Ecological analogies in the Pacific lamprey <Emphasis Type="Italic">Lethenteron camtschaticum</Emphasis> and the mykiss <Emphasis Type="Italic">Parasalmo mykiss</Emphasis> in Kamchatka

Ecological analogies between the Pacific lamprey Lethenteron camtschaticum and various species of salmonids (Salmonidae) are noted. Close analogies are found with the mykiss Parasalmo mykiss. The lamprey and mykiss are characterized by spawning in spring. In their populations there are specimens with anadromous and riverine life strategies. The mechanism of formation of life strategies seems to be similar in both species. The major role belongs to the trophic factor determining the level of energy resources necessary for maturation. Such analogies result from epigenetic changes in principal ecological parameters and are formed under the influence of similar environmental factors.     

Sequencing the genome of the Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis>)

The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids.     

Analysis of microsatellite DNA of rainbow trout (<Emphasis Type="Italic">Parasalmo</Emphasis> (<Emphasis Type="Italic">Oncorhynchus</Emphasis>) <Emphasis Type="Italic">mykiss</Emphasis>) of Kamchatka: Selection of loci and optimization of the method

The variation of a sample of rainbow trout (Parasalmo (Oncorhynchus) mykiss) from natural populations of several rivers of the Kamchatka Peninsula with respect to 43 microsatellite DNA loci has been studied. These loci were earlier used for analysis of Asian populations of closely related salmonids. Ten of them may be regarded as markers and seen promising for further studies on intraspecific relationships of rainbow trout of Kamchatka. Their use in studies on more numerous samples from different localities and populations of Parasalmo (O.) mykiss in the Asian part of the species range will ensure efficient population genetic analysis of the Kamchatka population group of this species.     

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

Salmonid fishes exhibit extensive local adaptations owing to abundant environmental variation and precise natal homing. This extensive local adaptation makes conservation and restoration of salmonids a challenge. For example, defining unambiguous units of conservation is difficult, and restoration attempts often fail owing to inadequate adaptive matching of translocated populations. A better understanding of the genetic architecture of local adaptation in salmonids could provide valuable information to assist in conserving and restoring natural populations of these important species. Here, we use a combination of laboratory crosses and next-generation sequencing to investigate the genetic architecture of the parallel adaptation of rapid development rate in two geographically and genetically distant populations of rainbow trout (Oncorhynchus mykiss). Strikingly, we find that not only is a parallel genetic mechanism used but that a conserved haplotype is responsible for this intriguing adaptation. The repeated use of adaptive genetic variation across distant geographical areas could be a general theme in salmonids and have important implications for conservation and restoration.     

The effects of introduced salmonids on two native stream‐dwelling salmonids through interspecific competition

Using an artificial stream, habitat use by two sympatric native salmonids in the presence and absence of introduced salmonid species was investigated experimentally. When only native white‐spotted charr Salvelinus leucomaenis and masu salmon Oncorhynchus masou were sympatric, they occupied different microhabitats. In the presence of introduced brown trout Salmo trutta or rainbow trout Oncorhynchus mykiss , however, white‐spotted charr and masu salmon were observed to use a similar habitat and interspecific competition between white‐spotted charr and masu salmon was initiated. The study suggested that the coexistence of native salmonids was negatively affected through interspecific competition between native and introduced salmonids.     

Assessment of genetic variation between reproductive ecotypes of Klamath River steelhead reveals differentiation associated with different run-timings

Seven microsatellite DNA loci were optimized to assess genetic differentiation in coastal steelhead (Oncorhynchus mykiss irideus) sampling groups from the lower Klamath River (California, USA). Genetic relationships among three winter‐run and two summer‐run groups were investigated. The different groups displayed high levels of allelic variation. Pairwise F_ST comparisons and Nei's genetic distance supported low, yet significant, genetic differentiation between summer and winter run‐timings similar to other studies of temporal variation in salmonids. Analysis of molecular variance showed that most of the genetic variation was at the individual level (97.9%), although significant genetic variation existed between timing of runs (2.59%). Additionally, at least one locus in each group was out of Hardy–Weinberg equilibrium due to a deficiency in heterozygotes, and significant F_IS values were observed in three temporal collections. Together, these results suggest stock admixture, caused by multiple populations of origin in each sampling group, better known as the Wahlund Effect. These observations are preliminary evidence for isolation by time between Klamath River steelhead runs during distinct periods.     

