Asynchrony in population dynamics of sockeye salmon in southwest Alaska

Ecologists have examined the synchronization of population dynamics across space as a means to understand how populations respond to climate variation. However, response diversity may reflect important variation among local population dynamics driven by population‐specific responses to regional environmental change. We used long‐term data on sockeye salmon Oncorhynchus nerka from pristine watersheds of southwestern Alaska to show that populations spawning in close proximity (<40 km) to one another have a limited degree of synchrony in their dynamics, even after accounting for density‐dependent processes. In fact, the dynamics of local populations of stream‐spawning sockeye salmon were no more coherent than those of stocks at a much coarser resolution across this region of Alaska. We examined four hypotheses to explain the observed patterns of asynchrony among stream‐spawning populations, and found that populations spawning in dissimilar habitats, and using different nursery lakes were less synchronized in their productivity. Similarity in the age structure of spawning adults was less correlated with synchrony in productivity. These results emphasize the importance of maintaining diverse spawning and rearing habitat for the conservation of Pacific salmon, and should guide conservation planning for Pacific salmon populations in regions where natural dynamics have been altered by habitat loss, hatchery practices, and over‐fishing.     

Climate effects on growth, phenology, and survival of sockeye salmon (Oncorhynchus nerka): a synthesis of the current state of knowledge and future research directions

Sockeye salmon (Oncorhynchus nerka) is one of the most iconic and valued species of Pacific salmon. Various studies have examined the potential effects of future climate change on sockeye salmon, but there is currently no synthesis of the documented effects of climate on this species. In this paper, we present a synthesis of 80 peer-reviewed publications in the English language evaluating the effects of climate on sockeye salmon growth, phenology, and survival. The great majority of studies examined have been conducted with stocks from North America (90?% of studies). Survival (55?%) has been the most frequently studied aspect of the sockeye salmon life history in relation to climate, followed by growth (45?%) and phenology (30?%), with temperature (83.4?%) being the climate-related variable most frequently examined in such studies. Across life stages, the effects of climate-related variables have been most frequently studied on fry (36.3?%) and least studied on spawners (7.5?%). Our synthesis revealed that associations between temperature and growth, phenology, or survival have been uncovered for all the life stages of sockeye salmon, whereas relationships with other climate-related variables have been sparse. There is substantial evidence that sockeye salmon are influenced by thermal conditions experienced at regional, rather than ocean- or continental-wide scales, and that responses to temperature vary among and within stocks. The mechanisms by which climate affect sockeye salmon during the early stages in freshwater and while at sea are still poorly understood and warrant future research. More research on the effects of non-temperature, climate-related variables (e.g. stream flow, ocean pH), inter-generational and carry-over effects of climate, interaction between climate and non-climate stressors, and adaptation to climate change are also needed. Such information will be critical to advance our understanding of how sockeye salmon stocks will fare with future climate change.     

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.     

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.     

Going with the Flow: Spatial Distributions of Juvenile Coho Salmon Track an Annually Shifting Mosaic of Water Temperature

A critical challenge for ecologists is to understand the functional significance of habitat heterogeneity and connectivity for mobile animals. Here, we explore how a thermo-regulating fish responds to annual variation in the spatial patterning of thermal and trophic resources. In a third-order stream in coastal Alaska, juvenile coho salmon forage on sockeye salmon eggs at night in cold water and then move to warmer water to increase their digestive capacity. We mapped the spatial distributions of water temperature, juvenile coho salmon, and spawning sockeye salmon across a 5-year period during which summer discharge varied by greater than fivefold. In low flow years, warm water (9–12°C) was only available in thalweg (that is, main-channel) habitat at least approximately 400 m upstream of the cooler habitat (3–7°C) where sockeye salmon spawned. In high flow years, the entire stream thalweg was isothermal at 7–8°C, but inundated off-channel areas generated warm habitats (9–12°C) laterally adjacent to the downstream regions where sockeye salmon spawned. The daytime spatial distribution of juvenile coho salmon shifted from headwater thalweg habitats in low flow years, to downstream off-channel habitats in high flow years. In all years, the majority of juvenile coho salmon sampled during the daytime were found in warm habitat units without sockeye salmon present, yet they exhibited diet contents comprised virtually entirely of sockeye salmon eggs. Thus, thermoregulatory movements by coho salmon were able to track an annually shifting mosaic of water temperature. Our results demonstrate how the spatial habitat heterogeneity and connectivity of intact floodplains can in turn buffer aquatic organisms from high levels of temporal variation in habitat conditions and resource abundance.     

