Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (Oncorhynchus mykiss).

Multiple studies in a range of taxa have found links between structural variants and the development of ecologically important traits. Such variants are becoming easier to find due, in large part, to the increase in the amount of genome-wide sequence data in nonmodel organisms. The salmonids (salmon, trout, and charr) are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture, fisheries, and variation in multiple ecologically important life-history traits. Previous research on rainbow trout (Oncorhynchus mykiss) has documented a large pericentric (∼55 Mb) chromosomal inversion (CI) on chromosome 5 (Omy05) and a second smaller (∼14 Mb) chromosome inversion on Omy20. While the Omy05 inversion appears to be associated with multiple adaptive traits, the inversion on Omy20 has received far less attention. In this study, we re-analyze RAD-seq and amplicon data from several populations of rainbow trout (O. mykiss) to better document the structure and geographic distribution of variation in the Omy20 CI. Moreover, we utilize phylogenomic techniques to characterize both the age- and the protein-coding gene content of the Omy20 CI. We find that the age of the Omy20 inversion dates to the early stages of O. mykiss speciation and predates the Omy05 inversion by ∼450,000 years. The 2 CIs differ further in terms of the frequency of the homokaryotypes. While both forms of the Omy05 CI are found across the eastern Pacific, the ancestral version of the Omy20 CI is restricted to the southern portion of the species range in California. Furthermore, the Omy20 inverted haplotype is comparable in genetic diversity to the ancestral form, whereas derived CIs typically show substantially reduced genetic diversity. These data contribute to our understanding of the age and distribution of a large CI in rainbow trout and provide a framework for researchers looking to document CIs in other nonmodel species.

Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish.

Recent work has revealed the importance of contemporary evolution in shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here, we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead and resident rainbow trout (Oncorhynchus mykiss). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident O. mykiss populations may be connected via gene flow, with important ecological consequences. Such eco-evolutionary processes should be considered when managing recently diverged populations connected by gene flow.

Monitoring post-spawning movement, habitat use, and survival of adult anadromous rainbow smelt using acoustic telemetry in a New Hampshire estuary.

Anadromous rainbow smelt (Osmerus mordax, [Mitchill 1814]) are found along the northeast Atlantic coastline of North America, with their range now limited to north of Cape Cod, Massachusetts, USA. Although their anadromous life cycles are described broadly, gaps remain regarding how adult rainbow smelt use estuaries post-spawning, including movement behaviors, habitats used, and specific timing of emigration to coastal waters. In spring 2021, we used acoustic telemetry to characterize movements during and after the spawning season of rainbow smelt captured in tributaries to Great Bay, New Hampshire, USA, a large estuarine system near the southern edge of their range. Forty-four adult rainbow smelt (n = 35 male, n = 9 female) were tagged with Innovasea V5 180-kHz transmitters and an array of 22,180 kHz VR2W receivers were deployed throughout Great Bay to detect movements of tagged fish from March to October 2021. Rainbow smelt were detected 14,186 times on acoustic telemetry receivers, with 41 (93%) of the tagged individuals being detected at least once post-tagging. Individuals were detected moving between tributaries, revealing that rainbow smelt can use multiple rivers during the spawning season (March-April). Mark-recapture Cormack-Jolly-Seber models estimated 83% (95% confidence interval 66%-92%) of rainbow smelt survived to the mainstem Piscataqua River, and a minimum of 50% (22 of 44) reached the seaward-most receivers and were presumed to have survived emigration. Most individuals that survived remained in the estuary for multiple weeks (average = 19.47 ± 1.99 standard error days), displaying extended use of estuarine environments. Downstream movements occurred more frequently during ebb tides and upstream movements with flood tides, possibly a mechanism to reduce energy expenditures. Fish emigrated from the estuary by mid-May to the coastal Gulf of Maine. Our results underscore that rainbow smelt need access to a variety of habitats, including multiple tributaries and high-quality estuarine habitat, to complete their life cycle.

Ancestry and genetic structure of resident and anadromous rainbow trout (Oncorhynchus mykiss) in Argentina.

