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.     

Life history and ecological characteristics of humper and lean ecotypes of lake trout stocked in Lake Erie

Through combined effects of over-exploitation and predation by invasive non-native sea lamprey Petromyzon marinus (Linneaus 1958), the lake trout Salvelinus namaycush (Walbaum 1972) population in Lake Erie collapsed and was considered extirpated by 1950; annual stocking occurred in 1969 to bolster and maintain this population as natural recruitment ceased. While various hatchery strains of lean ecotype lake trout remain the focus of Lake Erie’s stocking, between 2004 and 2011 a humper-like ecotype was stocked to aid re-establishment efforts. We assessed ecotype performance via adult fish collected during the summer-stratified period (2004–2017) and evaluated if life history and ecological characteristics varied between stocked ecotypes. Ecotype-specific differences in survival, length-at-age, accumulation of weight with length, and diet were observed. Lean lake trout grew faster (length-at-age) and matured at larger sizes than the humper ecotype. Humper lake trout exhibited higher sea lamprey wounding and lower survival rates than lean lake trout. Humpers also consumed more benthic prey fish than lean lake trout, suggesting this ecotype may exhibit a more benthic orientation than leans. Our study represents the first evaluation of how a non-lean ecotype lake trout performs outside their native ecosystem and provides fishery managers with valuable information relevant to re-establishing lake trout populations in the Great Lakes.

     

Environmental factors and life histories of isolated river stocks of brown trout (Salmo trutta m. fario) in Søre Osa river system,Norway

Synopsis The brown trout in the Søre Osa river system are isolated from the lake above by a dam. They are generally of a small size, but their condition coefficient is high. They reach sexual maturity at an early age and have a short life span. The substratum in the Søre Osa mainly consists of large stones covered with a dense mossy vegetation that creates good fish cover. A high biomass of zoobenthos gives an adequate food supply throughout the year. The trout spawn mainly in tributaries, where the water level is unpredictable, some years being too low to permit successful spawning for the migrating individuals in the stock. The life history of these fish depends on the amount of food available in the habitat and on reproduction in unstable environments where density-independent mortality factors appear important. Many young migrate to the main stream during their first year. In the tributaries, there is an excess of resident males and it is hypothesized that a population structure with small resident males and large migratory males is maintained by partial inbreeding and kin selection. In the main stream the trout are larger and they have higher growth rates in the upper part than farther downstream. This is probably so because the food particles that are flushed down from the lake above provide a better supply of zoobenthic food.     

Among‐individual diet variation within a lake trout ecotype: Lack of stability of niche use

In a polyphenic species, differences in resource use are expected among ecotypes, and homogeneity in resource use is expected within an ecotype. Yet, using a broad resource spectrum has been identified as a strategy for fishes living in unproductive northern environments, where food is patchily distributed and ephemeral. We investigated whether specialization of trophic resources by individuals occurred within the generalist piscivore ecotype of lake trout from Great Bear Lake, Canada, reflective of a form of diversity. Four distinct dietary patterns of resource use within this lake trout ecotype were detected from fatty acid composition, with some variation linked to spatial patterns within Great Bear Lake. Feeding habits of different groups within the ecotype were not associated with detectable morphological or genetic differentiation, suggesting that behavioral plasticity caused the trophic differences. A low level of genetic differentiation was detected between exceptionally large‐sized individuals and other piscivore individuals. We demonstrated that individual trophic specialization can occur within an ecotype inhabiting a geologically young system (8,000–10,000 yr BP), a lake that sustains high levels of phenotypic diversity of lake trout overall. The characterization of niche use among individuals, as done in this study, is necessary to understand the role that individual variation can play at the beginning of differentiation processes.     

Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four lake trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (mean F_ST = 0.016) than between ecotypes within sites (mean F_ST = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions supports the presence of a continuum of divergence in lake trout.     