Watershed‐scale climate influences productivity of Chinook salmon populations across southcentral Alaska

The ecosystems supporting Pacific salmon (Oncorhynchus spp.) are changing rapidly as a result of climate change and habitat alteration. Understanding how—and how consistently—salmon populations respond to changes at regional and watershed scales has major implications for fisheries management and habitat conservation. Chinook salmon (O. tshawytscha) populations across Alaska have declined over the past decade, resulting in fisheries closures and prolonged impacts to local communities. These declines are associated with large‐scale climate drivers, but uncertainty remains about the role of local conditions (e.g., precipitation, streamflow, and stream temperature) that vary among the watersheds where salmon spawn and rear. We estimated the effects of these and other environmental indicators on the productivity of 15 Chinook salmon populations in the Cook Inlet basin, southcentral Alaska, using a hierarchical Bayesian stock‐recruitment model. Salmon spawning during 2003–2007 produced 57% fewer recruits than the previous long‐term average, leading to declines in adult returns beginning in 2008. These declines were explained in part by density dependence, with reduced population productivity following years of high spawning abundance. Across all populations, productivity declined with increased precipitation during the fall spawning and early incubation period and increased with above‐average precipitation during juvenile rearing. Above‐average stream temperatures during spawning and rearing had variable effects, with negative relationships in many warmer streams and positive relationships in some colder streams. Productivity was also associated with regional indices of streamflow and ocean conditions, with high variability among populations. The cumulative effects of adverse conditions in freshwater, including high spawning abundance, heavy fall rains, and hot, dry summers may have contributed to the recent population declines across the region. Identifying both coherent and differential responses to environmental change underscores the importance of targeted, watershed‐specific monitoring and conservation efforts for maintaining resilient salmon runs in a warming world.     

MOLECULAR GENETIC EVIDENCE FOR PARALLEL LIFE-HISTORY EVOLUTION WITHIN A PACIFIC SALMON (SOCKEYE SALMON AND KOKANEE,ONCORHYNCHUS NERKA)

The Pacific salmon Oncorhynchus nerka typically occurs as a sea-run form (sockeye salmon) or may reside permanently in lakes (kokanee) thoughout its native North Pacific. We tested whether such geographically extensive ecotypic variation resulted from parallel evolutionary divergence thoughout the North Pacific or whether the two forms are monophyletic groups by examining allelic variation between sockeye salmon and kokanee at two minisatellite DNA repeat loci and in mitochondrial DNA (mtDNA) Bgl II restriction sites. Our examination of over 750 fish from 24 populations, ranging from Kamchatka to the Columbia River, identified two major genetic groups of North Pacific O. nerka: a “northwestern” group consisting of fish from Kamchatka, western Alaska, and northwestern British Columbia, and a “southern” group consisting of sockeye salmon and kokanee populations from the Fraser and Columbia River systems. Maximum-likelihood analysis accompanied by bootstrapping provided strong support for these two genetic groups of O. nerka; the populations did not cluster by migratory form, but genetic affinities were organized more strongly by geographic proximity. The two major genetic groups resolved in our study probably stem from historical isolation and dispersal of O. nerka from two major Wisconsinan glacial refugia in the North Pacific. There were significant minisatellite DNA allele frequency differences between sockeye salmon and kokanee populations from different parts of the same watershed, between populations spawning in different tributaries of the same lake, and also between sympatric populations spawning in the same stream at the same time. MtDNA Bgl II restriction site variation was significant between sockeye salmon and kokanee spawning in different parts of the same major watershed but not between forms spawning in closer degrees of reproductive sympatry. Patterns of genetic affinity and allele sharing suggested that kokanee have arisen from sea-run sockeye salmon several times independently in the North Pacific. We conclude that sockeye salmon and kokanee are para- and polyphyletic, respectively, and that the present geographic distribution of the ecotypes results from parallel evolutionary origins of kokanee from sockeye (divergences between them) thoughout the North Pacific.     

