David J. Teel

LIFE-HISTORY DIVERGENCE IN CHINOOK SALMON: HISTORIC CONTINGENCY AND PARALLEL EVOLUTION

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 life‐history 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 GST, 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 (GST < 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 (GST˜ 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.

Seasonal Stock-Specific Migrations of Juvenile Sockeye Salmon along the West Coast of North America: Implications for Growth

Abstract 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 = 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 prox...

Genetic and otolith isotopic markers identify salmon populations in the Columbia River at broad and fine geographic scales

Processes occurring in freshwater, estuarine, and marine habitats strongly influence the growth, survival and reproductive success of salmonids. Nonetheless, implementing an ecosystem model explicitly linking these important habitats has been hindered by the inability to track the source identity of individuals where they co-occur. Here we explore the development and integration of natural markers- molecular and isotopic to characterize the natal sources of Chinook salmon (Oncorhynchus tshawytscha) in the Mid and Upper Columbia River summer/fall-run (UCR Su/F) population. Microsatellite DNA markers identified the majority of juveniles collected in rivers and hatcheries in the Mid and Upper Columbia River watershed to the Summer/Fall-run population in this watershed with 90% posterior probabilities of group membership. Strontium isotopes (87Sr/86Sr) measured in the natal rearing portion of the otolith showed significant geographic variation among natal rivers and hatcheries. Natal sites exhibited a wide dynamic range in 87Sr/86Sr source signatures (0.7043–0.7142), such that on average 61% of individuals were correctly classified to the location from which they were collected. We found that multilocus genotypes and otolith 87Sr/86Sr ratios collected on the same individuals were complementary markers when applied in a hierarchy. Microsatellites successfully assigned individuals to the broader UCR Su/F genetic group and 87Sr/86Sr provided finer-scale geographic assignments to five natal river and hatchery groups nested within the UCR Su/F population. The temporal stability of both genetic and 87Sr/86Sr markers, together with the coast-wide microsatellite baseline currently being used for mixed-stock fisheries management supports the further development and integration of 87Sr/86Sr markers to potentially achieve finer levels of stock resolution. Stock identification at the scales of individual rivers and hatcheries would help elucidate the abundance, distribution, and the relative contributions of natal sources important for the recovery and spatial management of Chinook salmon.

Genetic Population Structure and Origin of Life History Types in Chinook Salmon in British Columbia, Canada

Abstract We used protein electrophoresis to examine genetic population structure and origin of life history types of chinook salmon Oncorhynchus tshawytscha in British Columbia, Canada. Among 31 allozyme loci resolved in 91 samples from 63 populations of chinook salmon in rivers and hatcheries throughout British Columbia, population heterozygosities averaged 0.084 (range 0.048–0.108) and were typical of values for populations in other regions. A hierarchical gene diversity analysis indicated that 91.3% of the total allele-frequency diversity was attributable to within-population variability; the remaining 8.7% was attributable to geographic variability among populations, which was partitioned into among-river (3.3%), among-area (3.5%), and among-region (1.9%) components. Two major groups of populations appeared in the principal components analysis and in cluster analysis of genetic distances. A coastal group included populations in four subgroups: Central coast, Georgia Strait, lower Fraser River, and wes...

Juvenile Salmonid Use of Reconnected Tidal Freshwater Wetlands in Grays River, Lower Columbia River Basin

Abstract Degraded wetland systems with impaired hydraulic connections have resulted in diminished habitat opportunity for salmonid fishes and other native flora and fauna in the Pacific Northwest. Many of these lost habitats were once intertidal freshwater marshes and swamps. Restoration of these systems is effected in part by reestablishing tidal processes that promote connectivity, with a central goal of restoring rearing habitat for juvenile Pacific salmon Oncorhynchus spp. In the Grays River tidal freshwater system of Washington, we measured hydrologic changes that resulted from the removal of tide gates from diked pastureland and we determined the subsequent time series of salmonid abundance and size frequency in the restoring marshes. Dike breaching caused an immediate return of full semidiurnal tidal fluctuations to the pasturelands. Juvenile Pacific salmonids quickly expanded into this newly available habitat and used prey items that were presumably produced within the marshes. Habitat use varied ...