Wide but not impermeable: Testing the riverine barrier hypothesis for an Amazonian plant species

Wallace's riverine barrier hypothesis postulates that large rivers, such as the Amazon and its tributaries, reduce or prevent gene flow between populations on opposite banks, leading to allopatry and areas of species endemism occupying interfluvial regions. Several studies have shown that two major tributaries, Rio Branco and Rio Negro, are important barriers to gene flow for birds, amphibians and primates. No botanical studies have considered the potential role of the Rio Branco as a barrier, while a single botanical study has evaluated the Rio Negro as a barrier. We studied an Amazon shrub, Amphirrhox longifolia (A. St.‐Hil.) Spreng (Violaceae), as a model to test the riverine barrier hypothesis. Twenty‐six populations of A. longifolia were sampled on both banks of the Rio Branco and Rio Negro in the core Amazon Basin. Double‐digest RADseq was used to identify 8,010 unlinked SNP markers from the nuclear genome of 156 individuals. Data relating to population structure support the hypothesis that the Rio Negro acted as a significant genetic barrier for A. longifolia. On the other hand, no genetic differentiation was detected among populations spanning the narrower Rio Branco, which is a tributary of the Rio Negro. This study shows that the strength of riverine barriers for Amazon plants is dependent on the width of the river separating populations and species‐specific dispersal traits. Future studies of plants with contrasting life history traits will further improve our understanding of the landscape genetics and allopatric speciation history of Amazon plant diversity.     

Mainstem‐tributary linkages by mayfly migration help sustain salmonids in a warming river network

Animal migrations can link ecosystems across space. We discovered an aquatic insect that migrates between a river mainstem and its tributaries, and provides an important trophic subsidy for tributary predators. A mayfly, Ephemerella maculata, rears in a warm, sunlit productive river mainstem, then migrates as adults to cool, shaded unproductive tributaries where they oviposit and die. This migration tripled insect flux into a tributary for 1 month in summer. A manipulative field experiment showed that this E. maculata subsidy nearly tripled the growth of the young of the year steelhead trout (Oncorhynchus mykiss) in the recipient tributary over the summer months, and was more important than terrestrial invertebrate subsidies, which have been considered the primary food source for predators in small, forested creeks. By delivering food subsidies from productive but warming river mainstems to cool but food‐limited tributaries, aquatic insect migrations could enhance resilience to cool‐water predators in warming river networks.     

Ecological Forms of Black Sea Brown Trout (<Emphasis Type="Italic">Salmo trutta labrax</Emphasis>) in the Mzymta River as Manifestation of Ontogenetic Plasticity

Populations of brown trout in the Mzymta River and its tributaries include anadromous (mainly female) and resident (mainly males) fish. Some resident males in the basin of the Mzymty River attain sexual maturity at the age 1+, and resident females mature at the age 2+ or 3+. The maximum age of resident fish is 4+ in the samples studied. Migrations of anadromous brown trout to the sea occur at the ages 1+, 2+, or 3+. Future spawners spend from 1 to 4 years at feeding grounds in the sea. Smolts of the population are characterized by performing not only spring but also autumn migrations to the sea. One smolt specimen has been detected upstream from the dam in the river where spawners of anadromous brown trout do not migrate; this means that the capability for sea migrations persists long in the population represented only by resident specimens of brown trout. The diversity of life cycles and ecological forms in populations of brown trout is not lower than in populations of brown trout in Northern and Western Europe. The comparison of the data obtained with published data makes it possible to come to the conclusion about the high plasticity of ontogenesis of Black Sea brown trout.     

Influences of life history and environment on lake trout (Salvelinus namaycush) growth and longevity in the Husky Lakes of the Western Canadian Arctic

The interaction between an organism and its environment is a major determinant of an individual’s growth rate, longevity, and fitness. Such interactions and resultant variation in growth is particularly prevalent in salmonids where a diversity of life history types and morphotypes can be observed within a single ecosystem. Lake trout, Salvelinus namaycush, are typically considered freshwater residents. However, three life history types within the Husky Lakes estuary and connected lakes, NWT were recently documented, including semi-anadromous, brackish-water resident, and freshwater resident. To understand how use of brackish-water environments influences growth and longevity in lake trout, we assessed otolith increment widths, as a proxy for annual fish growth, and age-at- capture among life history types. Assessment of increments indicated that growth increased in brackish water for semi-anadromous lake trout, and that growth was faster for semi-anadromous and brackish-water residents than for freshwater residents (70 mm larger on average at age 15). In addition, age at capture was significantly older in brackish-water residents (3.8 years older) when compared to the other life histories. Together these results indicate that life in brackish water can have positive effects on growth and longevity for lake trout.