Decline of the Migratory Form in Bull Charr, Salvelinus Confluentus, and Implications for Conservation

Large-bodied, migratory life history forms of bull charr, Salvelinus confluentus, were historically abundant in northwestern North America, but many remaining populations of this now-threatened species presently persist as small-bodied residents isolated in headwater streams. We examined whether the migratory form has been lost from headwater populations of bull charr and their potential for re-establishment. Upstream and downstream movement of bull charr and other salmonids from three tributary populations in the Bitterroot River drainage, Montana, was measured with weirs over a 17-month period. The migratory life history was rare or absent in two tributaries but still present at a low level in a third. In contrast, substantial numbers (n = 1745) of juvenile and adults of other salmonids (brown trout, Salmo trutta, cutthroat trout, Oncorhynchus clarki, and mountain whitefish, Prosopium williamsoni) were captured near tributary mouths, indicating a migratory life history was common in other species. Apparent decline of the migratory life history in bull charr was not directly related to damming suggesting other downstream mortality factors (predation, temperature) also are involved. Isolated, nonmigratory forms have increased risk of extinction, and restoration of the population connectivity via the re-establishment of migratory stocks is an important conservation goal for bull charr recovery. However, the factors governing migratory tendency remain unclear.     

Ubiquitous genetic diversity in ISSR markers between and within populations of the asexually producing moss <Emphasis Type="Italic">Pleurochaete squarrosa</Emphasis>

This paper provides an analysis of genetic variability in local populations of the clonal moss Pleurochaete squarrosa, a Mediterranean moss typical of post-fire recovery, and characterised by asexual reproduction. ISSR (Internal Simple Sequence Repeats) primers and trnL_UAA (intron of plastid gene for Leu tRNA) length polymorphism were employed to evaluate genetic structure in five southern Italy populations of this moss. Both molecular tools highlight high values of genetic diversity with geographic structure of sampled populations and a low gene flow among the investigated sites. Gene diversity is significant at every hierarchical level of sampling, and generally increases from lower to higher hierarchical levels. Among other factors, the ubiquitous genetic variability detected in P. squarrosa can be related to continuous, occasionally massive, short-range recruitment of propagules, and to the high degree of intermingling, both favoured by the modality of vegetative reproduction and growth occurring in the species.     

Allopatric and sympatric diversification within roach (Rutilus rutilus) of large pre‐alpine lakes

Intraspecific differentiation in response to divergent natural selection between environments is a common phenomenon in some northern freshwater fishes, especially salmonids and stickleback. Understanding why these taxa diversify and undergo adaptive radiations while most other fish species in the same environments do not, remains an open question. The possibility for intraspecific diversification has rarely been evaluated for most northern freshwater fish species. Here, we assess the potential for intraspecific differentiation between and within lake populations of roach (Rutilus rutilus)—a widespread and abundant cyprinid species—in lakes in which salmonids have evolved endemic adaptive radiations. Based on more than 3,000 polymorphic RADseq markers, we detected low but significant genetic differentiation between roach populations of two ultraoligotrophic lakes and between these and populations from other lakes. This, together with differentiation in head morphology and stable isotope signatures, suggests evolutionary and ecological differentiation among some of our studied populations. Next, we tested for intralacustrine diversification of roach within Lake Brienz, the most pristine lake surveyed in this study. We found significant phenotypic evidence for ecological intralacustrine differentiation between roach caught over a muddy substrate and those caught over a rocky substrate. However, evidence for intralacustrine genetic differentiation is at best subtle and phenotypic changes may therefore be mostly plastic. Overall, our findings suggest roach can differ between ecologically distinct lakes, but the extent of intralacustrine ecological differentiation is weak, which contrasts with the strong differentiation among endemic species of whitefish in the same lakes.     

