Sockeye Salmon Oncorhynchus Nerka Research Articles

Establishing present‐day Sockeye Salmon (Oncorhynchus nerka|sćwin) spawning capacity in the highly impacted sq,awsitkʷ|Okanagan River to guide population conservation and restoration

AbstractThe presence of dams on the Columbia River (CR) has reduced Sockeye Salmon (Oncorhynchus nerka|sćwin) numbers to a fraction of their historic numbers. The Syilx Okanagan Nation Alliance (SONA) has led voices of concern regarding the impacts of diminishing Sockeye Salmon numbers on the ecosystem health of the sawsitkʷ|Okanagan River (s|OR), a tributary of the CR. In the early 2000s efforts commenced to rehabilitate the s|OR Sockeye population. These efforts have seen the population rise from a running average of 40,000 to 200,000. However, the contemporary spawning capacity of the s|OR is unknown, and this metric is critical to guide the conservation and restoration of this keystone species. We employed a spawning capacity model relating fish length and gravel size to spawning potential. We collected substrate data at 49 sites throughout our 37‐km study area, and used fish length and egg numbers from n = 269 Sockeye Salmon to establish s|OR specific fecundity metrics. The model estimated the s|OR has the capacity to support 147,687 (±33,346) Sockeye spawners, in its current condition. Whilst our model has limitations, we suggest a minimum escapement of 147,687 Sockeye spawners ought to be passed to the s|OR per annum. These fish will have broad ecosystem benefits and will be culturally beneficial to SONA peoples. Finally, continued restoration of s|OR habitat should enhance opportunities for Sockeye Salmon to continue their remarkable recovery.

Opening a can of worms: Archived canned fish fillets reveal 40 years of change in parasite burden for four Alaskan salmon species.

How has parasitism changed for Alaskan salmon over the past several decades? Parasitological assessments of salmon are inconsistent across time, and though parasite data are sometimes noted when processing fillets for the market, those data are not retained for more than a few years. The landscape of parasite risk is changing for salmon, and long-term data are needed to quantify this change. Parasitic nematodes of the family Anisakidae (anisakids) use salmonid fishes as intermediate or paratenic hosts in life cycles that terminate in marine mammal definitive hosts. Alaskan marine mammals have been protected since the 1970s, and as populations recover, the density of definitive hosts in this region has increased. To assess whether the anisakid burden has changed in salmonids over time, we used a novel data source: salmon that were caught, canned, and thermally processed for human consumption in Alaska, USA. We examined canned fillets of chum (Oncorhynchus keta, n = 42), coho (Oncorhynchus kisutch, n = 22), pink (Oncorhynchus gorbuscha, n = 62), and sockeye salmon (Oncorhynchus nerka, n = 52) processed between 1979 and 2019. We dissected each fillet and quantified the number of worms per gram of salmon tissue. Anisakid burden increased over time in chum and pink salmon, but there was no change in sockeye or coho salmon. This difference may be due to differences in the prey preferences of each species, or to differences in the parasite species detected across hosts. Canned fish serve as a window into the past, providing information that would otherwise be lost, including information on changes over time in the parasite burden of commercially, culturally, and ecologically important fish species.

Biological and environmental covariates of juvenile sockeye salmon distribution and abundance in the southeastern Bering Sea, 2002-2018.

Climate change is altering the distribution and abundance of marine species, especially in Arctic and sub-Arctic regions. In the eastern Bering Sea, home of the world's largest run of sockeye salmon (Oncorhynchus nerka), juvenile sockeye salmon abundance has increased and their migration path shifted north with warming, 2002-2018. The reasons for these changes are poorly understood. For these sockeye salmon, we quantify environmental and biological covariate effects within spatio-temporal species distribution models. Spatio-temporally, with respect to juvenile sockeye salmon densities: (1) sea surface temperature had a nonlinear effect, (2) large copepod, Calanus, a minor prey item, had no effect, (3) age-0 pollock (Gadus chalcogrammus), a major prey item during warm years, had a positive linear effect, and (4) juvenile pink salmon (O. gorbuscha) had a positive linear effect. Temporally, annual biomass of juvenile sockeye salmon was nonlinearly related to sea temperature and positively related to age-0 pollock and juvenile pink salmon abundance. Results indicate that sockeye salmon distributed with and increased in abundance with increases in prey, and reached a threshold for optimal temperatures in the eastern Bering Sea. Changes in population dynamics and distribution of sockeye salmon in response to environmental variability have potential implications for projecting specific future food securities and management of fisheries in Arctic waters.