Juvenile sockeye salmon distribution, size, condition and diet during years with warm and cool spring sea temperatures along the eastern Bering Sea shelf

Interannual variations in distribution, size, indices of feeding and condition of juvenile Bristol Bay sockeye salmon Oncorhynchus nerka collected in August to September (2000–2003) during Bering–Aleutian Salmon International Surveys were examined to test possible mechanisms influencing their early marine growth and survival. Juvenile sockeye salmon were mainly distributed within the southern region of the eastern Bering Sea, south of 57°0' N during 2000 and 2001 and farther offshore, south of 58°0' N during 2002 and 2003. In general, juvenile sockeye salmon were significantly larger ( P < 0·05) and had significantly higher indices of condition ( P < 0·05) during 2002 and 2003 than during 2000 and 2001. The feeding index was generally higher for age 1.0 year sockeye salmon than age 2.0 year during all years. Among-year comparisons suggested that Pacific sand lance Ammodytes hexapterus were important components of the juvenile sockeye salmon diet during 2000 and 2001 (20 to 50% of the mean wet mass) and age 0 year walleye pollock Theragra chalcogramma were important components during 2002 and 2003 (50 to 60% of the mean wet mass). Warmer sea temperatures during spring and summer of 2002 and 2003 probably increased productivity on the eastern Bering Sea shelf, enhancing juvenile sockeye salmon growth.     

The distribution of juvenile Pacific salmon and associated fish species in Lake Sopochnoye,Iturup Island

A single survey using a minnow seine net showed that juvenile chum and sockeye salmon are distributed extremely unevenly along the shoreline of Lake Sopochnoye, on Iturup Island. Young-of-the-year chum salmon aggregate mainly near the estuaries of the rivers that flow into the lake; young-of-the-year and 2-year-old sockeye salmon aggregate closer to the central part of the lake. The distribution of associated fish species is also very uneven, but none of them dominates within the zone of catches; the abundance of each of these species is comparable to that of the juvenile Pacific salmon.     

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.     

Age‐related thermal habitat use by Pacific salmon Oncorhynchus spp.

Age‐related thermal habitat use by sockeye Oncorhynchus nerka, chum Oncorhynchus keta and pink Oncorhynchus gorbuscha salmon was examined using trawl data obtained in spring in the North Pacific Ocean. Thermal habitat use differed by species and age. Larger and older fishes inhabited cooler areas, whereas smaller and younger fishes inhabited warmer areas.     

Comparative anatomy of the dorsal hump in mature Pacific salmon

Mature male Pacific salmon (Genus Oncorhynchus ) demonstrate prominent morphological changes, such as the development of a dorsal hump. The degree of dorsal hump formation depends on the species in Pacific salmon. It is generally accepted that mature males of sockeye (O. nerka ) and pink (O. gorbuscha ) salmon develop most pronounced dorsal humps. The internal structure of the dorsal hump in pink salmon has been confirmed in detail. In this study, the dorsal hump morphologies were analyzed in four Pacific salmon species inhabiting Japan, masu (O. masou ), sockeye, chum (O. keta ), and pink salmon. The internal structure of the dorsal humps also depended on the species; sockeye and pink salmon showed conspicuous development of connective tissue and growth of bone tissues in the dorsal tissues. Masu and chum salmon exhibited less‐pronounced increases in connective tissues and bone growth. Hyaluronic acid was clearly detected in dorsal hump connective tissue by histochemistry, except for in masu salmon. The lipid content in dorsal hump connective tissue was richer in masu and chum salmon than in sockeye and pink salmon. These results revealed that the patterns of dorsal hump formation differed among species, and especially sockeye and pink salmon develop pronounced dorsal humps through both increases in the amount of connective tissue and the growth of bone tissues. In contrast, masu and chum salmon develop their dorsal humps by the growth of bone tissues, rather than the development of connective tissue.     

Thermal adaptation and phenotypic plasticity in a warming world: Insights from common garden experiments on Alaskan sockeye salmon

