Juvenile Chinook salmon (<Emphasis Type=Italic>Oncorhynchus tshawytscha</Emphasis>) growth in off-channel and main-channel habitats on the Sacramento River,CA using otolith increment widths

Few studies have quantified juvenile salmon growth among different habitats or evaluated the mechanisms controlling salmon growth and survival. We used otolith microstructure to compare daily relative growth rates among main-channel riverine areas, off-channel ponds, and non-natal seasonal tributaries of the Sacramento River, CA. We compared prey availability, prey preference, and stomach fullness between these sites. We observed larger average otolith growth increments, higher prey densities, and warmer water temperatures in both off-channel ponds and non-natal seasonal tributaries compared to the main-channel areas in both 2001 and 2002. Our findings suggest that warmer temperatures and abundant prey in off-channel habitats during Central Valley Chinook salmon rearing periods may lead to higher growth rates, which in turn may improve juvenile survival. Our results suggest that off-channel habitats may be critical habitats to include in conservation and management plans for juvenile salmon.     

Non-direct homing behaviours by adult Chinook salmon in a large, multi-stock river system

Two non-direct homing behaviours, overshoot of natal tributaries and temporary non-natal tributary use, were evaluated for 5150 radio-tagged spring–summer Chinook salmon Oncorhynchus tshawytscha from 40 populations in the large Columbia River system. Over 7 years, 2–44% (mean = 15%) of individuals within each group temporarily entered presumed non-natal tributaries. In addition, many Chinook salmon from lower river tributaries initially travelled 3 to >250 km upstream in the main-stem river beyond confluences with presumed natal tributaries before returning to the natal sites ('overshoot'). Both overshoot and temporary tributary use behaviours declined exponentially with increasing distance from the natal tributary. Non-direct homing also increased later in the season as water temperatures rose and was associated with hatchery origin in some cases. The behaviours may reflect a mix of active searching for olfactory cues from natal sites, behavioural thermoregulation and orientation challenges in a large-river migration corridor transformed by dams and reservoirs. While anadromous salmonid homing is generally accurate and precise, these results indicate that route finding can be non-direct, potentially increasing energetic costs and harvest risks during migration.     

Behavioural response of juvenile Chinook salmon Oncorhynchus tshawytscha during a sudden temperature increase and implications for survival

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Juvenile Chinook salmon Oncorhynchus tshawytscha survival and behaviour were evaluated during a temperature increase from 8.8 to 23.2 °C.     

Upstream migration rates of radio‐tagged adult Chinook salmon in riverine habitats of the Columbia River basin

Upstream migration rates were assessed for 1801 radio‐tagged adult spring–summer Chinook salmon Oncorhynchus tshawytscha through 12 unimpounded river reaches in the Columbia River basin from 1997 to 2002. Reaches were 36 to 241 km long (mean = 130 km) and included sections of the large Columbia and Snake Rivers and smaller free‐flowing tributaries. Median Chinook salmon migration rates ranged from <10 km day⁻¹ in the Deschutes and Clearwater Rivers to >35 km day⁻¹ in the Columbia and Snake Rivers. Using multivariate analyses, migration date explained the most variance in Chinook salmon migration rates while river discharge, migration year and migration reach were secondary. Both within and between years, Chinook salmon migrated more rapidly as migration date increased and more slowly when discharge was high. Arrival at high elevation spawning grounds at appropriate times and increased metabolic activity and reproductive maturation may explain the greater power of migration date, relative to river discharge, in predicting migration rates of Columbia basin spring–summer Chinook salmon.     

The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad‐scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad‐scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin‐wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.     

Beavers (Castor canadensis) influence habitat for juvenile salmon in a large Alaskan river floodplain

Our aim was to determine how beavers affect habitats and food resources for juvenile salmon in the Kwethluk River in western Alaska.