Assessing the impacts of environmental and ecological variables on the performance of Fraser sockeye salmon forecast

The Canadian Fraser River sockeye salmon ( Oncorhynchus nerka) is one of the largest stock complexes in North America, supporting major commercial, recreational, and First Nations fisheries. Sockeye fisheries management relies on an annual pre-season forecast of adult returns. In this study, we developed a comprehensive framework for visualization with a Taylor diagram to evaluate pre-season forecast models annually and identify external drivers important for forecasting sockeye returns. Specifically, we incorporated five new covariates, including sea surface temperature in the Gulf of Alaska and the abundance of salmon species, into the existing forecast models. Results revealed better performances by both the Ricker and Power models when coupled with the newly included covariates. Moreover, models selected over a decade ago underperformed compared to those selected based on our recent retrospective analysis from 2009 to 2020. We advocate for continuous evaluation of forecast models in the face of environmental change, emphasizing the necessity of developing models that incorporate non-stationary processes and assess the impacts of environmental and ecological factors on Fraser sockeye dynamics.

Variability of biological indices and abundance dynamics of the Ozernaya River sockeye salmon Oncorhynchus nerka (Walbaum) stock in the modern period (1971–2020)

Results of analyzing the spawning sockeye salmon age structure, length-weight composition and absolute fecundity are demonstrated for the Ozernaya River stock. In the course of maturation the sockeye salmon individuals can return into the Ozernaya River for spawning in the ages 3+, 4+, 5+, 6+ or 7+. A positive trend has been figured out for relative abundance of the 5+ and 6+ sockeye salmon individuals and generation abundances, a negative trend – for the 4+ individuals. Negative dynamics has described for the averaged length-weight indices and the mean absolute fecundity of sockeye salmon of the Ozernaya in the research period. Patterns of changes in biological indicators of the fi sh depending on density factors in the period1971–2020 have been identified.

Genetic features of the island populations of sockeye salmon Oncorhynchus nerka (Walbaum, 1792) in Russian part of the species range

Sockeye salmon genetic diversity in the Kuril Islands (Iturup, Urup, Paramushir, Shumshu) and the Commander Islands (Bering Island) was examined on 7 microsatellite loci. Average estimates of the heterozygocity observed on different loci vary from 0.300 to 0.858. General estimate of genetic differentiation θst is 15%, with a 95% confidence bootstrap interval [10.40–21.18%]. The results obtained in the program BOTTLENECK 1.2.02 made it possible to identify the passage of the “bottle neck” by all island populations. Unique properties and significant differences from each other are shown for allfivчe populations examined. The level of sockeye salmon intrapopulation diversity found in the Kuril and Commander Islands is significantly lower compared to that in the continental water bodies, what is generally typical for marginal populations of the species range.

Physiological condition infers habitat choice in juvenile sockeye salmon.

The amount of time that juvenile salmon remain in an estuary varies among and within populations, with some individuals passing through their estuary in hours while others remain in the estuary for several months. Underlying differences in individual physiological condition, such as body size, stored energy and osmoregulatory function, could drive individual variation in the selection of estuary habitat. Here we investigated the role of variation in physiological condition on the selection of estuarine and ocean habitat by sockeye salmon (Oncorhynchus nerka) smolts intercepted at the initiation of their 650-km downstream migration from Chilko Lake, Fraser River, British Columbia (BC). Behavioural salinity preference experiments were conducted on unfed smolts held in fresh water at three time intervals during their downstream migration period, representing the stage of migration at lake-exit, and the expected timing for estuary-entry and ocean-entry (0, 1 and 3 weeks after lake-exit, respectively). In general, salinity preference behaviour varied across the three time periods consistent with expected transition from river to estuary to ocean. Further, individual physiological condition did influence habitat choice. Smolt condition factor (K) and energy density were positively correlated with salinity preference behaviour in the estuary and ocean outmigration stages, but not at lake-exit. Our results suggest that smolt physiological condition upon reaching the estuary could influence migratory behaviour and habitat selection. This provides evidence on the temporally dependent interplay of physiology, behaviour and migration in wild juvenile Pacific salmon, with juvenile rearing conditions influencing smolt energetic status, which in turn influences habitat choice during downstream migration. The implication for the conservation of migratory species is that the relative importance of stopover habitats may vary as a function of initial condition.