     

A small number of anadromous females drive reproduction in a brown trout (Salmo trutta) population in an English chalk stream

相似文献   

The origins of ecotypic variation of rainbow trout: a test of environmental vs. genetically based differences in morphology

Although morphological plasticity has been observed in a variety of taxa, few experimental studies have compared the relative proportion of morphological variability that is accounted for by environmentally induced plasticity, and how much is because of genetically based differences among populations. We compared the morphology of six rainbow trout (Oncorhynchus mykiss) populations from different ecotypic categories that were raised under flowing vs. standing-water conditions. Our data indicate that both environmental conditions and ecotypic differences account for a significant proportion of variation in morphology. Among ecotype effects, however, accounted for a much larger proportion of morphological variability than environmental conditions. Rainbow trout from stream populations had deeper caudal peduncles, and longer fins than lake populations, and rainbow trout from a piscivorous population had larger mouth and head lengths than all other ecotypes. Environmentally induced differences in morphology were primarily related to differences in mouth and head lengths, as well as fin length. Relative to morphometric differences from natural rainbow trout populations, most characteristics deviated in the same direction in our experimental populations. Our data indicate that morphological differences across rainbow trout populations have a genetic basis and may represent locally adaptive characteristics and highlight the role of ecology in promoting phenotypic divergence.     

Responses to simulated winter conditions differ between threespine stickleback ecotypes

Abiotic factors can act as barriers to colonization and drive local adaptation. During colonization, organisms may cope with changes in abiotic factors using existing phenotypic plasticity, but the role of phenotypic plasticity in assisting or hindering the process of local adaptation remains unclear. To address these questions, we explore the role of winter conditions in driving divergence during freshwater colonization and the effects of plasticity on local adaptation in ancestral marine and derived freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We found that freshwater‐resident stickleback had greater tolerance of acute exposure to low temperatures than marine stickleback, but these differences were abolished after acclimation to simulated winter conditions (9L:15D photoperiod at 4 °C). Plasma chloride levels differed between the ecotypes, but showed a similar degree of plasticity between ecotypes. Gene expression of the epithelial calcium channel (ECaC) differed between ecotypes, with the freshwater ecotype demonstrating substantially greater expression than the marine ecotype, but there was no plasticity in this trait under these conditions in either ecotype. In contrast, growth (assessed as final mass) and the expression of an isoform of the electroneutral Na⁺/H⁺ exchanger (NHE3) exhibited substantial change with temperature in the marine ecotype that was not observed in the freshwater ecotype under the conditions tested here, which is consistent with evolution of these traits by a process such as genetic assimilation. These data demonstrate substantial divergence in many of these traits between freshwater and marine stickleback, but also illustrate the complexity of possible relationships between plasticity and local adaptation.     

Migratory behaviour shapes spatial genetic structure of cyprinid fishes within the Lake Malawi catchment

• Genetic differences among freshwater fish populations are dependent on life‐history characteristics of the species, including the range of adult dispersal and the extent of homing to natal breeding grounds. However, the effects of variation in such characteristics on population genetic connectivity are rarely studied comparatively among closely related species.
• We studied population genetic structure within three congeneric cyprinid species from the Lake Malawi catchment that differ substantially in life‐history traits and conservation status, using a combination of microsatellite and mitochondrial DNA markers. Mpasa (Opsaridium microlepis) is a large (70 cm total length) migratory species that spawns in rivers, but as an adult is exclusively known from the main lake body. Sanjika (Opsaridium microcephalum), is a medium size (30 cm total length) species that exists in lake breeding, river‐lake migratory and apparently landlocked populations. Dwarf sanjika (Opsaridium tweddleorum) is a small non‐migratory species (15 cm total length) that persists in small tributaries surrounding the main lake and adjoining rivers.
• The results revealed striking differences among the three species in spatial genetic structuring. The river‐lake migratory mpasa showed only weak yet significant population genetic structure within the main Lake Malawi catchment, suggesting that there is no strong natal homing. The habitat‐generalist sanjika showed only weak spatial genetic differentiation at microsatellite loci within the Lake Malawi catchment, but moderate structure in mitochondrial DNA, potentially reflecting male‐biased dispersal. The river‐restricted dwarf sanjika showed strong genetic structure in both microsatellite and mitochondrial DNA, suggesting strictly limited dispersal at both adult and juvenile stages.
• We conclude that contrasting migration life histories have resulted in dramatically different patterns of population genetic structure among these congeneric species. The observed patterns demonstrate how divergent life‐history evolution may strongly influence broader patterns of population genetic connectivity in freshwater fish, with consequences for management and conservation. Specifically the results suggesting gene flow among Lake Malawi populations of mpasa, an IUCN red‐listed ‘Endangered’ species endemic to the lake catchment, imply that conservation initiatives operating at both local and catchment scales are needed to reverse local population decline.