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Adult spawners: A critical period for subarctic Chinook salmon in a changing climate

Concurrent, distribution-wide abundance declines of some Pacific salmon species, including Chinook salmon (Oncorhynchus tshawytscha), highlights the need to understand how vulnerability at different life stages to climate stressors affects population dynamics and fisheries sustainability. Yukon River Chinook salmon stocks are among the largest subarctic populations, near the northernmost extent of the species range. Existing research suggests that Yukon River Chinook salmon population dynamics are largely driven by factors occurring between the adult spawner life stage and their offspring's first summer at sea (second year post-hatching). However, specific mechanisms sustaining chronic poor productivity are unknown, and there is a tremendous sense of urgency to understand causes, as declines of these stocks have taken a serious toll on commercial, recreational, and indigenous subsistence fisheries. Therefore, we leveraged multiple existing datasets spanning parent and juvenile stages of life history in freshwater and marine habitats. We analyzed environmental data in association with the production of offspring that survive to the marine juvenile stage (juveniles per spawner). These analyses suggest more than 45% of the variability in the production of juvenile Chinook salmon is associated with river temperatures or water discharge levels during the parent spawning migration. Over the past two decades, parents that experienced warmer water temperatures and lower discharge in the mainstem Yukon River produced fewer juveniles per spawning adult. We propose the adult spawner life stage as a critical period regulating population dynamics. We also propose a conceptual model that can explain associations between population dynamics and climate stressors using independent data focused on marine nutrition and freshwater heat stress. It is sobering to consider that some of the northernmost Pacific salmon habitats may already be unfavorable to these cold-water species. Our findings have immediate implications, given the common assumption that northern ranges of Pacific salmon offer refugia from climate stressors.     

Changes along a disturbance gradient in the density and composition of propagule banks in floodplain aquatic habitats

This study used germination methods to examine the density, species composition and functional composition of propagule banks in a series of riverine wetland aquatic habitats subject to varying degrees of hydrological and management-related disturbance. Under permanent inundation (the conditions prevailing at most sites during the growing season) propagule germination and species richness was low, with floodplain perennials and helophytes particularly affected. Densities of floodplain annuals were largely maintained through continued germination of a few flooding tolerant species. On damp mud (conditions associated with hydrological instability) total seedling number and species richness increased significantly, but species richness of germinating hydrophytes declined. Mean seedling density at 0–0.1m depth was 15450 ± 4400 m–2, reaching a maximum (162 050 m–2) in temporary backwaters. Annual (e.g., Lindernia dubia, Cyperus fuscus) and facultative ruderal species (e.g., Lythrum salicaria and Alisma plantago-aquatica) predominated. Vertical zonation of the propagule bank was weakly developed. The numbers of individuals and species germinating varied significantly between sites. The seasonal, most intensely disturbed sites (temporary backwaters) supported a numerically large, species-rich propagule bank based on floodplain annuals, while the permanent, less disturbed sites (ditches and an oxbow pond) had a small, species-poor propagule bank composed of hydrophytes and helophytes supplemented by allochthonous seed inputs. Sites intermediate on the gradient had a propagule bank dominated by facultative amphibious, ruderal hydrophytes. The composition of the seed bank and the established vegetation was most similar at the heavily disturbed sites where the seed bank was maintained by vigorously fruiting annuals and supplemented by inputs from temporary habitats upstream. At permanent sites much of the propagule bank composition could be accounted for by inputs of floodborne seed from the immediately adjacent floodplain. The established vegetation at such sites appeared to be maintained mainly by vegetative propagation with recruitment from the propagule bank likely only after severe disturbance. The potential contribution of functionally diverse propagule banks to sucessional processes within fluvially dynamic floodplain aquatic habitats is emphasised.     