Habitat modulates population-level responses of freshwater salmon growth to a century of change in climate and competition.

The impacts of climate change are widespread and threaten natural systems globally. Yet, within regions, heterogeneous physical landscapes can differentially filter climate, leading to local response diversity. For example, it is possible that while freshwater lakes are sensitive to climate change, they may exhibit a diversity of thermal responses owing to their unique morphology, which in turn can differentially affect the growth and survival of vulnerable biota such as fishes. In particular, salmonids are cold-water fishes with complex life histories shaped by diverse freshwater habitats that are sensitive to warming temperatures. Here we examine the influence of habitat on the growth of sockeye salmon (Oncorhynchus nerka) in nursery lakes of Canada's Skeena River watershed over a century of change in regional temperature and intraspecific competition. We found that freshwater growth has generally increased over the last century. While growth tended to be higher in years with relatively higher summer air temperatures (a proxy for lake temperature), long-term increases in growth appear largely influenced by reduced competition. However, habitat played an important role in modulating the effect of high temperature. Specifically, growth was positively associated with rising temperatures in relatively deep (>50 m) nursery lakes, whereas warmer temperatures were not associated with a change in growth for fish among shallow lakes. The influence of temperature on growth also was modulated by glacier extent whereby the growth of fish from lakes situated in watersheds with little (i.e., <5%) glacier cover increased with rising temperatures, but decreased with rising temperatures for fish in lakes within more glaciated watersheds. Maintaining the integrity of an array of freshwater habitats-and the processes that generate and maintain them-will help foster a diverse climate-response portfolio for important fish species, which in turn can ensure that salmon watersheds are resilient to future environmental change.

Brown bear (Ursus arctos) foraging in a mosaic of spatially discrete and variable habitats over 25 years of shifting Pacific salmon densities

Many foraging models assume “perfect information” and “free movement” when describing predator foraging behavior, although this is rare in nature. Here, we quantified predation by brown bears ( Ursus arctos Linnaeus, 1758) on adult sockeye salmon ( Oncorhynchus nerka (Walbaum, 1792)) in a series of spatially proximate ponds that largely satisfied both assumptions. Salmon abundance varied among years, but pond area and depth were fixed, allowing us to examine interactions between prey abundance and habitat features. We applied versions of two models to 25 years of data on the number and proportion of salmon killed by bears, modifying these models to include habitat features and temporal variability. The functional response model with a year effect fit the data well, indicating bears could take almost all salmon in ponds when salmon were scarce, but bears were sated when salmon were abundant. The proportion of salmon killed by bears was similar across habitats after correcting for pond depth and area. Overall, bears foraged across all habitats but killed higher proportions of salmon in smaller and shallower habitats, consistent with ease of capture.

Genomic vulnerability of a freshwater salmonid under climate change.

Understanding the adaptive potential of populations and species is pivotal for minimizing the loss of biodiversity in this era of rapid climate change. Adaptive potential has been estimated in various ways, including based on levels of standing genetic variation, presence of potentially beneficial alleles, and/or the severity of environmental change. Kokanee salmon, the non-migratory ecotype of sockeye salmon (Oncorhynchus nerka), is culturally and economically important and has already been impacted by the effects of climate change. To assess its climate vulnerability moving forward, we integrated analyses of standing genetic variation, genotype-environment associations, and climate modeling based on sequence and structural genomic variation from 224 whole genomes sampled from 22 lakes in British Columbia and Yukon (Canada). We found that variables for extreme temperatures, particularly warmer temperatures, had the most pervasive signature of selection in the genome and were the strongest predictors of levels of standing variation and of putatively adaptive genomic variation, both sequence and structural. Genomic offset estimates, a measure of climate vulnerability, were significantly correlated with higher increases in extreme warm temperatures, further highlighting the risk of summer heat waves that are predicted to increase in frequency in the future. Levels of standing genetic variation, an important metric for population viability and resilience, were not correlated with genomic offset. Nonetheless, our combined approach highlights the importance of integrating different sources of information and genomic data to formulate more comprehensive and accurate predictions on the vulnerability of populations and species to future climate change.

