Life history and genetic characterisation of sea trout Salmo trutta in the Adriatic Sea

1. The brown trout Salmo trutta is characterised by both anadromous (sea trout) and resident populations, naturally occurring in Atlantic and Ponto-Caspian rivers. Sea trout are currently considered absent from rivers of the Mediterranean area, probably because of the non-optimal chemical–physical characteristics of the Mediterranean Sea. However, the occasional bycatch of smoltified S. trutta in the Adriatic Sea is well known among fishermen and the biological explanation of this phenomenon is still controversial. The aim of this study was to compare the genetic diversity of freshwater and marine brown trout to try to understand the factors underlying the presence of putative anadromous brown trout in the Adriatic Sea.
2. In this study, we analysed the genetic diversity of: (1) wild brown trout collected from the Esino River (central Italy); (2) a domestic strain of brown trout used for stocking the study area; and (3) a sample of Adriatic sea trout collected near the outlet of the Esino River. Together with genetic analysis, we carried out scale analysis in order to track the freshwater/marine stages of the life cycle in the sea trout samples. The genetic characterisation was carried out by polymerase chain reaction–restriction fragment length polymorphism analysis of the mtDNA fragment ND-5/6 and the nuclear locus LDH-C1* and by genotyping 15 microsatellite loci. The genetic polymorphism obtained was used to investigate intra- and inter-population genetic diversity, rates of genetic introgression between wild and domestic samples and the origin of sea trout specimens by using assignment tests.
3. Our genetic analyses demonstrated that the sea trout analysed in this study are from the domestic strain of Atlantic origin used in central Italy for stocking activities. The level of genetic introgression between native and domestic samples is high in the Esino River. The populations more resilient to introgressive hybridisation appeared to be those living in the portion of the river network dominated by carbonate rocks. Assignment tests (GeneClass) suggest the existence of a link between stocking efforts and the freshwater origin of the sea trout. In addition, data obtained from the analysis of scales, size measurement, and sex determination showed a pattern of smolt age, size, and sex ratio very similar to those observed in other anadromous populations.
4. In conclusion, the present study highlighted that sea trout from the central Adriatic Sea originated from brown trout of Atlantic origin inhabiting the Esino River. Their seaward migratory behaviour could represent a consequence of an active migration instead of a passive displacement by water flow. Our results also showed that traditional stocking practices represent a negative activity for the conservation of the last Mediterranean native S. trutta populations.

     

The effects of trout on epibenthic odonate naiads in stream pools

• 1 In a southern Califomian stream naiads of a lestid damselfly (Archilestes grandis Rambur) were much less abundant, moved less, exhibited fewer conspicuous behaviours, were more likely to occur in refuge areas, and had different diets in pools containing versus pools lacking rainbow trout (Oncorhynchus mykiss Richardson). To determine if trout were responsible for these patterns, we removed trout from some stream pools and added them to pools lacking trout, with unmanipulated trout and troutless pools acting as controls.
• 2 The abundance and emergence of A. grandis were drastically reduced, and the proportion of lestid populations in refuge areas greatly increased, when trout were added to pools; however, the removal of trout had less drastic effects on lestid abundance and distribution, Aeshna walkeri (Kennedy) was also more abundant in pools lacking than in pools containing trout.
• 3 Trout manipulations affected lestid behaviour, with swimming being observed only in troutless pools and movement tending to be greater in pools lacking rather than containing trout.
• 4 One week after manipulations started, the number of prey items per lestid gut was higher in troutless control than in trout addition pools. Ostracods and chironomids were more abundant, and mayflies were less abundant, in the diets of lestids from pools lacking versus containing trout. Comparisons of the environmental abundances of prey taxa and lestid diet composition indicated that lestid selectivities for Caenis were higher, and those for Paraleptophlebia, ostracods, and Eubrianax lower, in trout than in troutless pools.
• 5 Although similar at the beginning of manipulations, head widths of lestids in troutless control pools were greater than those in trout addition pools after 3 weeks.

     

Heritable morphological differentiation in salmonids from two distinct stream types

We tested for phenotype-to-habitat associations in brown trout Salmo trutta populations from two ecologically different habitat types; i.e., groundwater and surface-water-fed streams. Additionally, we raised captive offspring from two such populations under standardised conditions to test whether potential phenotypic differentiation would be passed on to offspring. We found analogous differentiation by habitat in multiple wild populations. Some of these morphological differences were at least partially inherited by offspring. We suggest that this could have implications for both scientists and fisheries authorities studying or managing trout populations.     

