Juvenile coho salmon track a seasonally shifting thermal mosaic across a river floodplain

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How Stock of Origin Affects Performance of Individuals across a Meta-Ecosystem: An Example from Sockeye Salmon

Connectivity among diverse habitats can buffer populations from adverse environmental conditions, influence the functioning of meta-ecosystems, and ultimately affect the reliability of ecosystem services. This stabilizing effect on populations is proposed to derive from complementarity in growth and survival conditions experienced by individuals in the different habitats that comprise meta-ecosystems. Here we use the fine scale differentiation of salmon populations between diverse lake habitats to assess how rearing habitat and stock of origin affect the body condition of juvenile sockeye salmon. We use genetic markers (single nucleotide polymorphisms) to assign individuals of unknown origin to stock group and in turn characterize ecologically relevant attributes across habitats and stocks. Our analyses show that the body condition of juvenile salmon is related to the productivity of alternative habitats across the watershed, irrespective of their stock of origin. Emigrants and residents with genetic origins in the high productivity lake were also differentiated by their body condition, poor and high respectively. These emigrants represented a substantial proportion of juvenile sockeye salmon rearing in the lower productivity lake habitat. Despite emigrants originating from the more productive lake, they did not differ in body condition from the individuals spawned in the lower productivity, recipient habitat. Genetic tools allowed us to assess the performance of different stocks groups across the diverse habitats comprising their meta-ecosystem. The ability to characterize the ecological consequences of meta-ecosystem connectivity can help develop strategies to protect and restore ecosystems and the services they provide to humans.     

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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Juvenile Salmon Usage of the Skeena River Estuary

Migratory salmon transit estuary habitats on their way out to the ocean but this phase of their life cycle is more poorly understood than other phases. The estuaries of large river systems in particular may support many populations and several species of salmon that originate from throughout the upstream river. The Skeena River of British Columbia, Canada, is a large river system with high salmon population- and species-level diversity. The estuary of the Skeena River is under pressure from industrial development, with two gas liquefaction terminals and a potash loading facility in various stages of environmental review processes, providing motivation for understanding the usage of the estuary by juvenile salmon. We conducted a juvenile salmonid sampling program throughout the Skeena River estuary in 2007 and 2013 to investigate the spatial and temporal distribution of different species and populations of salmon. We captured six species of juvenile anadromous salmonids throughout the estuary in both years, and found that areas proposed for development support some of the highest abundances of some species of salmon. Specifically, the highest abundances of sockeye (both years), Chinook in 2007, and coho salmon in 2013 were captured in areas proposed for development. For example, juvenile sockeye salmon were 2–8 times more abundant in the proposed development areas. Genetic stock assignment demonstrated that the Chinook salmon and most of the sockeye salmon that were captured originated from throughout the Skeena watershed, while some sockeye salmon came from the Nass, Stikine, Southeast Alaska, and coastal systems on the northern and central coasts of British Columbia. These fish support extensive commercial, recreational, and First Nations fisheries throughout the Skeena River and beyond. Our results demonstrate that estuary habitats integrate species and population diversity of salmon, and that if proposed development negatively affects the salmon populations that use the estuary, then numerous fisheries would also be negatively affected.     

After 100 years: hydroelectric dam-induced life-history divergence and population genetic changes in sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>)

Understanding the impact of barriers and habitat fragmentation on the ecology and genetics of species is of broad interest to many biologists. In aquatic systems, hydroelectric dams often present an impenetrable barrier to migratory fish and can have negative effects on their persistence. Hydroelectric dams constructed in the Coquitlam and Alouette Rivers in the Fraser River drainage (British Columbia, Canada) in the early 1900s were thought to have led to complete loss of anadromous sockeye salmon from both rivers. For both reservoirs, recent water release programs resulted in the unexpected downstream migration of juvenile sockeye salmon and the subsequent upstream migration of adults towards the reservoir 2 years later. Here we investigate the evolutionary impact of dams on the sockeye salmon migration behavior by investigating the genetic distinction between migratory and non-migratory individuals within the Alouette and Coquitlam reservoirs. We also compare historical and contemporary genetic connectivity among 11 Lower Fraser River sockeye sites to infer recent population connectivity changes that might have been influenced by anthropogenic activities. Our molecular genetic analyses show a genetic distinction between the sea-run and resident individuals from the Coquitlam reservoir and population splitting time estimates suggest a very recent divergence between them. These results indicate a genetic component to migration behavior. For our broader survey from 11 sites, our comparisons suggest a general decline in gene flow, with a few interesting exceptions. In summary, our results suggest (i) early stage divergence between life history forms of sockeye salmon within one reservoir, and (ii) recent changes in genetic connectivity among Lower Fraser River populations; both of these results have potential recovery implications for historically migratory populations that were affected by anthropogenic barriers such as hydroelectric dams.     

