High level of population genetic structuring in lake-run brown trout, Salmo trutta, of the Inari Basin, northern Finland

Rivers draining into (Lake) Inarijärvi, northern Finland, sustain a number of lake‐run brown trout, Salmo trutta, populations but, as with most lake‐run S. trutta systems, the level of population genetic structuring among populations is unknown. To address this and to assist fish stock management in the region, the population genetic structure of S. trutta collected from 28 sampling sites in rivers flowing into Inarijärvi was studied using 13 microsatellite loci. Populations were clustered into three separate groups, largely corresponding to geographic regions, with between‐region F_ST values ranging from 0·11 to 0·16. The significant differentiation observed between most populations within each region also implies that individual populations should be recognized as separate management units and actions to improve, and subsequently maintain, conditions for natural spawning should be prioritized. The results of this study further indicate that the trout from each of these regions may have different biological characteristics, such as local‐lake feeding behaviour among the western populations and strong isolation among the northern stocks. As a consequence, further research is warranted to better understand the level of ecological uniqueness of lake‐run S. trutta populations.     

Telemetry and genetics reveal asymmetric dispersal of a lake‐feeding salmonid between inflow and outflow spawning streams at a microgeographic scale

The degree of natal philopatry relative to natal dispersal in animal populations has important demographic and genetic consequences and often varies substantially within species. In salmonid fishes, lakes have been shown to have a strong influence on dispersal and gene flow within catchments; for example, populations spawning in inflow streams are often reproductively isolated and genetically distinct from those spawning in relatively distant outflow streams. Less is known, however, regarding the level of philopatry and genetic differentiation occurring at microgeographic scales, for example, where inflow and outflow streams are separated by very small expanses of lake habitat. Here, we investigated the interplay between genetic differentiation and fine‐scale spawning movements of brown trout between their lake‐feeding habitat and two spawning streams (one inflow, one outflow, separated by <100 m of lake habitat). Most (69.2%) of the lake‐tagged trout subsequently detected during the spawning period were recorded in just one of the two streams, consistent with natal fidelity, while the remainder were detected in both streams, creating an opportunity for these individuals to spawn in both natal and non‐natal streams. The latter behavior was supported by genetic sibship analysis, which revealed several half‐sibling dyads containing one individual that was sampled as a fry in the outflow and another that was sampled as fry in the inflow. Genetic clustering analyses in conjunction with telemetry data suggested that asymmetrical dispersal patterns were occurring, with natal fidelity being more common among individuals originating from the outflow than the inflow stream. This was corroborated by Bayesian analysis of gene flow, which indicated significantly higher rates of gene flow from the inflow into the outflow than vice versa. Collectively, these results reveal how a combination of telemetry and genetics can identify distinct reproductive behaviors and associated asymmetries in natal dispersal that produce subtle, but nonetheless biologically relevant, population structuring at microgeographic scales.     

Complex genetic diversity patterns of cryptic,sympatric brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) populations in tiny mountain lakes

Intraspecific genetic variation can have similar effects as species diversity on ecosystem function; understanding such variation is important, particularly for ecological key species. The brown trout plays central roles in many northern freshwater ecosystems, and several cases of sympatric brown trout populations have been detected in freshwater lakes based on apparent morphological differences. In some rare cases, sympatric, genetically distinct populations lacking visible phenotypic differences have been detected based on genetic data alone. Detecting such “cryptic” sympatric populations without prior grouping of individuals based on phenotypic characteristics is more difficult statistically, though. The aim of the present study is to delineate the spatial connectivity of two cryptic, sympatric genetic clusters of brown trout discovered in two interconnected, tiny subarctic Swedish lakes. The structures were detected using allozyme markers, and have been monitored over time. Here, we confirm their existence for almost three decades and report that these cryptic, sympatric populations exhibit very different connectivity patterns to brown trout of nearby lakes. One of the clusters is relatively isolated while the other one shows high genetic similarity to downstream populations. There are indications of different spawning sites as reflected in genetic structuring among parr from different creeks. We used >3000 SNPs on a subsample and find that the SNPs largely confirm the allozyme pattern but give considerably lower F _ST values, and potentially indicate further structuring within populations. This type of complex genetic substructuring over microgeographical scales might be more common than anticipated and needs to be considered in conservation management.     