     

Genetic population structure in prickly sculpin (Cottus asper) reflects isolation‐by‐environment between two life‐history ecotypes

Life‐history transitions have evolved repeatedly in numerous taxa, although the ecological and evolutionary conditions favouring such transitions in the presence of gene flow remain poorly understood. The present study aimed to disentangle the effects of isolation‐by‐distance and isolation‐by‐environment on genetic differentiation between two sympatric life‐history ecotypes. Using 14 microsatellite loci, we first characterized amphidromous and freshwater groups of Cottus asper in a high gene flow setting in the Lower Fraser River system (south‐western British Columbia, Canada) to test for the effects of habitat and geographical distance on the distribution of life‐history ecotypes. Within the main river channel, no genetic differentiation was found, whereas tributaries even close to the estuary were genetically differentiated. Partial mantel tests confirmed that genetic differentiation between river tributaries and the main channel was independent from geographical distance, with distance‐scaled migration rates indicating reduced gene flow from the main channel into the tributaries. Our results suggest that isolation‐by‐environment can play an important role for the early stage of life‐history transitions, and may promote differentiation among life‐history ecotypes despite the presence of gene flow. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 943–957.     

Strontium content of scales as a marker for distinguishing between sea trout and brown trout

Strontium was determined in trout scales from a river where it is often difficult to distinguish between sea trout and resident brown trout by coloration or other visual marks. Sr values were compared with values in scales from brown trout caught above the anadromous stretch of the same river and in scales from a river where sea trout coloration is typical. In the first river, the Sr concentration was generally low, and as a mean only 50 ppm higher in scales from individuals classified as sea trout from the anadromous stretch than in brown trout scales from the upper stretch. There was no consistency between fish coloration and Sr concentration in scales from presumed sea trout on the anadromous stretch. Individuals with a typical sea trout coloration could have a lower concentration of Sr than individuals that were classified as uncertain sea trout by coloration. Fish weight did not seem to influence Sr levels. The mean Sr concentration in scales from the typical sea trout colored population in the second river was 2.8 times higher than that of the anadromous part of the first river. The high variability of Sr concentration in sea trout scales may be explained by differences in individual and population life history. The Sr levels reflect differences in saltwater exposure, either expressed by length of stay or concentration of salt in marine habitats. The study has shown that fish coloration is an inadequate mean to distinguish between resident and migratory trout. Nor is Sr determination of scales alone sufficient, because of low inter-group and high intra-group variability in some rivers. However, Sr values can give valuable information on individual and population migration on a large scale.     

Ecosystem-level evidence for top-down and bottom-up control of production in a grassland stream system

Ecosystem-wide effects of introduced brown trout (Salmo trutta L.) and native river galaxias (Galaxiaseldoni McDowall) were studied by analysing ecosystem production budgets for two adjacent tributaries of a grassland stream-system in the South Island of New Zealand. One tributary was inhabited by brown trout, the other by river galaxias. No other fish species were present in either stream. The budget for the river galaxias stream indicated little top-down control of invertebrates by fish predation (river galaxias consumed ∼18% of available prey production). A large proportion of annual net primary production was required to support production by invertebrates (invertebrates consumed an average of ∼75% of available primary production), and mean surplus primary production (i.e. not consumed) was not significantly different from zero. Primary and secondary production were presumably mutually limiting in this system (i.e. controlled by simultaneous top-down and bottom-up mechanisms). In contrast, the budget for the brown trout stream indicated extreme top-down control of invertebrate populations by fish predation; essentially all invertebrate production (∼100%) was required to support trout production. Invertebrate production required only a minor portion of annual net primary production (∼21%) and primary production was presumably controlled by mechanisms other than grazing (e.g. sloughing, nutrient limitation). Predatory invertebrates had little quantitative effect on prey populations in either stream. Recent experimental studies of invertebrate behaviour, fish behaviour, and food-web structure in New Zealand streams with physically stable channels indicate that a trophic cascade should be observed in streams inhabited by brown trout, in contrast to those inhabited by native fish. The results reported here provide ecosystem-level evidence supporting this prediction. Received: 10 March 1997 / Accepted: 12 December 1997     

Invasive brown trout Salmo trutta induce differential growth strategies in the native snow trout Schizothorax richardsonii of Himalaya: Are natives in unaltered rivers better at picking the gauntlet of invasion?