Development and validation of methods for measuring multiple biochemical indices of condition in juvenile fishes

The investigation established and validated methods to measure multiple biochemical indices of condition (whole body total lipids, whole body triglycerides, muscle RNA : DNA ratio and muscle protein) simultaneously in the same individual juvenile fish. It also provided examples of their application using a species comparison (salmonids and cyprinids) of the degree of change in these indices after food deprivation. The results showed that juvenile rainbow trout Oncorhynchus mykiss were much more susceptible to a decline in all biochemical indices of condition than juvenile fathead minnows Pimephales promelas upon food deprivation. The combination of these techniques can be used to accurately assess condition and growth potential of individuals from wild fish populations.     

A comparative mitogenomic analysis of the potential adaptive value of Arctic charr mtDNA introgression in brook charr populations (Salvelinus fontinalis Mitchill)

Wild brook charr populations (Salvelinus fontinalis) completely introgressed with the mitochondrial genome (mtDNA) of arctic charr (Salvelinus alpinus) are found in several lakes of northeastern Québec, Canada. Mitochondrial respiratory enzymes of these populations are thus encoded by their own nuclear DNA and by arctic charr mtDNA. In the present study we performed a comparative sequence analysis of the whole mitochondrial genome of both brook and arctic charr to identify the distribution of mutational differences across these two genomes. This analysis revealed 47 amino acid replacements, 45 of which were confined to subunits of the NADH dehydrogenase complex (Complex I), one in the cox3 gene (Complex IV), and one in the atp8 gene (Complex V). A cladistic approach performed with brook charr, arctic charr, and two other salmonid fishes (rainbow trout [Oncorhynchus mykiss] and Atlantic salmon [Salmo salar]) revealed that only five amino acid replacements were specific to the charr comparison and not shared with the other two salmonids. In addition, five amino acid substitutions localized in the nad2 and nad5 genes denoted negative scores according to the functional properties of amino acids and, therefore, could possibly have an impact on the structure and functional properties of these mitochondrial peptides. The comparison of both brook and arctic charr mtDNA with that of rainbow trout also revealed a relatively constant mutation rate for each specific gene among species, whereas the rate was quite different among genes. This pattern held for both synonymous and nonsynonymous nucleotide positions. These results, therefore, support the hypothesis of selective constraints acting on synonymous codon usage.     

Patterns of density‐dependent growth in juvenile stream‐dwelling salmonids

Literature data for 19 populations from 16 different studies of six species of stream‐dwelling salmonids were analysed to test the hypothesis that density‐dependent growth is stronger at low rather than at high population density. Fifteen of 19 populations showed evidence of a significant decrease in growth rate with increasing density. In 11 of these 15 populations, the pattern of density‐dependent growth was better described by a negative power curve than by a linear regression ( i.e . Akaike Information Criterion, AIC _linear −  AIC _power > 2), whereas only one population was better described by a linear regression than by a negative power curve; three populations were adequately described by both models ( AIC  < 2). In 10 of the 11 populations that were best described by a negative power curve, most of the decrease in growth rate occurred at population densities <1 fish m⁻², when space limitation is unlikely. This analysis provides broad support for the hypothesis that density‐dependent growth in stream salmonids occurs primarily at low population densities, probably due to exploitative competition.     

Patterns of subspecific anthropogenic introgression in two salmonid genera

Introgressive hybridizations have often been observed between native and introduced trouts of North America (Oncorhynchus spp.) and Europe (Salmo spp.), including some lineages that have been isolated for more than a million years. These observations have suggested that introgression is the expected result between introduced and indigenous conspecific salmonids. However, an examination of published information reveals a high variability in such anticipated gene flow. Many studies have noted the relative ease of translocating freshwater over anadromous salmonids, and this difference has been related to the more complex adaptations of anadromous populations (e.g., freshwater and marine residence, smoltification, juvenile and adult migration) that obstruct their translocation to conspecifically colonized areas. This contrast extends to introgressive capabilities where examples of introgression among freshwater populations predominate. Despite intensive introductions of non-native salmonids, indigenous anadromous populations commonly resist introgression. However, within major lineages, anadromous populations appear to be more susceptible to introgression. Measuring the extent and dynamics of such introgressions remains challenging because subgroups within major lineages lie on or below the threshold for detection by molecular genetic markers. These substructures appear to reflect the more rapid evolution of directional selection promoting, for instance, temporal or microgeographic divergence within a population unit defined by genetic markers. Consequently, management that assumes panmixia within a particular region based on even intensive molecular genetic analysis will inevitably erode and prevent reformation of this substructure to the detriment of the overall genetic variability and productivity.     