Use of cover habitat by bull trout, <Emphasis Type="Italic">Salvelinus confluentus</Emphasis>, and lake trout, <Emphasis Type="Italic">Salvelinus namaycush</Emphasis>, in a laboratory environment

Lacustrine-adfluvial bull trout, Salvelinus confluentus, migrate from spawning and rearing streams to lacustrine environments as early as age 0. Within lacustrine environments, cover habitat provides refuge from potential predators and is a resource that is competed for if limiting. Competitive interactions between bull trout and other species could result in bull trout being displaced from cover habitat, and bull trout may lack evolutionary adaptations to compete with introduced species, such as lake trout, Salvelinus namaycush. A laboratory experiment was performed to examine habitat use and interactions for cover by juvenile (i.e., <80 mm total length) bull trout and lake trout. Differences were observed between bull trout and lake trout in the proportion of time using cover (F _1,22.6 = 20.08, P < 0.001) and bottom (F _1,23.7 = 37.01, P < 0.001) habitat, with bull trout using cover and bottom habitats more than lake trout. Habitat selection ratios indicated that bull trout avoided water column habitat in the presence of lake trout and that lake trout avoided bottom habitat. Intraspecific and interspecific agonistic interactions were infrequent, but approximately 10 times greater for intraspecific interactions between lake trout. Results from this study provide little evidence that juvenile bull trout and lake trout compete for cover, and that species-specific differences in habitat use and selection likely result in habitat partitioning between these species.     

Lack of parallel genetic patterns underlying the repeated ecological divergence of beach and stream‐spawning kokanee salmon

Recent progress in methods for detecting adaptive population divergence in situ shows promise for elucidating the conditions under which selection acts to generate intraspecific diversity. Rapid ecological diversification is common in fishes; however, the role of phenotypic plasticity and adaptation to local environments is poorly understood. It is now possible to investigate genetic patterns to make inferences regarding phenotypic traits under selection and possible mechanisms underlying ecotype divergence, particularly where similar novel phenotypes have arisen in multiple independent populations. Here, we employed a bottom‐up approach to test for signatures of directional selection associated with divergence of beach‐ and stream‐spawning kokanee, the obligate freshwater form of sockeye salmon (Oncorhynchus nerka). Beach‐ and stream‐spawners co‐exist in many post‐glacial lakes and exhibit distinct reproductive behaviours, life‐history traits and spawning habitat preferences. Replicate ecotype pairs across five lakes in British Columbia, Canada were genotyped at 57 expressed sequence tag‐linked and anonymous microsatellite loci identified in a previous genome scan. Fifteen loci exhibited signatures of directional selection (high F_ST outliers), four of which were identified in multiple lakes. However, the lack of parallel genetic patterns across all lakes may be a result of: 1) an inability to detect loci truly under selection; 2) alternative genetic pathways underlying ecotype divergence in this system; and/or 3) phenotypic plasticity playing a formative role in driving kokanee spawning habitat differences. Gene annotations for detected outliers suggest pathogen resistance and energy metabolism as potential mechanisms contributing to the divergence of beach‐ and stream‐spawning kokanee, but further study is required.     

Recent local adaptation of sockeye salmon to glacial spawning habitats

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

The impact of an introduced predator on a threatened galaxiid fish is reduced by the availability of complex habitats

1. The availability of complex habitats such as macrophytes may be vital in determining the outcomes of interactions between introduced predators and native prey. Introduced brown trout (Salmo trutta) have impacted numerous small native freshwater fishes in the southern hemisphere, but the potential role of complex habitats in determining the direct outcomes of brown trout – native fish interactions has not been experimentally evaluated. 2. An in‐lake enclosure experiment was used to evaluate the importance of structurally complex habitats in affecting the direct impacts of brown trout on a threatened galaxiid fish. Five Galaxias auratus and a single brown trout were added to enclosures containing one of three different habitat types (artificial macrophytes, rocks and bare silt substrate). The experiment also had control enclosures without brown trout. Habitat‐dependence of predation risk was assessed by analysis of G. auratus losses to predation, and stomach contents of remaining fish were analysed to determine if brown trout directly affect the feeding of G. auratus and whether this is also habitat‐dependent. 3. Predation risk of G. auratus differed significantly between habitat types, with the highest mortality in enclosures with only bare silt substrate and the lowest in enclosures containing artificial macrophytes. This result highlights the importance of availability of complex habitats for trout – native fish interactions and suggests that increasing habitat degradation and loss in fresh waters may exacerbate the direct impacts of introduced predators. 4. Stomach contents analyses were restricted to fish in enclosures with artificial macrophytes and rocks, as most fish were consumed in enclosures with brown trout and only bare silt substrate. These analyses suggest that brown trout do not directly affect the feeding of G. auratus in complex habitats, but it is still unknown whether its feeding is reduced if complex habitats are unavailable.     

Inter and intra‐population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus,a rare freshwater fish in Scotland

This study revealed between‐lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (F_ST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common‐garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (F_ST = 0·001–0·024) and evidence of private alleles related to the basin structure of the lake. Within‐lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.     