Hydrothermal impacts of water release on early life stages of white sturgeon in the Nechako river, B.C. Canada

Water temperature plays a crucial role in the physiology of aquatic species, particularly in their survival and development. Thus, resource programs are commonly used to manage water quality conditions for endemic species. In a river system like the Nechako River system, central British Columbia, a water management program was established in the 1980s to alter water release in the summer months to prevent water temperatures from exceeding a 20 °C threshold downstream during the spawning season of Sockeye salmon (Oncorhynchus nerka). Such a management regime could have consequences for other resident species like the white sturgeon (Acipenser transmontanus). Here, we use a hydrothermal model and white sturgeon life stage-specific experimental thermal tolerance data to evaluate water releases and potential hydrothermal impacts based on the Nechako water management plan (1980–2019). Our analysis focused mainly on the warmest five-month period of the year (May to September), which includes the water release management period (July–August). Our results show that the thermal exposure risk, an index that measures temperature impact on species physiology of Nechako white sturgeon across all early life stages (embryo, yolk-sac larvae, larvae, and juvenile) has increased substantially, especially in the 2010s relative to the management program implementations’ first decade (the 1980s). The embryonic life stage was the most impacted, with a continuous increase in potential adverse thermal exposure in all months examined in the study. We also recorded major impacts of increased thermal exposure on the critical habitats necessary for Nechako white sturgeon recovery. Our study highlights the importance of a holistic management program with consideration for all species of the Nechako River system and the merit of possibly reviewing the current management plan, particularly with the current concerns about climate change impacts on the Nechako River.

Using repeat injury assessments in adult sockeye salmon (Oncorhynchus nerka) to predict spawning success and describe severity of migration conditions

Pacific salmon (Oncorhynchus spp.) are semelparous and anadromous, and during their up-river migration to spawn can experience injuries and mortality from fisheries interactions and adverse environmental conditions. There is the potential to improve models used to predict those losses by including information on surficial fish condition, but for this information to be useful, we need to understand how injuries change over time, and how injury type influences this change. To do this, we used repeated individual assessments to examine whether injuries accrued during migration on Fraser River sockeye salmon (O. nerka), assessed in the last leg of their migration or on arrival at the spawning grounds, could be used to predict their final injury score at death after spawning. We found that injury scores increased over the spawning period, but this was not driven by any specific type of migration-related injury, and fish initially scored as ‘uninjured’ had the largest increase in injury score, indicating a ceiling effect to our scoring method. Females with higher migration-related injury scores were more likely to experience pre-spawn mortality. Initial injury score accrued during migration was positively correlated with final injury score after spawning but only when initially assessed 45 km from the spawning grounds, and females that spawned accrued more injuries than females that did not spawn. Thus our method was able to use pre-spawn injury scores to predict spawning success but was limited in its ability to use post-spawn injury scores to describe severity of migration conditions. This highlights the need to better understand injury and disease dynamics and further refine injury assessment and scoring methods at the individual level if information on surficial fish condition is to be used to either describe or predict migration severity or pre-spawn mortality at the population level.

Metabolic constraints and individual variation shape the trade-off between physiological recovery and antipredator responses in adult sockeye salmon.

Metabolic scope represents the aerobic energy budget available to an organism to perform non-maintenance activities (e.g., escape a predator, recover from a fisheries interaction, compete for a mate). Conflicting energetic requirements can give rise to ecologically relevant metabolic trade-offs when energy budgeting is constrained. The objective of this study was to investigate how aerobic energy is utilized when individual sockeye salmon (Oncorhynchus nerka) are exposed to multiple acute stressors. To indirectly assess metabolic changes in free swimming individuals, salmon were implanted with heart rate biologgers. Animals were then exercised to exhaustion or briefly handled as a control, and allowed to recover from this stressor for 48-h. During the first two hours of the recovery period, individual salmon were exposed to 90ml of conspecific alarm cues or water as a control. Heart rate was recorded throughout the recovery period. Recovery effort and time was higher in exercised fish, relative to control fish, whereas exposure to an alarm cue had no effect on either of these metrics. Individual routine heart rate was negatively correlated with recovery time and effort. Together, these findings suggest that metabolic energy allocation towards exercise recovery (i.e., an acute stressor; handling, chase, etc.) trumps antipredator responses in salmon, although individual variation may mediate this effect at the population level. This article is protected by copyright. All rights reserved.

