Abstract. By jointly considering patterns of genetic and life-history diversity in over 100 populations of Chinook salmon from California to British Columbia, we demonstrate the importance of two different mechanisms for lifehistory evolution. Mapping adult run timing (the life-history trait most commonly used to characterize salmon populations) onto a tree based on the genetic data shows that the same run-time phenotypes exist in many different genetic lineages. In a hierarchical gene diversity analysis, differences among major geographic and ecological provinces explained the majority (62%) of the overall G ST , whereas run-time differences explained only 10%. Collectively, these results indicate that run-timing diversity has developed independently by a process of parallel evolution in many different coastal areas. However, genetic differences between coastal populations with different run timing from the same basin are very modest (G ST Ͻ 0.02), indicating that evolutionary divergence of this trait linked to reproductive isolation has not led to parallel speciation, probably because of ongoing gene flow. A strikingly different pattern is seen in the interior Columbia River Basin, where run timing and other correlated life-history traits map cleanly onto two divergent genetic lineages (G ST ϳ 0.15), indicating that some patterns of life-history diversity have a much older origin. Indeed, genetic data indicate that in the interior Columbia Basin, the two divergent lineages behave essentially as separate biological species, showing little evidence of genetic contact in spite of the fact that they comigrate through large areas of the river and ocean and in some locations spawn in nearly adjacent areas.Key words. Allozymes, gene diversity analysis, life-history evolution, Pacific salmon, parallel speciation, run timing. The question of how rapidly and by what mechanisms adaptive differences arise among populations is of central interest to both evolutionary biologists and conservation biologists. Evidence is accumulating that evolution can occur at a rate high enough to be amenable to experimental observation within the lifetime of humans (Thompson 1998;Hendry and Kinnison 1999;Reznick and Ghalambor 2001). In addition, a number of recent studies have demonstrated the importance of parallel evolution, or repeated evolution of ecologically equivalent traits within a taxon (Reznick et al. 1996;Pigeon et al. 1997;Rundle et al. 2000;Johannesson 2001;Johnson 2001). Both types of studies raise questions about the importance of conserving existing life-history diversity and the likelihood that traits, once lost, will evolve once again-questions that are increasingly relevant to understanding the consequences of current rates of decline in biodiversity (Bernatchez 1995;Pimm and Raven 2000;Myers and Knoll 2001).Understanding the evolution of life-history diversity in salmon is particularly challenging, both because of the enormous complexity in life-history traits expressed by these species (Groot and Margolis 1991;Waples ...

An international multi‐laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha). This project was in response to the needs of the Chinook Technical Committee of the Pacific Salmon Commission to identify stock composition of Chinook salmon caught in fisheries during their oceanic migrations. Nine genetics laboratories identified 13 microsatellite loci that could be reproducibly assayed in each of the laboratories. To test that the loci were reproducible among laboratories, blind tests were conducted to verify scoring consistency for the nearly 500 total alleles. Once standardized, a dataset of over 16,000 Chinook salmon representing 110 putative populations was constructed ranging throughout the area of interest of the Pacific Salmon Commission from Southeast Alaska to the Sacramento River in California. The dataset differentiates the major known genetic lineages of Chinook salmon and provides a tool for genetic stock identification of samples collected from mixed fisheries. A diverse group of scientists representing the disciplines of fishery management, genetics, fishery administration, population dynamics, and sampling theory are now developing recommendations for the integration of these genetic data into ocean salmon management.