Minimal gene flow from introduced brown trout (Salmo trutta L.) after 30 years of stocking

Lake Tinnsjø, Norway, has been heavily stocked over three decades with two different brown trout stocks. A population genetic survey based on 13 allozyme coding loci was conducted to investigate the genetic composition of the present trout population and the genetic impact of the two donors. Contrary to expectations, highly significant differences in allelic frequencies between Lake Tinnsjø trout and the two donor stocks were found at several loci, suggesting minimal gene flow from stocked trout to the wild populations. Pairwise genetic distance values were several times higher between donor stocks and Lake Tinnsjø samples than between the various spawning inlets to Lake Tinnsjø. F_st increased from 0.024 to 0.090, when samples from the donor stocks were included in the material. There were no deviations from expected Hardy–Weinberg distribution of genotypes in the spawning inlets. It was concluded that the donor stocks contributed little to the trout gene pool in the lake. A possible exception is the trout population below the lake outlet.     

Patterns of genetic structuring in a brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis> L.) metapopulation

One main challenge in conservation biology is to preserve genetic variability and adaptive variation within and among populations. However, constant anthropogenic habitat modifications have severe effects on the evolutionary dynamics shaping wild populations and pose a serious threat to the natural evolution of biodiversity. The aim of the present study was to unravel the genetic structuring of brown trout (Salmo trutta) populations in the largest freshwater catchment in Ireland, whose habitats have experienced major human-mediated changes over at least two centuries. A total of 419 juvenile fish were sampled from nine main rivers in the Corrib catchment and were genotyped using 12 microsatellites. Both Bayesian clustering and F _ST-based analyses of genetic variance sorted these populations into five main genetically distinct groups, characterized by different extent of genetic differentiation among populations. These groups were also characterized by some degree of admixture, which can be partly explained by recent gene flow. Overall, the study suggests that the Corrib trout may conform to a metapopulation model with local populations that show different degrees of isolation and are interconnected by various level of gene flow. Results add further insights into metapopulation evolutionary dynamics and provide a useful basis to implement appropriate conservation strategies.     

Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout

Migratory behaviour patterns in animals are controlled by a complex genetic architecture. Rainbow trout (Oncorhynchus mykiss) is a salmonid fish that spawns in streams but exhibits three primary life history pathways: stream‐resident (fluvial), lake‐migrant (adfluvial) and ocean‐migrant (anadromous). Previous studies examining fluvial and anadromous O. mykiss have identified several genes associated with life history divergence including the presence of an inversion complex within chromosome 5 (Omy05) that appears to maintain a suite of linked genes controlling migratory behaviour. However, adfluvial trout are migratory without being anadromous, and the genetic basis for this life history has not been investigated from evolutionary perspectives. We sampled wild, native nonanadromous rainbow trout occupying connected stream and lake habitats in a southwest Alaskan watershed to determine whether these fish exhibit genetic divergence between fluvial and adfluvial ecotypes, and whether that divergence parallels that documented in fluvial and anadromous O. mykiss. Data from restriction site‐associated DNA (RAD) sequencing revealed an association between frequencies of both the Omy05 inversion complex and other single nucleotide polymorphisms (SNPs) with habitat type (stream or lake), supporting the genetic divergence of fluvial and adfluvial individuals in sympatry. The presence of a genetic basis for migration into lakes, analogous to that documented for anadromy, indicates that the adfluvial ecotype must be recognized separately from the fluvial form of O. mykiss even though neither is anadromous. These results highlight the genetic architecture underlying migration and the importance of chromosomal inversions in promoting and sustaining intraspecific diversity.     

Disentangling stocking introgression and natural migration in brown trout: survival success and recruitment failure in populations with semi‐supportive breeding

1. Introgression into natural salmonid populations from stocked conspecifics has been widely studied. Outcomes vary from no effect even after decades of stocking, to population replacement after only a couple of generations. Potential introgression caused by semi‐supportive breeding (i.e. using a mixture of local strains as brood stock) is, however, less well studied. 2. We investigated population structure of brown trout (Salmo trutta) in a regulated alpine lake with three natural, environmentally contrasting tributaries used as spawning and rearing habitat. Massive semi‐supportive breeding of admixed local strains has been implemented for decades. Stocked trout represented c. 17% of the total lake population, and a substantial post‐release survival reflects a considerable potential for introgression. However, the mark‐recapture studies indicate no spawning runs of stocked fish. 3. Using 13 polymorphic microsatellite loci, we found natural straying and non‐native reproduction, especially among wild populations inhabiting environmentally unstable habitat. Retained genetic structure across tributaries indicated low reproductive success of wild‐born non‐natives. Moreover, the genetic structure among tributaries has probably not been influenced by semi‐supportive breeding, because of recruitment failure of stocked trout.     