Genetic quality and offspring performance in Chinook salmon: implications for supportive breeding

Each year salmon and other fishes are caught and used for supportive breeding programs that attempt to augment natural populations that are threatened with extinction. These programs typically mate individuals randomly and as such they overlook the importance of genetic quality to offspring fitness and ultimately to ensuring population health. Here, we use Chinook salmon (Oncorhynchus tshawytscha) and a fully crossed quantitative genetic breeding design to partition genetic variance in offspring performance (growth and survival) to additive and non-additive genetic effects as well as maternal effects. We show that these three effects contribute about equally to the variation in survival, but only non-additive genetic and maternal effects contribute to variation in growth. Some of the genetic effects could be assigned to variation at the class IIB locus of the major histocompatibility complex, but the maternal effects were not associated with egg size and we found no relationship between dam phenotypic measures and offspring survival or growth. We also found no relationship between sire sexually selected characters and offspring survival or growth, which is inconsistent with a “good genes” hypothesis. Finally, we show that incorporation of genetic quality into supportive breeding programs can increase offspring growth or survival by between 3% and 19% during the endogenous feeding stage alone, and projections to adulthood suggest that survivorship could be over four fold higher. Electronic Supplementary Material  Supplementary material is available in the online version of this article at and is accessible for authorised users.     

Rearing and migration of juvenile Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) in a large river floodplain

Off-channel habitat has become increasingly recognized as key for migratory fishes such as juvenile Chinook salmon (Oncorhynchus tshawytscha). Hence, floodplain habitat has been identified as critical for the continued persistence of California’s Central Valley salmon, particularly the Yolo Bypass, the primary floodplain of the Sacramento River. To provide insight into factors supporting juvenile salmon use of this 240 km², partially leveed floodplain, we examined inter- and intra-annual relationships between environmental correlates and residency time, apparent growth, emigration, migratory phenotype, and survival over more than a decade for natural-origin (“wild”) fish and experimentally-released hatchery fish. Flood duration was positively associated with hatchery juveniles residing longer and achieving larger size. Wild juveniles grew larger and emigrated later with cumulative temperature experience (accumulated thermal units) and warmer average annual temperatures during flood years. Within years, both wild and hatchery salmon departed the floodplain as flood waters receded. Parr-sized juveniles dominated outmigrant composition, though fry and smolt-sized juveniles were also consistently observed. Survival to the ocean fishery was not significantly different between hatchery fish that reared in the Yolo Bypass versus those that reared in the main stem Sacramento River. Our study indicates improved frequency and duration of connectivity between the Sacramento River and the Yolo Bypass could increase off-channel rearing opportunities that expand the life history diversity portfolio for Central Valley Chinook salmon.     

Seasonal variation in density of juvenile Atlantic salmon in fluvial shoreline habitats of a large subarctic river

The densities of Atlantic salmon fry (0+ years) and parr (1+ years and older) in shoreline habitats of the large River Teno watercourse and its tributary, the River Utsjoki generally fluctuated considerably, showing an increase from early summer towards late August and a subsequent decline towards autumn. The seasonal pattern of variation in density was more distinct for parr than for fry. In the period between late July and early September, parr density followed a sinusoidal curve, being highest in late August and lowest in early August and in September. Fry density had a weaker seasonal profile than parr, being highest in late August and in early September. Frequency distributions of the parr age groups (1+, 2+ and 3+ years) were mainly independent of the sampling month.     