Abstract. By jointly considering patterns of genetic and life-history diversity in over 100 populations of Chinook salmon from California to British Columbia, we demonstrate the importance of two different mechanisms for lifehistory evolution. Mapping adult run timing (the life-history trait most commonly used to characterize salmon populations) onto a tree based on the genetic data shows that the same run-time phenotypes exist in many different genetic lineages. In a hierarchical gene diversity analysis, differences among major geographic and ecological provinces explained the majority (62%) of the overall G ST , whereas run-time differences explained only 10%. Collectively, these results indicate that run-timing diversity has developed independently by a process of parallel evolution in many different coastal areas. However, genetic differences between coastal populations with different run timing from the same basin are very modest (G ST Ͻ 0.02), indicating that evolutionary divergence of this trait linked to reproductive isolation has not led to parallel speciation, probably because of ongoing gene flow. A strikingly different pattern is seen in the interior Columbia River Basin, where run timing and other correlated life-history traits map cleanly onto two divergent genetic lineages (G ST ϳ 0.15), indicating that some patterns of life-history diversity have a much older origin. Indeed, genetic data indicate that in the interior Columbia Basin, the two divergent lineages behave essentially as separate biological species, showing little evidence of genetic contact in spite of the fact that they comigrate through large areas of the river and ocean and in some locations spawn in nearly adjacent areas.Key words. Allozymes, gene diversity analysis, life-history evolution, Pacific salmon, parallel speciation, run timing. The question of how rapidly and by what mechanisms adaptive differences arise among populations is of central interest to both evolutionary biologists and conservation biologists. Evidence is accumulating that evolution can occur at a rate high enough to be amenable to experimental observation within the lifetime of humans (Thompson 1998;Hendry and Kinnison 1999;Reznick and Ghalambor 2001). In addition, a number of recent studies have demonstrated the importance of parallel evolution, or repeated evolution of ecologically equivalent traits within a taxon (Reznick et al. 1996;Pigeon et al. 1997;Rundle et al. 2000;Johannesson 2001;Johnson 2001). Both types of studies raise questions about the importance of conserving existing life-history diversity and the likelihood that traits, once lost, will evolve once again-questions that are increasingly relevant to understanding the consequences of current rates of decline in biodiversity (Bernatchez 1995;Pimm and Raven 2000;Myers and Knoll 2001).Understanding the evolution of life-history diversity in salmon is particularly challenging, both because of the enormous complexity in life-history traits expressed by these species (Groot and Margolis 1991;Waples ...

Information developed during recently completed evaluations of the status of seven species of anadromous Pacific salmonids (Oncorhynchus spp.) in the Pacific Northwest was used to characterize patterns of intraspecific diversity along three major axes: ecology, life history and biochemical genetics. Within the study area, the species' ranges, and therefore the number of distinct ecological regions inhabited differ considerably, with pink and chum salmon limited to the northern areas and chinook salmon and steelhead distributed over the widest geographic range. The species showed comparable differences in the patterns of life history and genetic diversity, with chinook and sockeye salmon and steelhead having the most major diversity groups and pink, chum and coho salmon having the least. Both life history and genetic diversity showed a strong, positive correlation with the extent of ecological diversity experienced by a species, and the correlation between the number of major genetic and life history groups within a species was even stronger (r=0·96; P<0·05). Departures from these general diversity relationships found in some species (especially sockeye and coho salmon and cutthroat trout) can be explained by different interactions with the freshwater environment and, for cutthroat trout, by the occurrence of substantial intrapopulational diversity in life history traits, a hierarchical level not considered in this study.

Knowledge of the migratory habits of juvenile Pacific salmon Oncorhynchus spp. is required to test the hypothesis that ocean food resources are a limiting factor in their production. Using DNA stock identification techniques, we reconstructed the regional and seasonal changes in the stock composition of juvenile sockeye salmon O. nerka (n ¼ 4,062) collected from coastal Washington to the Alaska Peninsula in coastal trawl surveys from May to February 1996-2007. Individuals were allocated to 14 regional populations. The majority were allocated to stocks from the Fraser River system (42%), while west coast Vancouver Island stocks accounted for 15% of the total catch; Nass and Skeena River sockeye salmon constituted 14% and Rivers Inlet 6% of the total. The remainder of the stocks identified individually contributed less than 5% of the sockeye salmon analyzed. These proportions generally reflected the abundance of those populations. In spring and summer, the majority of fish were caught in close proximity to their rivers of origin, lending further support to the allocations. By fall, sockeye salmon were caught as far north and west as the Alaska Peninsula, the majority being caught from central British Columbia to Southeast Alaska. Juvenile sockeye salmon generally disappeared from the coast by winter, suggesting dispersion into the Gulf of Alaska. Within each region, the proportional stock composition changed as the seasons progressed, with northward (and in some cases, rapid) migration along the coast. We also demonstrated stock-specific differences in migration patterns. For each stock identified, body size and energy density were higher at northern latitudes, suggesting that there is an environmental or food web influence on growth or that faster growing fish initiated their northward migration earlier.