Since the first introduction from North America more than a century ago, rainbow trout (Oncorhynchus mykiss) have rapidly established self-sustaining populations in major river basins of Patagonia. Many generations later, only the freshwater resident life history is expressed in the Chubut and Negro rivers of northern Argentinian Patagonia, whereas both the resident and anadromous life histories are found in the Santa Cruz River of southern Argentina. Despite previous studies that have tried to identify the sources of these introduced populations, uncertainty still exists. Here we combined data from many single-nucleotide polymorphisms and microsatellite loci in O. mykiss populations from Argentina and North America to evaluate putative source populations, gene flow between Argentinian river basins, and genetic diversity differences between Argentinian and North American populations. We found that populations from northern and southern Patagonia are highly differentiated and have limited gene flow between them. Phylogeographic analysis also confirmed that they have separate origins, with the northern populations most closely related to the domesticated rainbow trout strains that are raised worldwide and the Santa Cruz River populations most closely related to North American populations from California and Oregon that have an anadromous component. In addition, fish with different life histories in the Santa Cruz River were found to constitute a single interbreeding population. No evidence was found of reduced genetic variation in introduced rainbow trout, suggesting multiple contributing sources. In spite of these advances in understanding, significant questions remain regarding the origins and evolution of the introduced O. mykiss in Patagonia.

Balancing risks and rewards of alternate strategies in the seaward extent, duration and timing of fjord use in contemporary anadromy of brown trout (Salmo trutta).

BACKGROUND: Anadromy comprises a successful life-cycle adaptation for salmonids, with marine migration providing improved feeding opportunities and thus improved growth. These rewards are balanced against costs from increased energy expenditure and mortality risk. Anthropogenic-induced environmental changes that reduce benefits and/or increase costs of migration e.g., aquaculture and hydropower, may therefore result in adaptations disfavouring anadromy. We tagged brown trout (Salmo trutta) smolts (N = 175) and veteran migrants (N = 342), from five adjacent riverine populations located in Sognefjorden, the longest Norwegian fjord-system supporting anadromous brown trout populations (209 km). Over four years, 138 acoustic telemetry receivers were deployed to track migrations of tagged individuals from freshwater and throughout Sognefjorden. Detected movements were used to fit migration models and multi-state mark-recapture models of survival and movement for each life-stage. Seaward migration distance was modelled to examine the fitness consequences from alternate migration strategies, with these models used to simulate the extent of fjord-use by individuals and accompanying growth, fecundity and survival consequences. We compared these findings with mark-recapture data collected prior to aquaculture and hydropower development. RESULTS: The telemetry data revealed that the outermost-fjord region was utilised by all populations albeit by few individuals. However, historical recaptures were located at a greater distance from the river mouth (87.7 ± 70.3 km), when compared to maximum migration distances of present-day counterparts (58.6 ± 54.9 km). River of origin influenced observed migratory behaviour and differential survival was estimated for each population and life-stage. The simulations based on telemetry-data models revealed a 30% and 23% difference in survival among populations for smolts and veteran migrants, respectively. At the individual-level, a long-distance migration strategy was rewarded with enhanced fecundity. However, the main contribution to population-level fecundity was overwhelmingly derived from middle-distance migrants, due to higher mortality rates and limited numbers of long-distant migrants. CONCLUSIONS: We conclude that present-day anadromy is precarious, but potential risk varies considerably between life-stages and populations, even within a single fjord system. Our findings suggest that selection for extended migration is under pressure, we therefore stress the importance of monitoring and management actions to secure genetic variation pertinent to preserve fitness gains of anadromy.

Genetic structure of Ponto-Caspian trout populations shows gene flow among river drainages and supports resident Salmo rizeensis as a genetically distinct taxon.