Brown trout Salmo trutta is a potent global invader and its establishments have progressively altered physiologies, life-histories and niche-availabilities for native fish species. River impoundments further escalate its invasion potential. The Himalayan rivers however, stay uncharted for the effects of brown trout interactions with the native fish fauna. Snow trout Schizothorax richardsonii a Himalayan cold-water native, concerningly overlaps its range with brown trout. To understand its responses to invasion pressures, we investigated brown trout effects on the age and growth of snow trout populations in three rivers with varying levels of perturbation: (a) a dammed and (b) an undammed river with the invasive brown trout in comparison to (c) an undammed river without invasion pressures. We found sympatric snow trout in the undammed river to respond to brown trout invasion with fast life history responses, showing an early age-at-maturity (A₅₀ = 1.2 years) and fast growth with a higher growth constant (K = 0.40 yr⁻¹) and specific rate of linear growth across life. On the contrary, sympatric snow trout in the dammed river showed an explicitly slow life-history by maturing at a higher age (A₅₀ = 2.9 years) and a slow growth, with a lower growth constant (K = 0.26 yr⁻¹) and specific linear growth rates. Our findings suggest that, the snow trout appear to present stronger response to brown trout invasions when the river is unaltered and free from hydropower operations and damming. Further research is strongly warranted from other high-altitude Himalayan basins to delineate the variation in growth strategies exhibited by snow trout in sympatry with the invasives.     

Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses

Repeated adaptive ecological diversification has commonly been reported in fish and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous lake trout ecotypes from Laurentian Shield lakes, Canada. This was achieved by documenting the extent of morphological differentiation using geometric morphometrics and linear measurements as well as the pattern of genomic divergence by means of RADseq genotyping (3925 filtered SNPs) in 12 lakes. Our results indicate that the two ecotypes evolved distinct body shape and several linear measurements in parallel. Neutral genetic differentiation was pronounced between all isolated populations (Mean F_ST = 0.433), indicating no or very limited migration and pronounced genetic drift. Significant genetic differentiation also suggested partial reproductive isolation between ecotypes in the two lakes where they are found in sympatry. Combining different outlier detection methods, we identified 48 SNPs putatively under divergent selection between ecotypes, among which 10 could be annotated and related to functions such as developmental processes and ionic regulation. Finally, our results indicate that parallel morphological divergence is accompanied by both parallel and nonparallel genomic divergence, which is associated with the use of different trophic niches between ecotypes. The results are also discussed in the context of management and conservation of this highly exploited species throughout northern North America.     

Lake bathymetry and species occurrence predict the distribution of a lacustrine apex predator

This study examined the abiotic and biotic characteristics of ecosystems that allow expression of a life history called ferox trout, the colloquial name given to brown trout Salmo trutta adopting a piscivorous life history strategy, an apex predator in post‐glacial lakes in northern Europe. One hundred and ninety‐two lakes in Scotland show evidence of currently, or historically, supporting ferox S. trutta; their presence was predicted in logistic models by larger and deeper lakes with a large catchment that also support populations of Arctic charr Salvelinus alpinus.     

Winter ecology of Arctic charr (<Emphasis Type="Italic">Salvelinus alpinus</Emphasis>) and brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) in a subarctic lake,Norway

We studied habitat choice, diet, food consumption and somatic growth of Arctic charr (Salvelinus alpinus) and brown trout (Salmo trutta) during the ice-covered winter period of a subarctic lake in northern Norway. Both Arctic charr and brown trout predominantly used the littoral zone during winter time. Despite very cold winter conditions (water temperature <1°C) and poor light conditions, both fish species fed continuously during the ice-covered period, although at a much lower rate than during the summer season. No somatic growth could be detected during the ice-covered winter period and the condition factor of both species significantly declined, suggesting that the winter feeding rates were similar to or below the maintenance requirements. Also, the species richness and diversity of ingested prey largely decreased from summer to winter for both fish species. The winter diet of Arctic charr <20 cm was dominated by benthic insect larvae, chironomids in particular, and Gammarus lacustris, but zooplankton was also important in December. G. lacustris was the dominant prey of charr >20 cm. The winter diet of brown trout <20 cm was dominated by insect larvae, whereas large-sized trout mainly was piscivorous, feeding on juvenile Arctic charr. Piscivorous feeding behaviour of trout was in contrast rarely seen during the summer months when their encounter with potential fish prey was rare as the small-sized charr mainly inhabited the profundal. The study demonstrated large differences in the ecology and interactions of Arctic charr and brown trout between the winter and summer seasons.