Recent reductions in the abundance of all Pacific salmon species (Oncorhynchus spp.), coupled with large increases in artificial productioq demand that careful attention be paid to genetic changes occurring in both wild and cultured populations. Analysis of electrophoretic data for chinook salmon (O. tshawytscha) from the Pacific coast of Oregon revealed substantial allele frequency changes over 24 years in hatchery, but not wild populations. Unfortunately, our understanding of the causes of this result is hampered by a lack of theoretical models designed for organisms with life history features like those of Pacific salmon. We used computer simulations to provide a context for understanding genetic changes observed in the hatchery populations. Simulation results indicated that annual fluctuations in population allele frequencies due to genetic drift can typically be expected to be several percent, with the absolute magnitude determined primarily by the effective number of spawners each year rather than the age structure. Changes over 10‐ to 25‐year periods were only slightly greater than short‐term changes (1–5 years). The magnitude of allele frequency change over time was different for juvenile and adult samples. The probability of a significant test statistic comparing allele frequencies in temporally spaced samples increased with the ratio of sample size to effective number of breeders per year. This is an important consideration for conservation biologists, who typically are concerned with populations of small effective size. Simulation results indicate that it is necessary to postulate unrealistically large selection coefficients to explain the genetic changes in the hatchery populations by natural selection. The changes observed are consistent with a pure drift model provided that the effective number of breeders was as small as about 25–50 per year. Analysis of brood stock information for the hatcheries indicates that the effective population number may indeed have been this low, although the number of returning adults was often much larger. This conclusion underlines the importance of monitoring the genetic consequences of the large‐scale artificial propagation program involving Pacific salmon.

We monitored fish assemblages monthly at estuarine and tidal freshwater sites in the lower Columbia River and estuary from January 2002 through September 2007 in order to identify specific salmon stocks and migration stages that may benefit from habitat restoration initiatives. We report landscape‐scale and seasonal variation in abundance, size, hatchery production (based on adipose fin clips), and genetic stock of origin of juvenile Chinook salmon Oncorhynchus tshawytscha. From fish implanted with coded wire tags (CWTs), we also determined the sites of release and inferred migration patterns. Chinook salmon were found in diverse life history stages and forms, including fry migrants, fingerlings, and (fewer) yearlings. Abundance increased in February and decreased in August, but salmon were present in all months each year. Spatial gradients in abundance and size were strong, with fewer but larger fish in brackish than in tidal freshwater zones. Overall, 30% of the Chinook salmon measured were fry (≤60 mm) that were likely naturally produced fish. These occurred at higher mean monthly proportions in tidal freshwater than in estuarine zones. In contrast, most larger fish were probably raised in hatcheries. Genetic stock assessment revealed that the majority of the Chinook salmon analyzed were from fall‐run stock groups originating in the lower Columbia River, with 15% originating from other stock groups. Of these minority contributors, about 6% were identified as upper Columbia River summer–fall‐run Chinook salmon while seven other stock groups accounted for the remainder, including 3% from transplants originating in southern Oregon's Rogue River. Recaptures of tagged fish revealed maximum migration times of 143 d for subyearlings and 52 d for yearlings, and both CWT and genetic data indicated that fall Chinook salmon from coastal rivers occasionally entered the estuary. These data demonstrated a widespread temporal and spatial distribution of subyearling Chinook salmon in shallow‐water habitats of the lower Columbia River and estuary. Received June 28, 2011; accepted February 28, 2012

Early ocean residence is considered a critical period for juvenile salmon although specific survival mechanisms are often unidentified and may vary by species or life stage. Columbia River spring-run Chinook salmon Oncorhynchus tshawytscha abundance has declined dramatically since the early 1900s. To elucidate mechanisms of early marine survival, we tested the 'bigger-is-better' and 'stage-duration' aspects of the 'growth-mortality' hypothesis, which posits that size and growth rate are important for future abundance. We tested the 'match-mismatch' hypothesis to determine whether early marine growth was related to indices related to regional productivity, including spring transition timing and copepod community composition. We generated estimates of individual size at ocean entry and capture, marine growth rate, early marine migration rate, and emigration timing using data from ocean surveys, genetic stock-assignment, and otolith analyses of juveniles collected across 8 yr between 1998 and 2008. Size at capture and marine growth rate after ~30 d marine residence were positively related to future adult returns, whereas size at marine entry was not. Growth rate was not significantly related to indices of secondary production, but size at capture was significantly greater when lipid-rich copepods dominated. Although future adult abundance was not related to emigration timing, juveniles migrated more slowly when copepod biomass was high, perhaps responding to foraging conditions. Overall, processes during early ocean residence appear to be more important for cohort size establishment than those at marine entry. Approaches that combine genetic and otolith analyses have great potential to provide information on stock-specific variation in survival mechanisms.