Changes in infectious agent profiles and host gene expression during spawning migrations of adult sockeye salmon (Oncorhynchus nerka)

During spawning migrations, adult Pacific salmon ( Onco rhynchus spp.) must undergo a suite of morphological and physiological changes to prepare for spawning. Modern genomics approaches can be used to conduct nonlethal assessments of physiology and infectious agent presence in migrating salmon. We investigated gene expression changes and shifts in the prevalence and load of 18 infectious agents in the gill tissue of adult sockeye salmon ( Oncorhynchus nerka) during the final 50 km of their freshwater migration. We found 77% of fish successfully migrated to spawning grounds. Fish exhibited a decrease in thermal stress gene expression following lake migration, consistent with the hypothesized benefits of thermal refugia during spawning migrations. We also found evidence of cooler water selection (∼1.5 °C) during lake migration for fish with higher infection burden, suggesting behavioural changes for fish suffering higher infection burdens and potential benefits of thermal refuges for reducing the negative impacts of infection for migrating salmon. Collectively, our findings provide further evidence that fish behaviourally regulate exposure to stressful conditions such as high temperature that may undermine survival.

A century-long time series reveals large declines and greater synchrony in Nass River sockeye salmon size-at-age

The ability to comprehend the nature of changes in body size is often limited by time series of relatively short duration. Using archival records of 118 573 individual measurements, we developed a 106-year time series of mean size-at-age, by sex, of Nass River sockeye salmon ( Oncorhynchus nerka). Size-at-age declined during the last century in several distinct stanzas. Until the 1930s, there was weak covariation in size-at-age among age classes of both sexes. Thereafter, all time series exhibited a coherent cyclical pattern, superimposed on an underlying decline, reaching smallest average size-at-age in 2019. Age classes sharing the same years of ocean growth had more similar patterns of variation than those sharing a common brood year, suggesting a dominant role of marine life history. Since 1914, mean size-at-age declined from 5% up to 13% depending on age class and sex, resulting in an estimated 7%–19% decline in fecundity, which is likely to reduce the productivity of these populations. In the absence of increased survival, management targets based on fixed adult escapements may result in overexploitation.

Life Cycle Model Reveals Sensitive Life Stages and Evaluates Recovery Options for a Dwindling Pacific Salmon Population

AbstractPopulation models, using empirical survival rate estimates for different life stages, can help managers explore whether various management options could stabilize a declining population or restore it to former levels of abundance. Here we used two decades of data on five life stages of the population of Sockeye SalmonOncorhynchus nerkain the Cedar River to create and parameterize a life cycle model. This formerly large but unproductive population is now in steep decline despite hatchery enhancement. We gathered population‐specific data on survival during five stages: (1) egg to fry, (2) fry to presmolt, (3) presmolt to adult return from the ocean, (4) adult en route from the ocean to the spawning grounds, and (5) reproduction. We ground‐truthed the model to ensure its fit to the data, and then we modified survival and other parameters during various stages to examine future scenarios. Our analyses revealed that low survival of juveniles in Lake Washington (stage 2: averaging only 3% over the past 20 years), survival of adults returning to freshwater to spawn (stage 4), and survival of adults on spawning grounds to reproduce (stage 5) are likely limiting factors. Combined increases in these stages and others (specifically, the proportion of fish taken into the hatchery to be spawned) might also recover the population. As in other integrated hatchery populations, managers must weigh options relating to balancing the fraction of natural‐ and hatchery‐origin fish, and our results showed that increasing the fraction of fish taken into the hatchery alone will not recover the population. Our model brings together population‐specific data to help managers weigh conservation strategies and understand which stages and habitats are most limiting and how much survival must increase to achieve recovery targets. By extension, our analyses also reveal the utility of such models in other cases where stage‐specific data are available.