Genetic Analyses Provide Insight into the Early Ocean Stock Distribution and Survival of Juvenile Coho Salmon off the Coasts of Washington and Oregon

Abstract Estimating the stock proportions of mixed-stock fishery samples by means of genetic stock identification has played an important role in the management of salmon fisheries. In addition, stock identification of individual fish has applications for population studies, forensic cases, and management issues. We examined 11 microsatellite DNA loci in 84 populations of coho salmon Oncorhynchus kisutch sampled at 78 locations from southern British Columbia to northern California to construct a database of microsatellite allele frequencies. We then evaluated the applicability of the database for estimating stock proportions in a mixed fishery and assigning individuals to their regions of origin. The loci were highly polymorphic: observed heterozygosity ranged from 0.754 to 0.943. Using genetic distance calculations, we identified six major geographic regions and 15 smaller subregions into which the populations grouped. Computer simulations and a sample of 143 coho salmon with known origins showed that th...

Spatial and trophic overlap of marked and unmarked Columbia River Basin spring Chinook salmon during early marine residence with implications for competition between hatchery and naturally produced fish

Ecological interactions between natural and hatchery juvenile salmon during their early marine residence, a time of high mortality, have received little attention. These interactions may negatively influence survival and hamper the ability of natural populations to recover. We examined the spatial distributions and size differences of both marked (hatchery) and unmarked (a high proportion of which are natural) juvenile Chinook salmon in the coastal waters of Oregon and Washington from May to June 1999–2009. We also explored potential trophic interactions and growth differences between unmarked and marked salmon. Overlap in spatial distribution between these groups was high, although catches of unmarked fish were low compared to those of marked hatchery salmon. Peak catches of hatchery fish occurred in May, while a prolonged migration of small unmarked salmon entered our study area toward the end of June. Hatchery salmon were consistently longer than unmarked Chinook salmon especially by June, but unmarked salmon had significantly greater body condition (based on length-weight residuals) for over half of the May sampling efforts. Both unmarked and marked fish ate similar types and amounts of prey for small (station) and large (month, year) scale comparisons, and feeding intensity and growth were not significantly different between the two groups. There were synchronous interannual fluctuations in catch, length, body condition, feeding intensity, and growth between unmarked and hatchery fish, suggesting that both groups were responding similarly to ocean conditions.

Genetic population structure of central Oregon Coast coho salmon (Oncorhynchus kisutch)

We surveyed microsatellite variation from 22 spawning populations of coho salmon (Oncorhynchus kisutch) from the Oregon Coast to help identify populations for conservation planning. All of our samples were temporally replicated, with most samples obtained in 2000 and 2001. We had three goals: (1) to confirm the status of populations identified on the basis of spawning location and life history; (2) to estimate effective population sizes and migration rates in order to determine demographic independence at different spatial scales; and (3) to determine if releases of Washington hatchery coho salmon in the 1980s into Oregon Coast streams resulted in measurable introgression into nearby wild Oregon Coast coho populations. For the last question, our study included a hatchery broodstock sample from 1985, after the Puget Sound introduction, and a 1975 sample taken from the same area prior to the introduction. Our results generally supported previously hypothesized population structure. Most importantly, we found unique lake-rearing groups identified on the basis of a common life-history type were genetically related. Estimates of immigrant fraction using several different methods also generally supported previously identified populations. Estimates of effective population size were highly correlated with estimates of spawning abundance. The 1985 hatchery sample was genetically similar to contemporary Washington samples, and the contemporary Oregon Coast samples were similar to the 1975 Oregon Coast sample, suggesting that introductions of Washington coho salmon did not result in large scale introgression into Oregon populations.

Genetic Stock Composition of Subyearling Chinook Salmon in Seasonal Floodplain Wetlands of the Lower Willamette River, Oregon

Abstract We used genetic identification methods to examine the stock composition of subyearling Chinook salmon Oncorhynchus tshawytscha in floodplain wetland and main-stem habitats of the lower Willamette River, Oregon. Using a microsatellite DNA baseline of 13 standardized loci and 30 Columbia River basin populations, we analyzed 280 subyearlings collected in winter and spring 2005-2006 from wetland and main-stem river sites. Genetic stock identification analysis indicated that spring Chinook salmon originating from the Willamette River made up a substantial proportion of the samples and contributed 16-71% to sample mixtures representing the wetland habitat sites. Fall Chinook salmon from lower Columbia River sources were also present and contributed 58% of winter samples. Spring Chinook salmon from lower Columbia River populations were present in both wetland (17%) and river (16%) samples in spring 2005, and subyearlings from summer-fall-run populations in the middle and upper Columbia River contributed...

Distribution, Size, and Origin of Juvenile Chinook Salmon in Shallow-Water Habitats of the Lower Columbia River and Estuary, 2002–2007

Abstract 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 Oregons 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.