Functions of restored wetlands for juvenile salmon in an industrialized estuary

The Duwamish estuary is an industrialized waterway located in Seattle, WA, USA. Despite a history of habitat loss, naturally produced juvenile Chinook salmon use the estuary. In addition to experiencing degraded habitat in the estuary, wild salmon growth may be affected by competition with more than three million hatchery fish released yearly into the river. Restoring habitat to benefit salmon in the Duwamish River is a priority for trustees of public resources, and a number of wetland restoration sites have been created there. We tested the function of restored sites in the Duwamish estuary for juvenile Chinook salmon by comparing fish densities from enclosure nets or beach seines at three paired restored/un-restored sites and by applying environmental and diet data to a bioenergetics model. We also examined temporal and diet overlap of wild juvenile Chinook salmon with other salmon species and with hatchery-reared Chinook salmon using non-metric multidimensional scaling (NMDS). At a brackish upstream site with a relatively large opening to the river, we found higher densities of juvenile Chinook salmon at the restored site. NMDS results indicated that juvenile Chinook salmon fed on different taxa at the restored sites than at the reference sites. However, modeled growth was similar at restored and reference sites. Co-occurring juvenile chum and Chinook salmon fed differently, with chum eating smaller prey, and Chinook salmon eating larger prey. Co-occurring hatchery and wild juvenile Chinook salmon had similar diets, indicating that they may compete for prey. However, modeled growth was positive and did not differ between hatchery and wild fish, suggesting that food was not limiting. Bioenergetics models indicated that overall juvenile Chinook salmon growth potential at the brackish water site was consistently higher than at more saline sites. Our results suggest that restoration sites in the Duwamish estuary that have larger access openings and are located in brackish water may have increased function over other configurations.     

Characterization of a chromosomal rearrangement responsible for producing "apparent" XY-female fall-run Chinook salmon in California

Fluorescence in situ hybridization (FISH) was used to identify the X and Y chromosomes of offspring produced by normal and "apparent" XY-female fall-run Chinook salmon (Oncorhynchus tshawytscha) from California. FISH experiments were performed using probes to 2 sex-linked loci, growth hormone pseudogene (GH-Psi), and OtY1, as well as a probe to a sex-linked microsatellite (Omy7INRA). Comparison of FISH staining patterns between the offspring produced by normal and apparent XY-females revealed that the apparent XY-female examined transmitted a "Y-like" chromosome with an attenuated OtY1 and GH-Psi signal to half of its offspring. Segregation analysis of microsatellites derived from rainbow trout (Oncorhynchus mykiss) with respect to phenotypic sex was carried out for 2 normal and 2 apparent XY-female Chinook salmon families. Inheritance patterns of Omy7INRA were consistent with this locus being closely linked to GH-Psi in males and in apparent XY-females carrying the Y-like chromosome. Another microsatellite locus (Omm1077) was closely linked to the primary sex-determining locus (SEX) in males but not to GH-Psi/OtY1 in apparent XY-females. The FISH analyses suggest that apparent XY-female fall-run Chinook salmon in California are not the product of a Y chromosome to autosome translocation. Despite the combined FISH and inheritance analyses, we were unable to differentiate between 2 alternative explanations for apparent XY-females, namely, recombination of markers between the sex chromosomes, or a Y chromosome with a dysfunctional or missing sex-determining region.     

Just add water: sources of chironomid drift in a large river floodplain

Although seasonal floodplains represent one of the most dynamic and productive of aquatic ecosystems, the sources of this productivity are poorly understood. We examined composition and sources of chironomid drift in the Yolo Bypass, the primary floodplain of the Sacramento River. We found that invertebrate drift during winter floodplain inundation is dominated by a single species, the newly identified chironomid Hydrobaenus saetheri (Diptera: Chironomidae). In order to determine sources of chironomids in the Yolo Bypass, invertebrates were sampled from several potential sources prior to and during initial floodplain inundation. Rehydration of dried floodplain sediments from several locations showed that H. saetheri dominated insect emergence from this colonization pathway. By contrast, H. saetheri was not a substantial component of inundated floodplain ponds or of tributary inputs to the floodplain. We conclude that the initial pulse of invertebrate abundance in Yolo Bypass floodwaters is dominated by chironomid emergence from sediments in multiple regions of the floodplain. Handling editor: S. Declerck     

Climate impacts at multiple scales: evidence for differential population responses in juvenile Chinook salmon

1. We explored differential population responses to climate in 18 populations of threatened spring-summer Chinook salmon Onchorynchus tshawytscha in the Salmon River basin, Idaho. 2. Using data from a long-term mark-release-recapture study of juvenile survival, we found that fall stream flow is the best predictor of average survival across all populations. 3. To determine whether all populations responded similarly to climate, we used a cluster analysis to group populations that had similar annual fluctuations in survival. The populations grouped into four clusters, and different environmental factors were important for different clusters. 4. Survival in two of the clusters was negatively correlated with summer temperature, and survival in the other two clusters was positively correlated with minimum fall stream flow, which in turn depends on snow pack from the previous winter. 5. Using classification and regression tree analysis, we identified stream width and stream temperature as key habitat factors that shape the responses of individual populations to climate. 6. Climate change will likely have different impacts on different populations within this metapopulation, and recognizing this diversity is important for accurately assessing risks.     

