has increased in size due to the captive broodstock program (this study and Kalinowski et al. ()). Introgression with non‐native, stocked Kokanee, known to be introduced from unknown sources (Bowler, ), could also lead to increased divergence among populations, but Waples et al.…”

“…The presence of a residual life history in Redfish Lake may have been one means protecting the Redfish Lake population from going extinct during the time Sunbeam Dam (1910‐1934), a long‐time barrier to upstream migration, was in operation (Waples et al., ). The founders for the captive broodstock program for Redfish Lake Sockeye Salmon were collected in the years 1991–1998 and originated from a variety of life‐stages, including outmigrating smolts that were likely produced from both residual O. nerka , residual adult O. nerka , and returning anadromous Sockeye Salmon (Kalinowski et al., ; National Marine Fisheries Service ). Propagation of anadromous Sockeye Salmon in Redfish Lake has continued through the captive broodstock program, and future recovery strategies include restoring self‐sustaining, anadromous runs in Pettit and Alturas Lakes.…”

Search for the Smoking Gun: Identifying and Addressing the Causes of Postrelease Morbidity and Mortality of Hatchery‐Reared Snake River Sockeye Salmon Smolts

“…After securing the genetic legacy of Snake River Sockeye Salmon (Kalinowski et al. ) and increasing the size of the captive broodstock program (Kline and Flagg ), the program shifted toward rebuilding the anadromous life history component of the population. Rearing in captivity circumvents the high mortality rates observed in the natural environment and can quickly result in broodstock replacement and amplification for highly fecund salmonid species (Flagg et al.…”

Maintenance of Genetic Diversity in Natural Spawning of Captively-Reared Endangered Sockeye Salmon, Oncorhynchus nerka

“…Success of natural population recovery will depend on numerous environmental and genetic factors which are expected to influence fitness of individuals in the nascent wild population [10]. For salmon, captive breeding has been successful in maintaining the endangered Redfish Lake sockeye salmon population over a twenty year period, but the population is still receiving hatchery supplementation [11]. Similarly, all three federal captive breeding programs established for endangered salmon populations in Canada (Inner Bay of Fundy Atlantic salmon, Cultus Lake and Sakinaw Lake sockeye salmon) are ongoing [12][13][14][15].…”