Genetic evidence for seasonal consumption of monkfish (Lophius spp.) and salmonids (Salmo spp.) by gray seals

Recoveries of gray seal (Halichoerus grypus) populations across their eastern Atlantic distribution have led to a steady increase in seal-fishery interactions. Fishers have estimated depredation of salmonids (Salmo spp.) and monkfish (Lophius spp.) as high as 40% and 59% respectively in Ireland. However, empirical evidence for the consumption of these species has been extremely limited due to diagnostic hard part remains not being found in scats or stomach samples. We applied species-specific primers and tested for the presence of monkfish and salmonids in gray seal diet genetically using quantitative polymerase chain reaction (qPCR) on scats. Monkfish occurred in 29.7% of sampled scats, while salmonids occurred in 12.7%. Seasonal and regional variability in occurrence were noted for both species, likely related to the migratory behavior of the prey species and proximity of seal haul-outs to aquaculture sites. Traditional hard part analysis of scats, including scats that tested positive for monkfish and salmonid DNA, failed to find any evidence of either species. This study provides important empirical evidence for the consumption of these species in Ireland that can inform management.     

Life history influences the vulnerability of New Zealand galaxiids to invasive salmonids

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Neoparamoebic gill infections: host response and physiology in salmonids

Amoebic gill diseases (AGD) caused primarily by the amphizoic Neoparamoeba spp. have been identified as significant to fish health in intensive aquaculture. These diseases have consequently received significant attention with regard to disease pathophysiology. Neoparamoeba perurans has been putatively identified as the aetiological agent in salmonids, with other species such as turbot Psetta maxima and sea bass Dicentrarchus labrax also affected. Similarly, Neoparamoeba spp. have also been identified in co‐infections with other gill diseases in salmonids. While infection of the gills results in an acute multifocal hyperplastic host response, reduced gill surface area and increased mucous cell densities, ion regulation and respiration in terms of blood gasses are only marginally affected. This may be partially attributed to reserve respiratory capacity and a reduction in mucous viscosity allowing for a greater flushing of the gill, so reducing the gill mucus boundary layer. Clinical and acute infections result in significant cardiovascular compromise with increases in aortic blood pressure, and systemic vascular resistance in Atlantic salmon, Salmo salar, which are not seen in rainbow Oncorhynchus mykiss and brown trout Salmo trutta. Increases in vascular resistance appear to be due to vascular constriction potentially reducing blood flow to the heart in compromised fishes, the overall effect being to lead to a compensatory tissue remodelling and change in cardiac shape in chronically infected fishes. The combined effect of reduced gill surface area and cardiovascular compromise leads to a significant reduction in swimming performance and increases in the routine metabolic rate that lead to an increase in the overall metabolic cost of disease.     

Similarity of vasorelaxant effects of natriuretic peptides in isolated blood vessels of salmonids

Natriuretic peptides (NPs) have been implicated in cardiovascular regulation in rainbow trout (Oncorhyncus mykiss), and it has been observed that the vasorelaxant activity of distinct trout and human NPs is similar in isolated trout arteries. This study characterizes the response of a variety of vessels from rainbow trout and other salmonids to different NPs. The effects of heterologous (rat atrial and human atrial) and homologous (rainbow trout atrial and rainbow trout ventricular) NPs were examined in precontracted efferent branchial arteries from rainbow trout (O. mykiss, Kamloops strain), lake whitefish (Coregonus clupeaformis), and in rainbow trout celiacomesenteric arteries and anterior cardinal veins. The response to mammalian NPs was also examined in efferent branchial arteries from the steelhead (O. mykiss, Skamania strain), coho salmon (Oncorhyncus kisutch), brook trout (Salvelinus fontinalis), and brown trout (Salmo trutta). In general, there were relatively few differences that were species, peptide, or vessel specific. There was no difference in the sensitivity (concentration producing a half-maximal response EC(50)) or efficacy (percent relaxation, i.e., E(max)) of trout or whitefish efferent branchial arteries to any NP, except human NP, which was significantly less effective (greater EC(50) and lower E(max)) in whitefish arteries. There were no differences in E(max) of mammalian NPs in efferent branchial arteries from any species, and only coho and brook trout had significantly different EC(50)'s (coho, 1.0+/-0.2 nM; brook trout, 4. 2+/-0.6 nM; and other species, from 1.9 to 3.5 nM). Rainbow and coho anterior cardinal veins were less sensitive than arteries to mammalian NPs (EC(50)'s; 8.8+/-2.0, 2.0+/-0.1 vs. 3.0+/-0.9, 1.0+/-0. 2, respectively), whereas brown trout veins were more sensitive (1. 0+/-0.2, 3.5+/-1.3, respectively). Sodium nitroprusside (SNP), which activates soluble guanylate cyclase, was vasodilatory, albeit significantly less potent than all NPs, in efferent branchial arteries of all species. SNP was significantly more potent in trout than whitefish efferent branchial arteries, whereas it was equally efficacious in these vessels. These results demonstrate that multiple vessels from various salmonids are similarly responsive to the vasorelaxant effects of a variety of NPs and that the salmonid NP receptor has relatively little ability to discriminate between homologous and heterologous peptides. We conclude that the vascular NP receptor complex is highly conserved among salmonids. Further, salmonids utilize cyclic guanosine monophosphate (cGMP) elevations for reductions of vascular tonus by both particulate and soluble guanylate cyclase pathways.     

