2007 NWFSC Tidal Freshwater Genetics Results

Genetic Analysis of Juvenile Chinook Salmon for inclusion in 'Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta, lower Columbia River, 2007. Final report submitted to the Bonneville Power Administration, Contract DE-AC05-76RLO1830.' Genotypic data were collected for 108 Chinook salmon and used in the genetic stock identification analysis. Results of the mixture analysis are presented in Table 1. Percentage estimates for four genetic stock groups (West Cascade Tributary Fall, Willamette River Spring, Deschutes River Fall, and Upper Columbia River Summer/Fall) ranged from 11% to 43%, all with non-zero lower 95% confidence intervals. Small contributions were also estimated for the West Cascade Tributary Spring (3%) and Snake River Fall (6%) stock groups. Results of individual fish probability assignments were summed by collection date (Figure 1) and site (Figure 2). Assignment probabilities for the most likely stock group for each individual ranged from 0.51 to 1.00 with approximately 60% of the assignments greater than 0.90 (data not shown). Nearly all of the low probability assignments were fish with assignments split between the Deschutes River Fall and Upper Columbia River Summer/Fall groups

Manual for starch gel electrophoresis: A method for the detection of genetic variation

The procedure to conduct horizontal starch gel electrophoresis on enzymes is described in detail. Areas covered are (I) collection and storage of specimens, (2) preparation of tissues, (3) preparation of a starch gel, (4) application of enzyme extracts to a gel, (5) setting up a gel for electrophoresis, (6) slicing a gel, and (7) staining a gel. Recipes are also included for 47 enzyme stains and 3 selected gel buffers. (PDF file contains 26 pages.

Life-History Divergence In Chinook Salmon: Historic Contingency And Parallel Evolution

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 \u3c 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 co-migrate through large areas of the river and ocean and in some locations spawn in nearly adjacent areas

INEEL Greenhouse Gas Inventory and Trend Analysis

The objective of the INEEL GHG Inventory and Trend Analysis is to establish INEEL expertise in carbon management decision making and policy analysis. This FY-99 effort is the first step toward placing the INEEL in a leadership role within the DOE laboratories to support carbon management systems and analysis

Juvenile salmonid distribution, growth, condition, origin, and environmental and species associations in the Northern California Current

Information is summarized on juvenile salmonid distribution, size, condition, growth, stock origin, and species and environmental associations from June and August 2000 GLOBEC cruises with particular emphasis on differences related to the regions north and south of Cape Blanco off Southern Oregon. Juvenile salmon were more abundant during the August cruise as compared to the June cruise and were mainly distributed northward from Cape Blanco. There were distinct differences in distribution patterns between salmon species: chinook salmon were found close inshore in cooler water all along the coast and coho salmon were rarely found south of Cape Blanco. Distance offshore and temperature were the dominant explanatory variables related to coho and chinook salmon distribution. The nekton assemblages differed significantly between cruises. The June cruise was dominated by juvenile rockfishes, rex sole, and sablefish, which were almost completely absent in August. The forage fish community during June comprised Pacific herring and whitebait smelt north of Cape Blanco and surf smelt south of Cape Blanco. The fish community in August was dominated by Pacific sardines and highly migratory pelagic species. Estimated growth rates of juvenile coho salmon were higher in the GLOBEC study area than in areas farther north. An unusually high percentage of coho salmon in the study area were precocious males. Significant differences in growth and condition of juvenile coho salmon indicated different oceanographic environments north and south of Cape Blanco. The condition index was higher in juvenile coho salmon to the north but no significant differences were found for yearling chinook salmon. Genetic mixed stock analysis indicated that during June, most of the Chinook salmon in our sample originated from rivers along the central coast of Oregon. In August, chinook salmon sampled south of Cape Blanco were largely from southern Oregon and northern California; whereas most chinook salmon north of Cape Blanco were from the Central Valley in California

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades

Estimating behavior in a black box : how coastal oceanographic dynamics influence yearling Chinook salmon marine growth and migration behaviors

Ocean currents or temperature may substantially influence migration behavior in many marine species. However, high-resolution data on animal movement in the marine environment are scarce; therefore, analysts and managers must typically rely on unvalidated assumptions regarding movement, behavior, and habitat use. We used a spatially explicit, individual-based model of early marine migration with two stocks of yearling Chinook salmon to quantify the influence of external forces on estimates of swim speed, consumption, and growth. Model results suggest that salmon behaviorally compensate for changes in the strength and direction of ocean currents. These compensations can result in salmon swimming several times farther than their net movement (straight-line distance) would indicate. However, the magnitude of discrepancy between compensated and straight-line distances varied between oceanographic models. Nevertheless, estimates of relative swim speed among fish groups were less sensitive to the choice of model than estimates of absolute individual swim speed. By comparing groups of fish, this tool can be applied to management questions, such as how experiences and behavior may differ between groups of hatchery fish released early vs. later in the season. By taking into account the experiences and behavior of individual fish, as well as the influence of physical ocean processes, our approach helps illuminate the “black box” of juvenile salmon behavior in the early marine phase of the life cycle

Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon (Oncorhynchus tshawytscha