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.     

Physiological characterization of juvenile Chinook salmon utilizing different habitats during migration through the Columbia River Estuary

Although off-channel habitats in the estuaries of large rivers impart many benefits to fish that rear within them, it is less clear how these habitats benefit migrating anadromous species that utilize these habitats for short periods of time. We evaluated the physiological correlates (nutritional condition, growth, and smoltification) of habitat utilization (main-channel vs. off-channel) by juvenile Chinook salmon Oncorhynchus tshawytscha during emigration. Fish from the off-channel had higher condition factor scores and relative weights than fish from the main-channel throughout the study period. Plasma triglyceride and protein concentrations were significantly different between habitat types and across the sampling period, suggesting that fish utilizing the off-channel habitats were compensating for energy losses associated with emigration as compared to main-channel fish. Growth potential (RNA to DNA ratio) did not vary by habitat or sampling period, presumably due to short residency time. There were no differences in osmoregulatory capacity (gill Na(+), K(+)-ATPase activity) based on habitat type. Our results indicate that short-term off-channel habitat use may mitigate for energy declines incurred during migration, but likely does not impart significant gains in energy stores or growth.     

Use of glacier river-fed estuary channels by juvenile Coho Salmon: transitional or rearing habitats?

Estuaries are among the most productive ecosystems in the world and provide important rearing environments for a variety of fish species. Though generally considered important transitional habitats for smolting salmon, little is known about the role that estuaries serve for rearing and the environmental conditions important for salmon. We illustrate how juvenile coho salmon Oncorhynchus kisutch use a glacial river-fed estuary based on examination of spatial and seasonal variability in patterns of abundance, fish size, age structure, condition, and local habitat use. Fish abundance was greater in deeper channels with cooler and less variable temperatures, and these habitats were consistently occupied throughout the season. Variability in channel depth and water temperature was negatively associated with fish abundance. Fish size was negatively related to site distance from the upper extent of the tidal influence, while fish condition did not relate to channel location within the estuary ecotone. Our work demonstrates the potential this glacially-fed estuary serves as both transitional and rearing habitat for juvenile coho salmon during smolt emigration to the ocean, and patterns of fish distribution within the estuary correspond to environmental conditions.     

Inclusion of water temperature in a fuzzy logic Atlantic salmon (Salmo salar) parr habitat model

As water temperature is projected to increase in the next decades and its rise is clearly identified as a threat for cold water fish species, it is necessary to adapt and optimize the tools allowing to assess the quantity and quality of habitats with the inclusion of temperature. In this paper, a fuzzy logic habitat model was improved by adding water temperature as a key determinant of juvenile Atlantic salmon parr habitat quality. First, salmon experts were consulted to gather their knowledge of salmon parr habitat, then the model was validated with juvenile salmon electrofishing data collected on the Sainte-Marguerite, Matapedia and Petite-Cascapedia rivers (Québec, Canada). The model indicates that when thermal contrasts exist at a site, cooler temperature offered better quality of habitat. Our field data show that when offered the choice, salmon parr significantly preferred to avoid both cold areas (<15 °C) and warm areas (>20.5 °C). Because such thermal contrasts were not consistently present among the sites sampled, the model was only validated for less than 60% of the sites. The results nevertheless indicate a significant correlation between median Habitat Quality Index and parr density for the Sainte-Marguerite River (R² = 0.38). A less important, albeit significant (F-test; p = 0.036) relationship was observed for the Petite-Cascapedia river (R² = 0.14). In all instances, the four-variable (depth, velocity, substrate size and temperature) model provided a better explanation of parr density than a similar model excluding water temperature.     