Genetic variation and clonal diversity of <Emphasis Type="Italic">Bromus ircutensis</Emphasis> Kom. in the Otingdag sandy land detected by <Emphasis Type="Italic">ISSR markers</Emphasis>

Genetic variation and clonal diversity of nine populations of Bromus ircutensis Kom. from the Otingdag sandy land were investigated using Inter Simple Sequence Repeat (ISSR) markers. A total of 102 bands were amplified by using 11 ISSR primers chosen for the study. Among those 99% were polymorphic indicating high level of genetic variation at the species level with a mean genetic diversity (H) of 0.292 and Shannon information index (I) of 0.450. Percentage of polymorphic loci (PPL) of nine populations was 76.48% on average, which provides more evidence of considerable genetic variation at the population level. AMOVA analysis revealed that total genetic variation was higher within populations (87.06%) than between populations (12.94%), which is mainly the result of the extensive gene flow (Nm = 1.682) among B. ircutensis populations. UPGMA cluster analysis divided the nine populations into two groups. There was significant or moderate negative correlations between genetic diversity parameters (PPL, H, I) and longitude or latitude. Mantel test also showed a significant correlation between geographical distance and genetic distance (r = 0.681, p = 0.002). Our findings indicated that distribution of B. ircutensis populations was influenced by geographical and ecological factors. Clonal diversity was also high with 108 individuals identified by 11 ISSR primers being all of different genets. Our results provide a molecular basis for sustainable management and conservation of B. ircutensis in the study area.     

Predation by introduced fish constrains the thermal distribution of aquatic Coleoptera in mountain lakes

1. Most high mountain lakes were free of fish until humans stocked them. This provides the opportunity to study the extent to which predation constrains the thermal distribution of large macroinvertebrates, among lakes of a suitable temperature for them. 2. We analysed the distribution of aquatic beetles (Coleoptera, Dytisicidae, including the genera Agabus, Platambus, Hydroporus and Boreonectes) in a set of 82 lakes in the Pyrenees. Temperature was the most important variable explaining the overall distribution of dytiscids (out of 29 environmental variables considered). The presence of fish (i.e. salmonids) and macrophyte cover (plants provide refuge from predators) was also important. Indeed, either salmonids or macrophytes as single factors explained more of the variance in dytiscid distribution than temperature. 3. Further analysis showed that the presence of salmonids was particularly important for the medium‐sized dytiscid Agabus bipustulatus. This species is generally eurythermic, although in the Pyrenees it is found mainly in cold lakes. This is attributed to predation pressure from fish, since the latter are more likely to be present in warm lakes. As a consequence, salmonids increase fragmentation of A. bipustulatus with respect to populations occupying lowland habitats. 4. Predation can therefore constrain the distribution of species to a fraction of habitats that appear suitable based on simple thermal responses. As humans also facilitate the dispersal of non‐native fish, the consequent modification of distribution patterns in fresh waters could make it difficult to predict how distributions might change in relation to climate warming.