To assess the genetic structure of Ponto-Caspian brown trout (Salmo trutta complex) populations, we analyzed both mitochondrial DNA sequences and genotypes at 10 microsatellite loci of fish caught in the Black Sea and from nine river catchments in Georgia, flowing into either the Black or Caspian seas. The results show that: (1) there is substantial genetic differentiation among Ponto-Caspian trout populations, both among the populations of different nominal species and within those of the same species; (2) the genetic distance between conspecific populations from the Black and Caspian Sea basins exceeds that among the populations within the same basin. Moreover, within drainages, genetic distance correlates with the geographic distance; (3) the Black Sea itself is not a barrier to gene flow among the watersheds draining into the Black Sea; (4) some populations in the headwaters of the rivers draining into the Black Sea Basin fall out of this pattern and likely form a separate, non-anadromous (resident) taxon, previously described from northeastern Turkey as Salmo rizeensis. This hypothesis is supported by mitochondrial DNA phylogeny. The presence of both anadromous and resident populations in a single river basin calls for a substantial re-thinking of speciation patterns and taxonomy of Eurasian brown trout.

Geography, environment, and colonization history interact with morph type to shape genomic variation in an Arctic fish.

Polymorphic species are useful models for investigating the evolutionary processes driving diversification. Such processes include colonization history as well as contemporary selection, gene flow, and genetic drift, which can vary between intraspecific morphs as a function of their distinct life histories. The interactive and relative influence of such evolutionary processes on morph differentiation critically informs morph-specific management decisions and our understanding of incipient speciation. We therefore investigated how geographic distance, environmental conditions, and colonization history interacted with morph migratory capacity in the highly polymorphic fish species, Arctic Charr (Salvelinus alpinus). Using an 87 k SNP chip we genetically characterized recently evolved anadromous, resident, and landlocked charr collected from 45 locations across a secondary contact zone of three charr glacial lineages in eastern Canada. A strong pattern of isolation by distance across all populations suggested geographic distance principally shaped genetic structure. Landlocked populations had lower genetic diversities and higher genetic differentiation than anadromous populations. However, effective population size was generally temporally stable in landlocked populations in comparison to anadromous populations. Genetic diversity positively correlated with latitude, potentially indicating southern anadromous populations' vulnerability to climate change and greater introgression between the Arctic and Atlantic glacial lineages in northern Labrador. Local adaptation was suggested by the observation of several environmental variables strongly associating with functionally relevant outlier genes including a region on chromosome AC21 potentially associated with anadromy. Our results demonstrate that gene flow, colonization history, and local adaptation uniquely interact to influence the genetic variation and evolutionary trajectory of populations.

The Physiological Costs of Reproduction in a Capital Breeding Fish.

AbstractReproduction represents the most energetically demanding period of life for many organisms. Capital breeders, such as anadromous sea trout (Salmo trutta), provide a particularly interesting group of organisms to study within the context of reproduction because they rely on energy stores accrued before breeding to reproduce and sustain all phenotypic and behavioral changes related to reproduction. Energy allocation into current reproduction therefore cannot be mitigated via food intake, resulting in an important life history trade-off. For this reason, exploring indexes related to energetics in salmonids can provide powerful insights into the physiological costs of reproduction. In this study, we sampled blood from and PIT tagged 232 fish captured in the wild before the spawning season. We recaptured and resampled 74 individuals (53 females and 21 males) at the end of the spawning season. Females were further divided into spawning phases (nonspawned, partially spawned, and spawned individuals), though males could not be classified as such. We compared nutritional correlates (triglycerides, cholesterol, calcium, inorganic phosphorus, and total protein), stress correlates (cortisol, sodium, potassium, chloride, and glucose), and indexes of tissue damage (aspartate aminotransferase) between initial capture and recapture as well as among spawning phases in females. We found that nutritional status decreased in all fish throughout the spawning season but that it was substantially lower in females that had spawned. We further found that spawning itself appears stressful, with elevated glucose in partially spawned females and elevated cortisol in male sea trout at recapture. Our findings thus support the idea that the cost of reproduction is energetically high and that incurred stress and a decrease in nutritional status are important physiological costs.

Programmed acoustic tags reveal novel information on late-phase marine life in Atlantic salmon, Salmo salar.