Effects of river temperature and climate warming on stock‐specific survival of adult migrating Fraser River sockeye salmon (Oncorhynchus nerka)

Mean summer water temperatures in the Fraser River (British Columbia, Canada) have increased by ～1.5 °C since the 1950s. In recent years, record high river temperatures during spawning migrations of Fraser River sockeye salmon (Oncorhynchus nerka) have been associated with high mortality events, raising concerns about long‐term viability of the numerous natal stocks faced with climate warming. In this study, the effect of freshwater thermal experience on spawning migration survival was estimated by fitting capture–recapture models to telemetry data collected for 1474 adults (captured in either the ocean or river between 2002 and 2007) from four Fraser River sockeye salmon stock‐aggregates (Chilko, Quesnel, Stellako‐Late Stuart and Adams). Survival of Adams sockeye salmon was the most impacted by warm temperatures encountered in the lower river, followed by that of Stellako‐Late Stuart and Quesnel. In contrast, survival of Chilko fish was insensitive to the encountered river temperature. In all stocks, in‐river survival of ocean‐captured sockeye salmon was higher than that of river‐captured fish and, generally, the difference was more pronounced under warm temperatures. The survival–temperature relationships for ocean‐captured fish were used to predict historic (1961–1990) and future (2010–2099) survival under simulated lower river thermal experiences for the Quesnel, Stellako‐Late Stuart and Adams stocks. A decrease of 9–16% in survival of all these stocks was predicted by the end of the century if the Fraser River continues to warm as expected. However, the decrease in future survival of Adams sockeye salmon would occur only if fish continue to enter the river abnormally early, towards warmer periods of the summer, as they have done since 1995. The survival estimates and predictions presented here are likely optimistic and emphasize the need to consider stock‐specific responses to temperature and climate warming into fisheries management and conservation strategies.     

Spawning tactics of summer chum salmon Oncorhynchus keta in relation to channel complexity and hyporheic exchange

Vertical hydraulic gradient, channel hydraulic, and substratum data were collected at active chum salmon redds to evaluate their influence on redd site selection in the Kwethluk River, a wandering gravel-bedded tributary of Alaska’s Lower Kuskokwim River. Two distinct summer chum salmon spawning tacitcs: primary- and off-channel groups spawning in different hydraulic and thermal environments. Channel hydraulics, ground-surface water exchanges, and bed sediment data were collected throughout the range of topographic conditions at sites occupied and unoccupied by spawners. Analyses of these data showed that redd site selection was incoherent with channel hydraulics and substratum size, when all channel types were considered. Rather, spawning was associated with the exchange of river and groundwater at four spatial scales. In primary channels, chum salmon spawned only in reaches where the regional hydraulic gradient (regional scale) promoted the penetration of river water, or downwelling, into the bed sediments. Within these reaches, primary-channel spawning was influenced by bed topography (fluvial scale) that promoted strong localized downwelling; a logit model, fitted to constituent hydraulics, discriminated between selected and unselected sites with 89 % accuracy. In contrast, spawners in off-channel habitats (flood and spring channels) selected areas of upwelling groundwater, regardless of channel hydraulics and the regional hydraulic gradient. In parafluvial flood channels, spawners selected localized upwelling associated with short groundwater flow paths (parafluvial scale). In spring channels, within the floodplain’s forested riparia (orthofluvial scale), spawners eschewed areas of localized downwelling and uniformly selected upwelling zones feeding these channels. Thus, redd selectivity differentiated two spawning tactics (groups) in this complex channel network where ground and surface water exchange is an important predictor of spawning habitat.     

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.     

Methemoglobin reductase activity in fish erythrocytes

NADH-methemoglobin reductase activity of erythrocytes from the coho salmon, Oncorhynchus kisutch, sockeye salmon, Oncorhynchus nerka, and the rainbow trout, Salmo gairdneri exhibited a major band of activity that resembled the human enzyme in electrophoretic mobility. No polymorphism was found in 35 samples from rainbow trout, 4 samples from Dolly Varden, 29 samples from sockeye salmon, and 24 samples from coho salmon. All samples differed from the human enzyme in that they appeared to be membrane-bound and required the presence of a detergent, Triton X-100, for solubilization. Rainbow trout and coho salmon enzymatic activity is greater than the human enzyme activity at 15 degrees C.     

Idiosyncratic responses of Pacific salmon species to land cover,fragmentation, and scale