Evolutionary and Ecological Aspects of the Population Structure Formation of Sockeye Salmon Oncorhynchus nerka (Salmonidae) in Western Kamchatka

—The results of previous studies on the population structure of the sockeye salmon Oncorhynchus nerka of Western Kamchatka are revised based on the analysis of the variability of 45 single nucleotide polymorphism loci using both own data (seven samples from the water bodies of the western coast of the Kamchatka peninsula) and the data obtained by other researchers (seven samples from the basin of Lake Kurilskoye and one sample from the Bystraya River, basin of the Bolshaya River). All materials were re-analyzed to clarify the existing ideas about the origin and formation of the populations of sockeye salmon of the Western Kamchatka complex, as well as to reconstruct the historical and modern demographic and genetic processes that occur in these populations. According to the results of genetic differentiation tests, principal component analysis, and discriminant analysis of the principal components the sample set of lake sockeye salmon from the Ozernaya River (reproduction in the basin of Lake Kurilskoye) and Plotnikova River (predominantly the downstream migrants from Lake Nachikinskoye) differed the most from the other samples, represented mainly by river sockeye salmon. The results of the principal component analysis and the topology of the phylogenetic network for the sample sets from the basin of Lake Kurilskoye revealed their division in accordance with the periods of spawning grounds filling and with the geographical variability of the spawning periods of sockeye salmon in the lake basin.

Identification of upper thermal thresholds during development in the endangered Nechako white sturgeon with management implications for a regulated river.

Climate change-induced warming effects are already evident in river ecosystems, and projected increases in temperature will continue to amplify stress on fish communities. In addition, many rivers globally are impacted by dams, which have many negative effects on fishes by altering flow, blocking fish passage, and changing sediment composition. However, in some systems, dams present an opportunity to manage river temperature through regulated releases of cooler water. For example, there is a government mandate for Kenney dam operators in the Nechako river, British Columbia, Canada, to maintain river temperature <20°C in July and August to protect migrating sockeye salmon (Oncorhynchus nerka). However, there is another endangered fish species inhabiting the same river, Nechako white sturgeon (Acipenser transmontanus), and it is unclear if these current temperature regulations, or timing of the regulations, are suitable for spawning and developing sturgeon. In this study, we aimed to identify upper thermal thresholds in white sturgeon embryos and larvae to investigate if exposure to current river temperatures are playing a role in recruitment failure. We incubated embryos and yolk-sac larvae in three environmentally relevant temperatures (14, 18 and 21°C) throughout development to identify thermal thresholds across different levels of biological organization. Our results demonstrate upper thermal thresholds at 21°C across physiological measurements in embryo and yolk-sac larvae white sturgeon. Before hatch, both embryo survival and metabolic rate were reduced at 21°C. After hatch, sublethal consequences continued at 21°C because larval sturgeon had decreased thermal plasticity and a dampened transcriptional response during development. In recent years, the Nechako river has reached 21°C by the end of June, and at this temperature, a decrease in sturgeon performance is evident in most of the traits measured. As such, the thermal thresholds identified here suggest current temperature regulations may not be suitable for developing white sturgeon and future recruitment.

Evolutionary and Ecological Aspects of the Population Structure Formation of Sockeye Salmon Oncorhynchus nerka (Salmonidae) in Western Kamchatka

The results of previous studies on the population structure of the sockeye salmon Oncorhynchus nerka of Western Kamchatka are revised based on the analysis of the variability of 45 single nucleotide polymorphism loci using both own data (seven samples from the water bodies of the western coast of the Kamchatka peninsula) and the data obtained by other researchers (seven samples from the basin of Lake Kurilskoye and one sample from the Bystraya River, basin of the Bolshaya River). All materials were re-analyzed to clarify the existing ideas about the origin and formation of the populations of sockeye salmon of the Western Kamchatka complex, as well as to reconstruct the historical and modern demographic and genetic processes that occur in these populations. According to the results of genetic differentiation tests, principal component analysis, and discriminant analysis of the principal components the sample set of lake sockeye salmon from the Ozernaya River (reproduction in the basin of Lake Kurilskoye) and Plotnikova River (predominantly the downstream migrants from Lake Nachikinskoye) differed the most from the other samples, represented mainly by river sockeye salmon. The results of the principal component analysis and the topology of the phylogenetic network for the sample sets from the basin of Lake Kurilskoye revealed their division in accordance with the periods of spawning grounds filling and with the geographical variability of the spawning periods of sockeye salmon in the lake basin.

The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid.

Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.