This pilot study used programmed acoustic tags implanted into Salmo salar smolts, in conjunction with an extensive offshore marine receiver array, to investigate late-stage migratory behaviour and survival of returning adult salmon. A total of 100 smolts were tagged in 2020, and a number of individuals were successfully detected as returning adults in 2021. After detection efficiency was accounted for, 5-9 adults were estimated to have returned to the offshore array c. 45 km from the river mouth. A total of three fish were subsequently detected in the river. Losses of between 40% and 66% were evident during the final stages of ocean migration, and one tagged fish provided direct evidence of a predation event.

Spawning migration behaviour of sea trout (Salmo trutta L.) in a boreal river system: effects of flow conditions and obstacles on migratory activity.

In this study, radio telemetry was used to examine the upstream spawning migration behaviour of anadromous brown trout (sea trout), Salmo trutta L., in a boreal river system, the River Isojoki, western Finland. The aim was to study the movement activity and migration characteristics of trout during the upstream spawning migration, as well as to locate the important spawning habitats and study the spawning characteristics. Furthermore, the authors analysed how flow conditions and a hydropower dam, with adjacent fishways, affected the upstream spawning migration. Tagged trout spawned in both the main stem and four tributaries, with spawning taking place from early October to November. The movement activity of radio-tagged trout was influenced by a hydropower dam (Perus dam), with spring migrators spending prolonged periods at the dam area, postponing the migration upstream. Flow conditions affected the total time spent at the dam area, as well as the movement activity in the free-flowing sections above the dam, with increasing flow stimulating activity. In addition, time of river ascent and location of spawning area had a significant effect on the movement activity of tagged trout. These results are further evidence that synergistic effects of flow and migratory obstacles can negatively influence migrations of anadromous fish, regardless of constructed fishways. The management of flow regimes and the efficiency of fishways are vital, as climate change will likely influence the flow and increase the water temperature of boreal river systems, further aggravating issues caused by obstacles.

The speciation of arsenic in the muscle tissue of inland and coastal freshwater fish from a remote boreal region.

Elevated concentrations of total arsenic (As) have been reported in boreal freshwater fish in both human-impacted and relatively pristine areas. We assessed the arsenic speciation profiles in muscle tissue of six fish species (n = 300) sampled from nine locations across a remote freshwater watershed in northern Ontario, Canada, extending from inland headwater lakes to the coastal marine confluence. Of the five arsenic species measured, only arsenobetaine (AsB) and dimethylarsinic acid (DMA) were detected in these fish. Riverine fish had up to 10-fold higher total [As] when compared to lacustrine fish. On average, these riverine fish also had higher percentages of AsB (%AsB, 60 ± 26%) and lower percentages of unmeasured arsenic (%UNM, 20 ± 21%), compared to lacustrine fish (28 ± 18% and 52 ± 21% %AsB and %UNM, respectively). DMA percentages (%DMA) were relatively consistent across the watershed, averaging 20 ± 21% across all fish. We examined ecological drivers of As speciation and found that %AsB increased slightly with fish weight in large-body predatory fish, but not in forage fish or insectivores. Furthermore, %AsB was positively related to trophic elevation (inferred from δ15N) in lacustrine fish across 3 out of 4 communities and within some populations. Lastly, riverine fish with a more marine-based diet had markedly higher %AsB when compared to fish with more freshwater-based diets, indicating an effect of anadromy on arsenic speciation. Overall, knowledge on arsenic speciation in freshwater fish has been limited and these results indicate potential drivers that can be considered in future studies. Furthermore, the absence of toxic inorganic As species in these boreal fish is an important consideration for future environmental monitoring practices and risk assessments, some of which assume 10-20% of total [As] in fish is present as toxic inorganic As. Additional studies on As bioaccumulation and biotransformation are needed in freshwater systems, particularly at the base of aquatic food webs.

In-river behaviour and freshwater return rates of sea trout, Salmo trutta L., from two coastal river populations.