Salmon are critical to the ecology and livelihood of the Pacific Northwest, and are declining throughout much of their range. While much of their life cycle occurs in open ocean, freshwater conditions also contribute to population trends. Because stream habitats are connected to uplands by water flow, salmon can be influenced by the characteristics of terrestrial systems. We analyzed the relationships between the population trends of Pacific salmon (1953–2006) and land cover, fragmentation, and forest age derived from remotely‐sensed, landscape level datasets. Analyses included 425 populations of all native salmon species in 156 watersheds on Vancouver Island, British Columbia, Canada. Vancouver Island salmon escapements exhibited general patterns of decline, which may be largely controlled by broad‐scale marine conditions. The spatial variation in these population trends was related to landscape variables at watershed and riparian scales with regression trees. Results were found to be species specific, but characteristics indicating a legacy of historic and current forest management (such as fragmented forests and non‐forested or early‐successional forest cover) generally had negative effects, driven by a small subset of highly fragmented watersheds. Chum and coho had strong negative relationships with fragmentation, pink had a strong positive relationship with wetland abundance, and Chinook and sockeye were most closely related to geomorphology. There was no ‘single best’ scale of analysis. Salmon trends were generally more closely related to variables estimated over the entire watershed, however, the relative importances of watershed and riparian level predictors varied by both variable and species. Efforts to restore salmon habitat will be complicated by marine and freshwater processes, terrestrial conditions throughout watersheds, and the idiosyncratic requirements of each species.     

Climate variation is filtered differently among lakes to influence growth of juvenile sockeye salmon in an Alaskan watershed

The physical landscape filters regional climate variation such that the environmental conditions an organism experiences are unique to the characteristics of local habitat features. While it has become apparent that populations may show watershed‐specific responses to changing climate within a geographic region, the population dynamics of Pacific salmon Oncorhynchus spp. suggest that within watershed climate filtering is also important. Growth provides an integrated measure of habitat quality capturing the overall response of individuals to climate as filtered by their habitat and their response to the biological interactions in the ecosystem. We used two different long‐term datasets, scales from returning adults and juvenile length measurements, to assess the response of sockeye salmon O. nerka growth during their juvenile life phase to single and integrated measures of climate within a watershed between 1950 and 2010. Scale growth showed evidence for differences among stocks rearing in different lake habitats within the same Alaska Peninsula watershed. These lakes have substantially different morphometry and showed opposite responses to changes in spring and fall air temperatures. Juvenile length data were also available for one of these stocks and indicated that density effects were relatively weak in contrast to the effects of temperature. While direct measures of juvenile length and measures derived from adult scales showed some similarity in their trends over time, they indicated opposite effects of air temperature. Throughout the range of Pacific salmon, climate change is altering freshwater ecosystems through changes to temperature, precipitation and associated variables. These data suggest that sockeye salmon populations are experiencing climate filtering at a sub‐watershed scale. Maintaining connected, heterogeneous landscapes will therefore likely be important for providing productive habitat for sockeye salmon across a range of climate conditions that they are going to experience under new climate regimes.     

Recent local adaptation of sockeye salmon to glacial spawning habitats

Salmonids spawn in highly diverse habitats, exhibit strong genetic population structuring, and can quickly colonize newly created habitats with few founders. Spawning traits often differ among populations, but it is largely unknown if these differences are adaptive or due to genetic drift. To test if sockeye salmon (Oncorhynchus nerka) populations are adapted to glacial, beach, and tributary spawning habitats, we examined variation in heritable phenotypic traits associated with spawning in 13 populations of wild sockeye salmon in Lake Clark, Alaska. These populations were commonly founded between 100 and 400 hundred sockeye salmon generations ago and exhibit low genetic divergence at 11 microsatellite loci (F _ST < 0.024) that is uncorrelated with spawning habitat type. We found that mean P _ST (phenotypic divergence among populations) exceeded neutral F _ST for most phenotypic traits measured, indicating that phenotypic differences among populations could not be explained by genetic drift alone. Phenotypic divergence among populations was associated with spawning habitat differences, but not with neutral genetic divergence. For example, female body color was lighter and egg color was darker in glacial than non-glacial habitats. This may be due to reduced sexual selection for red spawning color in glacial habitats and an apparent trade-off in carotenoid allocation to body and egg color in females. Phenotypic plasticity is an unlikely source of phenotypic differences because Lake Clark sockeye salmon spend nearly all their lives in a common environment. Our data suggest that Lake Clark sockeye salmon populations are adapted to spawning in glacial, beach and tributary habitats and provide the first evidence of a glacial spawning ecotype in salmonids. Glacial spawning habitats are often young (i.e., <200 years old) and ephemeral. Thus, local adaptation of sockeye salmon to glacial habitats appears to have occurred recently.     