Static habitat partitioning and dynamic selection by sympatric young Atlantic salmon and brown trout in south-west England streams

Direct underwater observation of micro‐habitat use by 1838 young Atlantic salmon Salmo salar [mean L_T 7·9 ± 3.1(s.d.) cm, range 3·19] and 1227 brown trout Salmo trutta (L_T 10·9 ± 5·0 cm, range 3·56) showed both species were selective in habitat use, with differences between species and fish size. Atlantic salmon and brown trout selected relatively narrow ranges for the two micro‐habitat variables snout water velocity and height above bottom, but with differences between size‐classes. The smaller fishes <7 cm held positions in slower water closer to the bottom. On a larger scale, the Atlantic salmon more often used shallower stream areas, compared with brown trout. The larger parr preferred the deeper stream areas. Atlantic salmon used higher and slightly more variable mean water velocities than brown trout. Substrata used by the two species were similar. Finer substrata, although variable, were selected at the snout position, and differences were pronounced between size‐classes. On a meso‐habitat scale, brown trout were more frequently observed in slow pool‐glide habitats, while young Atlantic salmon favoured the faster high‐gradient meso‐habitats. Small juveniles <7 cm of both species were observed most frequently in riffle‐chute habitats. Atlantic salmon and brown trout segregated with respect to use of habitat, but considerable niche overlap between species indicated competitive interactions. In particular, for small fishes <7 cm of the two species, there was almost complete niche overlap for use of water depth, while they segregated with respect to water velocity. Habitat suitability indices developed for both species for mean water velocity and water depth, tended to have their optimum at lower values compared with previous studies in larger streams, with Atlantic salmon parr in the small streams occupying the same habitat as favoured by brown trout in larger streams. The data indicate both species may be flexible in their habitat selection depending on habitat availability. Species‐specific habitat overlap between streams may be complete. However, between‐species habitat partitioning remains similar.     

Temporal constraints on the potential role of fry odors as cues of past reproductive success for spawning lake trout

Deciding where to reproduce is a major challenge for most animals. Many select habitats based upon cues of successful reproduction by conspecifics, such as the presence of offspring from past reproductive events. For example, some fishes select spawning habitat following odors released by juveniles whose rearing habitat overlaps with spawning habitat. However, juveniles may emigrate before adults begin to search for spawning habitat; hence, the efficacy of juvenile cues could be constrained by degradation or dissipation rates. In lake trout (Salvelinus namaycush), odors deposited by the previous year's offspring have been hypothesized to guide adults to spawning reefs. However, in most extant populations, lake trout fry emigrate from spawning reefs during the spring and adults spawn during the fall. Therefore, we postulated that the role of fry odors in guiding habitat selection might be constrained by the time between fry emigration and adult spawning. Time course chemical, physiological, and behavioral assays indicated that the odors deposited by fry likely degrade or dissipate before adults select spawning habitats. Furthermore, fry feces did not attract wild lake trout to constructed spawning reefs in Lake Huron. Taken together, our results indicate fry odors are unlikely to act as cues for lake trout searching for spawning reefs in populations whose juveniles emigrate before the spawning season, and underscore the importance of environmental constraints on social cues.     

Short-and long term niche segregation and individual specialization of brown trout (Salmo trutta) in species poor Faroese lakes

Trophic niche divergence is considered to be a major process by which species coexistence is facilitated. When studying niche segregation in lake ecosystems, we tend to view the niche on a one-dimensional pelagic-littoral axis. In reality, however, the niche use may be more complex and individual fidelity to a niche may be variable both between and within populations. In order to study this complexity, relative simple systems with few species are needed. In this paper, we study how competitor presence affects the resource use of brown trout (Salmo trutta) in 11 species-poor Faroese lakes by comparing relative abundance, stable isotope ratios and diet in multiple habitats. In the presence of three-spined sticklebacks (Gasterosteus aculeatus), a higher proportion of the trout population was found in the pelagic habitat, and trout in general relied on a more pelagic diet base as compared to trout living in allopatry or in sympatry with Arctic charr (Salvelinus alpinus). Diet analyses revealed, however, that niche-segregation may be more complex than described on a one-dimensional pelagic-littoral axis. Trout from both littoral and offshore benthic habitats had in the presence of sticklebacks a less benthic diet as compared to trout living in allopatry or in sympatry with charr. Furthermore, we found individual habitat specialization between littoral/benthic and pelagic trout in deep lakes. Hence, our findings indicate that for trout populations interspecific competition can drive shifts in both habitat and niche use, but at the same time they illustrate the complexity of the ecological niche in freshwater ecosystems.     