The effective management of anadromous Salmo trutta resources is challenging because long-term data on life history, phenology and survival are sparse and most stocks across the range are highly diverse and data-limited. The current study employed acoustic telemetry to tag 448 sea trout across three life stages, to describe the phenology, spawning behaviour and return rates of smolts, finnock (0+ sea age) and adult (≥1+ sea age) sea trout in two Irish river systems during 2018-2021. Tagged smolts (n = 206) exhibited river to sea transition rates of 78%-92% and a number of surviving smolts returned to their natal river as 0+ sea age finnock, exhibiting overall smolt to finnock return rates of between 6% and 17%. Short-term vagrancy occurred among smolts, and 14 individuals were detected in adjacent non-natal rivers. Finnock tagged during the late summer (n = 205) exhibited a range of behaviours with a minority (<30%) ascending upstream to spawning areas. Tagged adult sea trout (n = 37) ascended upstream to the spawning grounds and between 50% and 80% successfully returned to sea as kelts after spawning. Subsequent return rates of kelts back to the river in the following year ranged from 9% to 40%. The current study indicated that body size was an influential predictor of behaviour and survival across all three life stages. Increased body size was positively associated with marine transition success in smolts, long-term marine survival in kelts and spawning behaviour in finnock. This work further demonstrates the complexity of sea trout life-history dynamics and provides a comparative perspective across different age classes. An understanding of life-history variation, behaviour and survival is fundamental for the successful management and conservation of sea trout stocks.

Surfing the tide: Homeward migration of sea trout (Salmo trutta) in a Patagonian river.

This study evaluates the influence of marine and freshwater conditions on the timing of river entry and upstream migration of sea trout (Salmo trutta) in the Grande River of Tierra del Fuego, Patagonia. We analysed the in-river catch-and-release records from a group of fishing lodges that dominate the Grande River fishery during January-April 2008 (n = 5029 fish) as a function of environmental variables: tidal amplitude, stage in the lunar cycle, river discharge, and river water temperature along the homeward migration season. We discuss the value of the daily catch rate as an abundance index in the Grande river, then analyse the temporal structure of the tidal cycle in the Grande River estuary, a macro-tidal environment with a mean tidal amplitude of 5.7 m, and analyse the fit of a generalized additive model to trout catches on a daily basis in four sections along the river to identify the environmental variables that may affect trout abundance throughout the homeward migration. Fish catches in each section of the river were differentially affected by specific environmental variables: tidal amplitude had a positive and significant effect on catches in the lower river sections, whereas water temperature and river discharge significantly affected catches in upper sections (positive effect of temperature; negative effect of discharge). Catches in the lower section clearly reflect the river entry stage of the homeward migration, with a bi-modal shape significantly correlated with the tidal cycle. The first peak was composed mainly of larger multi-sea-winter trout that move upstream, whereas the second one had a wider range of fish lengths, including a large proportion of small and maybe nonreproductive trout that overwinter in the lower river. Based on our results, we conclude that the large tides in the Grande River estuary strongly affect the river entry timing of sea trout. The underlying mechanisms of this effect may be a combination of increased olfactory recognition and increased tidal transport modulated by the seasonal tidal cycle, which operates on trout during coastal migration to produce the pulses observed in the Grande River sea trout run. In the middle and upper sections of the river, where the tidal effect at river entry was dissipated as upstream migration progressed, trout catches increased with water temperature and decreased with river discharge, which may operate through their influence on in-river migration rate and abundance, but also through changes in catchability.

Sea trout (Salmo trutta) straying rate decreases as distance from river mouth increases.

For both conservation and management purposes, it is important to identify the natal origin of migratory individuals entering a river, particularly in genetically spatially structured species like brown trout (Salmo trutta) where the migrant ecotype (called sea trout) can originate from different populations. Nonetheless, little attention has been paid to the spatial distribution of non-local fish at the level of an entire river catchment. The objective of the study was to quantify the proportion of non-local sea trout entering a river catchment (i.e., straying rate) and estimate the spatial extent of their upstream migration. Here, the authors considered dispersal in three distinct rivers, taking advantage of 10 sampling sites. Sea trout, either trapped or rod-caught, were genotyped and genetically assigned to their source populations using appropriate baselines. Based on 1437 sea trout fish classified as local or non-local, the authors empirically demonstrate that straying rate declines in each river as distance from the coast increases in a non-linear fashion. Straying rate exceeds 50% near the mouth, and then decreases gradually to reach <10% 40-50 km inland. A similar spatial pattern is found in the three rivers investigated suggesting an underlying common behaviour of non-local sea trout. The data and results presented here suggest that straying in is far more constrained spatially than first expected. The majority of non-local sea trout were found within the first 25 km of the estuary in the three rivers investigated.