Abstract: We evaluated the relative importance of "bottom-up" (production-limited) and "top-down" (predator-mediated) processes during early marine residence in a population of Chinook salmon (Oncorhynchus tshawytscha) from the upper Columbia River, USA. We examined length, mass, and condition index of age-0 juveniles collected in the ocean during June and September across 11 years in relation to conditions in the river, estuary, and coastal ocean and to future adult returns. Characteristics of juveniles in September, but not June, were related to adult returns. During years when coastal waters were relatively cool and productive, juveniles captured in September displayed relatively low condition and reduced otolith growth compared with years when coastal waters were relatively warm and unproductive; this contrast indicates that top-down effects such as selective mortality or competition are important during early marine residence. Key physical (river plume volume during emigration) and biological (condition) variables and their interaction accounted for >95% of the variation in adult returns. Future research should focus on evaluating predators and competitors and understanding how river plume structure influences survival. Résumé : Nous avons évalué l'importance relative des processus ascendants (limités par la production) et descendants (modulés par les prédateurs) au début du séjour en mer dans une population de saumons quinnat (Oncorhynchus tshawytscha) du cours supérieur du fleuve Columbia (États-Unis). Nous avons examiné la longueur, la masse et l'indice d'embonpoint de juvéniles de 0 an prélevés en océan durant les mois de juin et septembre pendant 11 ans, par rapport aux conditions dans le fleuve, l'estuaire et le littoral océanique, ainsi qu'aux retours d'adultes subséquents. Les caractéristiques des juvéniles en septembre, mais non en juin, étaient reliées aux retours d'adultes. Durant les années où les eaux côtières étaient relativement froides et productives, les juvéniles capturés en septembre présentaient des indices d'embonpoint et des taux de croissance des otolites relativement faibles par rapport à ceux des juvéniles capturés durant des années d'eaux côtières relativement chaudes et non productives. Ces différences indiquent que des effets descendants tels qu'une mortalité sélective ou la concurrence sont importants au début du séjour en mer. Des variables physiques (volume du panache fluvial durant l'émigration) et biologiques (embonpoint) clés et leur interaction expliquaient >95 % de la variabilité des retours d'adultes. Les travaux de recherche futurs devraient se pencher sur l'évaluation des prédateurs et des concurrents et la compréhension de l'influence de la structure du panache fluvial sur la survie. [Traduit par la Rédaction

Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon (Oncorhynchus tshawytscha)

We evaluated the relative importance of "bottom-up" (production-limited) and "top-down" (predator-mediated) processes during early marine residence in a population of Chinook salmon (Oncorhynchus tshawytscha) from the upper Columbia River, USA. We examined length, mass, and condition index of age-0 juveniles collected in the ocean during June and September across 11 years in relation to conditions in the river, estuary, and coastal ocean and to future adult returns. Characteristics of juveniles in September, but not June, were related to adult returns. During years when coastal waters were relatively cool and productive, juveniles captured in September displayed relatively low condition and reduced otolith growth compared with years when coastal waters were relatively warm and unproductive; this contrast indicates that top-down effects such as selective mortality or competition are important during early marine residence. Key physical (river plume volume during emigration) and biological (condition) variables and their interaction accounted for >95% of the variation in adult returns. Future research should focus on evaluating predators and competitors and understanding how river plume structure influences survival.Keywords: Survival, Chinook salmon (Oncorhynchus tshawytscha

Assessing the Relative Importance of Local and Regional Processes on the Survival of a Threatened Salmon Population

Research on regulatory mechanisms in biological populations often focuses on environmental covariates. An integrated approach that combines environmental indices with organismal-level information can provide additional insight on regulatory mechanisms. Survival of spring/summer Snake River Chinook salmon (Oncorhynchus tshawytscha) is consistently low whereas some adjacent populations with similar life histories experience greater survival. It is not known if populations with differential survival respond similarly during early marine residence, a critical period in the life history. Ocean collections, genetic stock identification, and otolith analyses were combined to evaluate the growth-mortality and match-mismatch hypotheses during early marine residence of spring/summer Snake River Chinook salmon. Interannual variation in juvenile attributes, including size at marine entry and marine growth rate, was compared with estimates of survival and physical and biological metrics. Multiple linear regression and multi-model inference were used to evaluate the relative importance of biological and physical metrics in explaining interannual variation in survival. There was relatively weak support for the match-mismatch hypothesis and stronger evidence for the growth-mortality hypothesis. Marine growth and size at capture were strongly, positively related to survival, a finding similar to spring Chinook salmon from the Mid-Upper Columbia River. In hindcast models, basin-scale indices (Pacific Decadal Oscillation (PDO) and the North Pacific Gyre Oscillation (NPGO)) and biological indices (juvenile salmon catch-per-unit-effort (CPUE) and a copepod community index (CCI)) accounted for substantial and similar portions of variation in survival for juvenile emigration years 1998–2008 (R² > 0.70). However, in forecast models for emigration years 2009–2011, there was an increasing discrepancy between predictions based on the PDO (50–448% of observed value) compared with those based on the NPGO (68–212%) or biological indices (CPUE and CCI: 83–172%). Overall, the PDO index was remarkably informative in earlier years but other basin-scale and biological indices provided more accurate indications of survival in recent years