An important unresolved question is how populations of coldwater‐dependent fishes will respond to rapidly warming water temperatures. For example, the culturally and economically important group, Pacific salmon (Oncorhynchus spp.), experience site‐specific thermal regimes during early development that could be disrupted by warming. To test for thermal local adaptation and heritable phenotypic plasticity in Pacific salmon embryos, we measured the developmental rate, survival, and body size at hatching in two populations of sockeye salmon (Oncorhynchus nerka) that overlap in timing of spawning but incubate in contrasting natural thermal regimes. Using a split half‐sibling design, we exposed embryos of 10 families from each of two populations to variable and constant thermal regimes. These represented both experienced temperatures by each population, and predicted temperatures under plausible future conditions based on a warming scenario from the downscaled global climate model (MIROC A1B scenario). We did not find evidence of thermal local adaptation during the embryonic stage for developmental rate or survival. Within treatments, populations hatched within 1 day of each other, on average, and among treatments, did not differ in survival in response to temperature. We did detect plasticity to temperature; embryos developed 2.5 times longer (189 days) in the coolest regime compared to the warmest regime (74 days). We also detected variation in developmental rates among families within and among temperature regimes, indicating heritable plasticity. Families exhibited a strong positive relationship between thermal variability and phenotypic variability in developmental rate but body length and mass at hatching were largely insensitive to temperature. Overall, our results indicated a lack of thermal local adaptation, but a presence of plasticity in populations experiencing contrasting conditions, as well as family‐specific heritable plasticity that could facilitate adaptive change.     

Stream network geomorphology mediates predicted vulnerability of anadromous fish habitat to hydrologic change in southeast Alaska

In rivers supporting Pacific salmon in southeast Alaska, USA, regional trends toward a warmer, wetter climate are predicted to increase mid‐ and late‐21st‐century mean annual flood size by 17% and 28%, respectively. Increased flood size could alter stream habitats used by Pacific salmon for reproduction, with negative consequences for the substantial economic, cultural, and ecosystem services these fish provide. We combined field measurements and model simulations to estimate the potential influence of future flood disturbance on geomorphic processes controlling the quality and extent of coho, chum, and pink salmon spawning habitat in over 800 southeast Alaska watersheds. Spawning habitat responses varied widely across watersheds and among salmon species. Little variation among watersheds in potential spawning habitat change was explained by predicted increases in mean annual flood size. Watershed response diversity was mediated primarily by topographic controls on stream channel confinement, reach‐scale geomorphic associations with spawning habitat preferences, and complexity in the pace and mode of geomorphic channel responses to altered flood size. Potential spawning habitat loss was highest for coho salmon, which spawn over a wide range of geomorphic settings, including steeper, confined stream reaches that are more susceptible to streambed scour during high flows. We estimated that 9–10% and 13–16% of the spawning habitat for coho salmon could be lost by the 2040s and 2080s, respectively, with losses occurring primarily in confined, higher‐gradient streams that provide only moderate‐quality habitat. Estimated effects were lower for pink and chum salmon, which primarily spawn in unconfined floodplain streams. Our results illustrate the importance of accounting for valley and reach‐scale geomorphic features in watershed assessments of climate vulnerability, especially in topographically complex regions. Failure to consider the geomorphic context of stream networks will hamper efforts to understand and mitigate the vulnerability of anadromous fish habitat to climate‐induced hydrologic change.     

Linking climate change projections for an Alaskan watershed to future coho salmon production

Climate change is predicted to dramatically change hydrologic processes across Alaska, but estimates of how these impacts will influence specific watersheds and aquatic species are lacking. Here, we linked climate, hydrology, and habitat models within a coho salmon (Oncorhynchus kisutch) population model to assess how projected climate change could affect survival at each freshwater life stage and, in turn, production of coho salmon smolts in three subwatersheds of the Chuitna (Chuit) River watershed, Alaska. Based on future climate scenarios and projections from a three‐dimensional hydrology model, we simulated coho smolt production over a 20‐year span at the end of the century (2080–2100). The direction (i.e., positive vs. negative) and magnitude of changes in smolt production varied substantially by climate scenario and subwatershed. Projected smolt production decreased in all three subwatersheds under the minimum air temperature and maximum precipitation scenario due to elevated peak flows and a resulting 98% reduction in egg‐to‐fry survival. In contrast, the maximum air temperature and minimum precipitation scenario led to an increase in smolt production in all three subwatersheds through an increase in fry survival. Other climate change scenarios led to mixed responses, with projected smolt production increasing and decreasing in different subwatersheds. Our analysis highlights the complexity inherent in predicting climate‐change‐related impacts to salmon populations and demonstrates that population effects may depend on interactions between the relative magnitude of hydrologic and thermal changes and their interactions with features of the local habitat.     