Thermal habitat of adult Atlantic salmon Salmo salar in a warming ocean

The year-round thermal habitat at sea for adult Atlantic salmon Salmo salar (n = 49) from northern Norway was investigated using archival tags over a 10 year study period. During their ocean feeding migration, the fish spent 90% of the time in waters with temperatures from 1.6–8.4°C. Daily mean temperatures ranged from −0.5 to 12.9°C, with daily temperature variation up to 9.6°C. Fish experienced the coldest water during winter (November–March) and the greatest thermal range during the first summer at sea (July–August). Trends in sea-surface temperatures influenced the thermal habitat of salmon during late summer and autumn (August–October), with fish experiencing warmer temperatures in warmer years. This pattern was absent during winter (November–March), when daily mean temperatures ranged from 3.4–5.0°C, in both colder and warmer years. The observations of a constant thermal habitat during winter in both warmer and colder years, may suggest that the ocean distribution of salmon is flexible and that individual migration routes could shift as a response to spatiotemporal alterations of favourable prey fields and ocean temperatures.     

Can intense predation by bears exert a depensatory effect on recruitment in a Pacific salmon population?

It has long been recognized that, as populations increase in density, ecological processes affecting growth and survival reduce per capita recruitment in the next generation. In contrast to the evidence for such “compensatory” density dependence, the alternative “depensatory” process (reduced per capita recruitment at low density) has proven more difficult to demonstrate in the field. To test for such depensation, we measured the spawner–recruit relationship over five decades for a sockeye salmon (Oncorhynchus nerka) population in Alaska breeding in high-quality, unaltered habitat. Twenty-five years of detailed estimates of predation by brown bears, Ursus arctos, revealed strong density dependence in predation rate; the bears killed ca. 80 % of the salmon in years of low salmon spawning abundance. Nevertheless, the reconstructed spawner–recruit relationship, adjusted to include salmon intercepted in the commercial fishery, provided no evidence of demographic depensation. That is, in years when few salmon returned and the great majority were killed by bears, the few that spawned were successful enough that the population remained highly productive, even when those killed by bears were included as potential spawners. We conclude that the high quality of breeding habitat at this site and the productive nature of semelparous Pacific salmon allowed this population to avoid the hypothesized depressed recruitment from depensatory processes expected at low density. The observed lack of demographic depensation is encouraging from a conservation standpoint because it implies that depleted populations may have the potential to rebound successfully given suitable spawning and rearing habitat, even in the presence of strong predation pressure.     

Immediate response of fish communities and water chemistry to causeway breaching and bridge installation in the Kaouk River estuary,British Columbia,Canada

The Kaouk River estuary is located on the northwest coast of Vancouver Island, British Columbia, Canada, in the Treaty Settlement Lands of the Ka:'yu:'k't'h'/Che:k'tles7et'h First Nations. Stretching across the widest point of this estuary is a causeway providing road access to Fair Harbour. This causeway was observed to decrease habitat connectivity throughout the estuary, specifically limiting juvenile salmon access to high‐quality rearing habitat in the tidal marsh. As such, the causeway was breached in 2019 and a bridge was installed. Juvenile salmon were observed using the new connection and were captured both up and downstream of the causeway immediately following breaching. Postbreach water chemistry (dissolved oxygen, pH, salinity, and temperature) near the causeway was recorded within the range of values observed throughout the estuary. Use of the breach by juvenile salmon and homogenized water chemistry indicate the project succeeded in improving habitat connectivity within the Kaouk River estuary and has enhanced juvenile salmon access to 2.7 km² of wetland rearing habitat.     

Amino acid cues emanating from Pacific salmon eggs and ovarian fluid

The eggs of salmonid fishes are an important food source for many aquatic predators that detect eggs using olfaction. Moreover, chemicals from eggs and ovarian fluid aid sperm cells in detecting and locating eggs for fertilization, and ovarian fluid is attractive to conspecific males. Thus chemicals from eggs and ovarian fluid may facilitate reproduction but may also attract egg predators. The authors sampled mature females of three Pacific salmon species – Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch) and sockeye (Oncorhynchus nerka) – and determined the proportional representation of amino acids, potent fish odorants, from their eggs and ovarian fluid (Chinook and coho salmon only). They then tested juvenile coho salmon, an egg predator, for responses to ovarian fluid and egg odours using the electro-olfactogram (EOG) recording technique. The amino acid compositions of the salmon species were significantly and positively correlated with each other, and the interspecific differences were comparable to those between individuals of the same species. The egg water samples were, on average, dominated by lysine, alanine and glutamine (12.6%, 12.4% and 10.9%, respectively). The ovarian fluid samples were dominated by lysine (20.5%), followed by threonine (9.7%), glycine (9.2%) and arginine (8.8%). EOG recordings demonstrated the ability of juvenile coho salmon to detect the chemical traces of eggs and ovarian fluid. It is concluded that salmon eggs are a potent source of odours for potential predators but likely not highly differentiated among salmon species.