Connectivity and complexity of floodplain habitats govern zooplankton dynamics in a large temperate river system

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A latitudinal cline in the Chinook salmon (Oncorhynchus tshawytscha) Clock gene: evidence for selection on PolyQ length variants

A critical seasonal event for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which adults migrate from the ocean to breed in freshwater. We investigated whether allelic variation at the circadian rhythm genes, OtsClock1a and OtsClock1b, underlies genetic control of migration timing among 42 populations in North America. We identified eight length variants of the functionally important polyglutamine repeat motif (PolyQ) of OtsClock1b while OtsClock1a PolyQ was highly conserved. We found evidence of a latitudinal cline in average allele length and frequency of the two most common OtsClock1b alleles. The shorter 335 bp allele increases in frequency with decreasing latitude while the longer 359 bp allele increases in frequency at higher latitudes. Comparison to 13 microsatellite loci showed that 335 and 359 bp deviate significantly from neutral expectations. Furthermore, a hierarchical gene diversity analysis based on OtsClock1b PolyQ variation revealed that run timing explains 40.9 per cent of the overall genetic variance among populations. By contrast, an analysis based on 13 microsatellite loci showed that run timing explains only 13.2 per cent of the overall genetic variance. Our findings suggest that length polymorphisms in OtsClock1b PolyQ may be maintained by selection and reflect an adaptation to ecological factors correlated with latitude, such as the seasonally changing day length.     

The importance of zooplankton in the diets of three native fish species in floodplain waterholes of a dryland river,the Macintyre River,Australia

The zooplankton of freshwater systems has been recognized as an important energy resource for fish of small body size that, in turn, provide energy to piscivorous fish consumers higher up the food web. This study evaluates the importance of zooplankton to the diets of three species of fish living in floodplain waterholes of an Australian dryland river. The species selected for study represent different trophic categories in waterhole food webs: Ambassis agassizii is a microcarnivore, Leiopotherapon unicolor is an omnivore, and Nematalosa erebi is a detritivore. Dietary differences among size classes of each species were also evaluated to understand possible ontogenetic shifts in zooplankton consumption. Ambassis agassizii fed primarily on zooplankton (99.9%, made up mostly of 81.6% Calanoida and 17.4% Moinidae), regardless of the size of individual fish. Leiopotherapon unicolor fed on zooplankton (47%, mostly Daphniidae and Moinidae) and aquatic insects (46.7%). Smaller individuals of Leiopotherapon unicolor (30–49 mm TL—total length) were responsible for 36.1% of the plankton consumed by the species. Nematalosa erebi fed on detritus (84.6%) with zooplankton (Calanoida, Moinidae, and Cyclopoida) contributing only 13.7% of the mean diet. Smaller individuals (40–69 mm TL) were responsible for 98% of the plankton consumed by Nematalosa erebi, and individuals of 40–49 mm (TL) fed exclusively on zooplankton (53.8% Moinidae and 46.2% Calanoida). Although the three fish species had different diets, reflecting differences in species-specific and ontogenetic morphological and behavioral characteristics, zooplankton formed the basis of the diet of all species when young. These results confirm the importance of zooplankton as a major food resource for three fish species and smaller size classes of these species in floodplain waterholes of the Macintyre River, Australia. Guest editors: U. M. Azeiteiro, I. Jenkinson & M. J. Pereira Plankton Studies