Escalating the conflict? Intersex genetic correlations influence adaptation to environmental change in facultatively migratory populations.

Males and females are often subject to different and even opposing selection pressures. When a given trait has a shared genetic basis between the sexes, sexual conflict (antagonism) can arise. This can result in significant individual-level fitness consequences that might also affect population performance, whilst anthropogenic environmental change can further exacerbate maladaptation in one or both sexes driven by sexual antagonism. Here, we develop a genetically explicit eco-evolutionary model using an agent-based framework to explore how a population of a facultatively migratory fish species (brown trout Salmo trutta) adapts to environmental change across a range of intersex genetic correlations for migration propensity, which influence the magnitude of sexual conflict. Our modelled focal trait represents a condition threshold governing whether individuals adopt a resident or anadromous (sea migration) tactic. Anadromy affords potential size-mediated reproductive advantages to both males and females due to improved feeding opportunities at sea, but these can be undermined by high background marine mortality and survival/growth costs imposed by marine parasites (sea lice). We show that migration tactic frequency for a given set of environmental conditions is strongly influenced by the intersex genetic correlation, such that one sex can be dragged off its optimum more than the other. When this occurred in females in our model, population productivity was substantially reduced, but eco-evolutionary outcomes were altered by allowing for sneaking behaviour in males. We discuss real-world implications of our work given that anadromous salmonids are regularly challenged by sea lice infestations, which might act synergistically with other stressors such as climate change or fishing that impact marine performance, driving populations towards residency and potentially reduced resilience.

Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss.

Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, whereas others undergo anadromous migration. Because there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous (n = 39) and resident (n = 78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA, with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single-nucleotide polymorphisms that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. Although a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR, and PYD domain-containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.

The Genomic Consistency of the Loss of Anadromy in an Arctic Fish (Salvelinus alpinus).

AbstractThe potentially significant genetic consequences associated with the loss of migratory capacity of diadromous fishes that have become landlocked in freshwater are poorly understood. Consistent selective pressures associated with freshwater residency may drive repeated differentiation both between allopatric landlocked and anadromous populations and within landlocked populations (resulting in sympatric morphs). Alternatively, the strong genetic drift anticipated in isolated landlocked populations could hinder consistent adaptation, limiting genetic parallelism. Understanding the degree of genetic parallelism underlying differentiation has implications for both the predictability of evolution and management practices. We employed an 87k single-nucleotide polymorphism (SNP) array to examine the genetic characteristics of landlocked and anadromous Arctic char (Salvelinus alpinus) populations from five drainages within Labrador, Canada. One gene was detected as an outlier between sympatric, size-differentiated morphs in each of two landlocked lakes. While no single locus differentiated all replicate pairs of landlocked and anadromous populations, several SNPs, genes, and paralogs were consistently detected as outliers in at least 70% of these pairwise comparisons. A significant C-score suggested that the amount of shared outlier SNPs across all paired landlocked and anadromous populations was greater than expected by chance. Our results indicate that despite their isolation, selection due to the loss of diadromy may drive consistent genetic responses in landlocked populations.

An opinion piece: the evolutionary and ecological consequences of changing selection pressures on marine migration in Atlantic salmon.