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small‐scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine‐scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F_ST = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite‐based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ_ST = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine‐scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter‐related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine‐scale population structure among bottlenose dolphins in Moreton Bay.     

Spatio-temporal genetic structuring of brown trout (Salmo trutta L.) populations within the River Luga, northwest Russia

The brown trout populations of the Baltic Sea region have been drastically affected by various human activities during the past century. Due to their propensity to home to their natal site to spawn and their tendency to evolve local adaptations, populations may be genetically differentiated in water systems where no physical barriers preventing interbreeding exist. Consequently, identification of management units, a prerequisite for appropriate conservation and management planning, cannot necessarily be deduced from the physical properties of the habitat. In this study, microsatellite markers were employed to assess the spatio-temporal genetic structuring of inter-connected brown trout populations from a river-system in Northwest Russia. Populations were found to be genetically differentiated from each other (global F _ST 0.06) and the genetic structuring within the river to follow an isolation by distance pattern. Indications of temporal stability were found in some populations, however others appeared to be temporally unstable suggesting differences in the demographic forces affecting the populations. Based on the observed isolation by distance pattern of genetic differentiation, preserving several breeding sites spaced evenly throughout the river-system would appear to be more appropriate than focussing conservation effort on any single stretch of the river. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hierarchical population structure and genetic diversity of lake trout (Salvelinus namaycush) in a dendritic system in Northern Labrador

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Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits

To study effects from natural selection acting on brown trout in a natural stream habitat compared with a hatchery environment, 3,781 single nucleotide polymorphism (SNP) markers were analyzed in three closely related groups of brown trout (Salmo trutta L.). Autumn (W/0+, n = 48) and consecutive spring (W/1+, n = 47) samples of brown trout individuals belonging to the same cohort and stream were retrieved using electrofishing. A third group (H/1+, n = 48) comprised hatchery‐reared individuals, bred from a mixture of wild parents of the strain of the two former groups and from a neighboring stream. Pairwise analysis of F_ST outliers and analysis under a hierarchical model by means of ARLEQUIN software detected 421 (10.8%) candidates of selection, before multitest correction. BAYESCAN software detected 10 candidate loci, all of which were included among the ARLEQUIN candidate loci. Body length was significantly different across genotypes at 10 candidate loci in the W/0+, at 34 candidate loci in the W/1+ and at 21 candidate loci in the H/1+ group. The W/1+ sample was tested for genotype‐specific body length at all loci, and significant differences were found in 10.6% of all loci, and of these, 14.2% had higher frequency of the largest genotype in the W/1+ sample than in W/0+. The corresponding proportion among the candidate loci of W/1+ was 22.7% with genotype‐specific body length, and 88.2% of these had increased frequency of the largest genotype from W/0+ to W/1+, indicating a linkage between these loci and traits affecting growth and survival under this stream's environmental conditions. Bayesian structuring of all loci, and of the noncandidate loci suggested two (K = 2), alternatively four clusters (K = 4). This differed from the candidate SNPs, which suggested only two clusters. In both cases, the hatchery fish dominated one cluster, and body length of W/1+ fish was positively correlated with membership of one cluster both from the K = 2 and the K = 4 structure. Our analysis demonstrates profound genetic differentiation that can be linked to differential selection on a fitness‐related trait (individual growth) in brown trout living under natural vs. hatchery conditions. Candidate SNP loci linked to genes affecting individual growth were identified and provide important inputs into future mapping of the genetic basis of brown trout body size selection.     

Divergence along a steep ecological gradient in lake whitefish (Coregonus sp.)

To understand mechanisms structuring diversity in young adaptive radiations, quantitative and unbiased information about genetic and phenotypic diversity is much needed. Here, we present the first in‐depth investigation of whitefish diversity in a Swiss lake, with continuous spawning habitat sampling in both time and space. Our results show a clear cline like pattern in genetics and morphology of populations sampled along an ecological depth gradient in Lake Neuchâtel. Divergent natural selection appears to be involved in shaping this cline given that trait specific P_ST‐values are significantly higher than F_ST‐values when comparing populations caught at different depths. These differences also tend to increase with increasing differences in depth, indicating adaptive divergence along a depth gradient, which persists despite considerable gene flow between adjacent demes. It however remains unclear, whether the observed pattern is a result of currently stable selection‐gene flow balance, incipient speciation, or reverse speciation due to anthropogenic habitat alteration causing two formerly divergent species to collapse into a single gene pool.