Trophic ecology of Pacific salmon (<Emphasis Type="Italic">Oncorhynchus</Emphasis> spp.) in the ocean: a synthesis of stable isotope research

Increasing interest in the marine trophic dynamics of Pacific salmon has been motivated by the recognition of their sensitivity to changing climate and to the competitive effects of hatchery fish on wild stocks. It has become more common to use stable isotopes to supplement traditional diet studies of salmon in the ocean; however, there have been no integrated syntheses of these data to determine whether stable isotope analyses support the existing conventional wisdom of feeding strategies of the Pacific salmon. We performed a meta-analysis of stable isotope data to examine the extent of trophic partitioning among five species of Pacific salmon during their marine lives. Pink, sockeye, and chum salmon showed very high overlap in resource use and there was no consistent evidence for chum relying on alternative food webs dominated by gelatinous zooplankton. δ¹⁵N showed that Chinook and coho salmon fed at trophic levels higher than the other three species. In addition, these two species were distinctly enriched in ¹³C, suggesting more extensive use of coastal food webs compared to the more depleted (pelagic) signatures of pink, sockeye, and chum salmon. This paper presents the first synthesis of stable isotope work on Pacific salmon and provides δ¹⁵N and δ¹³C values applicable to research on the fate of the marine derived nutrients these organisms transport to freshwater and riparian ecosystems.     

Perspectives on wild and hatchery salmon interactions at sea,potential climate effects on Japanese chum salmon,and the need for sustainable salmon fishery management reform in Japan

Pacific salmon (Oncorhynchus spp.) play an important role as a keystone species and provider of ecosystem services in the North Pacific ecosystem. We review our studies on recent production trends, marine carrying capacity, climate effects and biological interactions between wild and hatchery origin populations of Pacific salmon in the open sea, with a particular focus on Japanese chum salmon (O. keta). Salmon catch data indicates that the abundance of Pacific salmon increased since the 1976/77 ocean regime shift. Chum and pink salmon (O. gorbuscha) maintained high abundances with a sharp increase in hatchery-released populations since the late 1980s. Since the 1990s, the biomass contribution of hatchery returns to the total catch amounts to 50% for chum salmon, more than 10% for pink salmon, and less than 10% for sockeye salmon (O. nerka). We show evidence of density-dependence of growth and survival at sea and how it might vary across spatial scales, and we provide some new information on foraging plasticity that may offer new insight into competitive interactions. The marine carrying capacity of these three species is synchronized with long-term patterns in climate change. At the present time, global warming has positively affected growth and survival of Hokkaido populations of chum salmon. In the future, however, global warming may decrease the marine carrying capacity and the area of suitable habitat for chum salmon in the North Pacific Ocean. We outline future challenges for salmon sustainable conservation management in Japan, and recommend fishery management reform to sustain the hatchery-supported salmon fishery while conserving natural spawning populations.     

Patterns on a parr: Drivers of long‐term salmon parr length in U.K. and French rivers depend on geographical scale

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Sea louse infection of juvenile sockeye salmon in relation to marine salmon farms on Canada's west coast

Background

Pathogens are growing threats to wildlife. The rapid growth of marine salmon farms over the past two decades has increased host abundance for pathogenic sea lice in coastal waters, and wild juvenile salmon swimming past farms are frequently infected with lice. Here we report the first investigation of the potential role of salmon farms in transmitting sea lice to juvenile sockeye salmon (Oncorhynchus nerka).

Methodology/Principal Findings

We used genetic analyses to determine the origin of sockeye from Canada''s two most important salmon rivers, the Fraser and Skeena; Fraser sockeye migrate through a region with salmon farms, and Skeena sockeye do not. We compared lice levels between Fraser and Skeena juvenile sockeye, and within the salmon farm region we compared lice levels on wild fish either before or after migration past farms. We matched the latter data on wild juveniles with sea lice data concurrently gathered on farms. Fraser River sockeye migrating through a region with salmon farms hosted an order of magnitude more sea lice than Skeena River populations, where there are no farms. Lice abundances on juvenile sockeye in the salmon farm region were substantially higher downstream of farms than upstream of farms for the two common species of lice: Caligus clemensi and Lepeophtheirus salmonis, and changes in their proportions between two years matched changes on the fish farms. Mixed-effects models show that position relative to salmon farms best explained C. clemensi abundance on sockeye, while migration year combined with position relative to salmon farms and temperature was one of two top models to explain L. salmonis abundance.

Conclusions/Significance

This is the first study to demonstrate a potential role of salmon farms in sea lice transmission to juvenile sockeye salmon during their critical early marine migration. Moreover, it demonstrates a major migration corridor past farms for sockeye that originated in the Fraser River, a complex of populations that are the subject of conservation concern.     

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.