There are strong signals that the selection forces favouring the expression of long-distance sea migration by Atlantic salmon (Salmo salar) are changing. Unlike many other behavioural traits, the costs of migration are incurred before any fitness benefits become apparent to the migrant. The expression of this behaviour has thus been shaped by selection forces over multiple generations and cannot respond to short interval (within a single generation) environmental change as many other behavioural traits can. Here we provide a framework to examine the evolutionary and ecological consequences of a sustained increase in migration cost. We argue that Atlantic salmon may have entered an evolutionary trap, where long-distance sea migration has become maladaptive because of shifting environmental conditions. We predict that if higher migration costs (affecting survivorship and ultimately fitness) persist, then shifting selection pressures will result in continuing declines in population size. We suggest, however, that in some populations there is demonstrable capacity for evolutionary rescue responses within the species which is to be found in the variation in the expression of migration. Under a scenario of low to moderate change in the selection forces that previously promoted migration, we argue that disruptive, sex-based selection would result in partial migration, where females retain sea migration but with anadromy loss predominantly in males. With more acute selection forces, anadromy may be strongly selected against, under these conditions both sexes may become freshwater resident. We suggest that as the migration costs appear to be higher in catchments with standing waters, then this outcome is more likely in such systems. We also speculate that as a result of the genetic structuring in this species, not all populations may have the capacity to respond adequately to change. The consequences of this for the species and its management are discussed.

Exceptional longevity in a lightly exploited, semi-anadromous clupeid (Perth herring Nematalosa vlaminghi) within a degraded estuarine environment.

Many anadromous (and semi-anadromous) fish species, which migrate from marine to freshwater ecosystems to spawn and to complete their life cycle, are currently threatened by habitat degradation in the upper parts of estuaries and rivers, where spawning and juvenile nursery areas occur. This situation pertains to Nematalosa vlaminghi, a semi-anadromous gizzard shad (Clupeidae: Dorosomatinae) endemic to south-western Australia. More information on the biology of N. vlaminghi is required for its effective management and conservation. This study estimated growth, longevity and natural mortality of N. vlaminghi. Ages were determined by counting validated annual growth increments in thin sections of sagittal otoliths. Fish were sampled in the Swan-Canning Estuary, which historically hosted the main commercial fishery for N. vlaminghi. Since the late 1990s, however, only very minor catches of this species have been taken from this estuary and none since 2007. Given the essentially unexploited state of the current population, the estimate of total mortality (Z, y-1 ) from the catch curve analysis in this study provides a direct estimate of natural mortality (M, y-1 ) for N. vlaminghi. Somatic growth during this study was substantially slower than that historically reported for N. vlaminghi. Various processes operating in this estuary since the 1970s may have contributed to slower growth, including increased hypoxia, higher primary productivity due to eutrophication and cessation of fishing for N. vlaminghi. The maximum observed age of 19.8 years for N. vlaminghi is the highest reported for any gizzard shad globally and one of the highest reported for any clupeid species. This exceptional longevity is likely part of a life-history strategy that allows N. vlaminghi, which exhibits substantial variation in annual recruitment success, to persist in the intermittently closed estuaries of south-western Australia where environmental factors, including low flow and hypoxia, can create unfavourable conditions for reproduction for extended periods.

Freshwater early life growth influences partial migration in populations of Dolly Varden (Salvelinus malma malma).

Populations of northern Dolly Varden (Salvelinus malma malma) exhibit partial seaward migration, yet little is known about this phenomenon in Dolly Varden populations. Our study analyzed data from three different Dolly Varden populations in the western Canadian Arctic in order to determine if: (1) differences in size-at-first seaward migration exist between fish that migrate at early and late ages among populations inhabiting different river systems, and (2) annual growth influences anadromous or resident life history choice. Otolith strontium analysis and back-calculation were used to determine age- and size-at-first seaward migration, respectively. Differences in age- and size-at-first seaward migration were determined across river system and migration age. Back-calculated fish lengths were compared using a mixed effect model to determine how early growth influences migratory tactics (early or late aged smolt, or resident). Our results indicate that fish exhibiting faster early growth migrated in earlier years and at smaller sizes than slower growing fish, however size- and age-at first seaward migration varied by river system. Faster growing Dolly Varden tended to become either residents or early smolts, while slower growth was associated with smolting later in life. This is contrary to life history theory where the fastest growing fish in a population should mature as a resident. Our results indicate factors other than growth may be influencing life history 'decisions' in Dolly Varden. Future work on growth efficiencies and metabolic rates is needed to assess how they affect migratory behaviours.