The selection of the ‘wild’: A combined molecular approach for the identification of pure indigenous fish from hybridised populations

The identification of pure indigenous fish from hybridised populations represents a key issue in fisheries management and conservation biology. In the present study an approach for selection of purebred marble trout (Salmo trutta marmoratus C.) individuals out of admixed populations was set up and assessed. In a first step, baseline data sets of pure marble trout and pure brown trout specimens based on twelve microsatellite loci were used to simulate five consecutive generations of admixture. The baseline and the resulting simulation data sets were then combined with data of a ‘real’ hybridised marble trout population to perform a single individual assignment test as implemented in STRUCTURE. By this procedure the assignment approach was calibrated and it was possible to compare admixture coefficients obtained for individuals from different populations. The ranking of individual admixture coefficients on a plot and comparison with simulated data revealed that the test population was composed of pure marble trout individuals, first generation hybrids between marble trout and brown trout, and hybrid backcross specimens between both groups. However, by defining a critical q-value of 0.1 and additionally integrating individual sequence data of the mtDNA control region, it was possible to indicate individuals, which could be selected for the establishment of a pure marble trout strain.     

Effects of Large Woody Debris Addition on Stream Habitat and Brook Trout Populations in Appalachian Streams

Large woody debris (LWD) was added to eight streams in the central Appalachians of West Virginia to determine if stream habitat could be enhanced and brook trout (Salvelinus fontinalis) populations increased. Brook trout populations were assessed one year prior to habitat manipulation and 3 years post-habitat manipulation. LWD was added by felling approximately 15 trees per 300 m stream reach. Four of the streams had LWD added to one 300 m reach with 300 m unmanipulated reaches upstream and downstream of the manipulated reach to observe within-stream effects of LWD additions on brook trout density. The remaining four streams had LWD added to three 300 m reaches and these streams were compared to those with only a single 300 m manipulated reach to observe the effects of the extent of habitat manipulation on brook trout density. New pools were formed by the addition of LWD, but overall pool area did not increase significantly in reaches where LWD was added. The relatively high gradient and coarse substrate of these streams may have precluded the added LWD from having a significant influence on stream channel morphology and habitat complexity. No pools were formed in the highest gradient stream, while the stream with the most pools formed had the lowest gradient. Brook trout populations fluctuated following habitat manipulations, and there was no overall effect of the LWD additions on within-stream variability in brook trout density. When there were significant differences among-streams with different extents of LWD additions, those streams receiving LWD additions over a large extent had the greatest brook trout densities. The full potential of added LWD to change stream habitat and influence on brook trout populations may take more time to develop than the 3 years post-manipulation period of this study.     

Phylogeography and taxonomic status of trout and salmon from the Ponto‐Caspian drainages,with inferences on European Brown Trout evolution and taxonomy

Current taxonomy of western Eurasian trout leaves a number of questions open; it is not clear to what extent some species are distinct genetically and morphologically. The purpose of this paper was to explore phylogeography and species boundaries in freshwater and anadromous trout from the drainages of the Black and the Caspian Seas (Ponto‐Caspian). We studied morphology and mitochondrial phylogeny, combining samples from the western Caucasus within the potential range of five nominal species of trout that are thought to inhabit this region, and using the sequences available from GenBank. Our results suggest that the genetic diversity of trout in the Ponto‐Caspian region is best explained with the fragmentation of catchments. (1) All trout species from Ponto‐Caspian belong to the same mitochondrial clade, separated from the other trout since the Pleistocene; (2) the southeastern Black Sea area is the most likely place of diversification of this clade, which is closely related to the clades from Anatolia; (3) The species from the Black Sea and the Caspian Sea drainages are monophyletic; (4) except for the basal lineage of the Ponto‐Caspian clade, Salmo rizeensis, all the lineages produce anadromous forms; (5) genetic diversification within the Ponto‐Caspian clade is related to Pleistocene glacial waves; (6) the described morphological differences between the species are not fully diagnostic, and some earlier described differences depend on body size; the differences between freshwater and marine forms exceed those between the different lineages. We suggest a conservative taxonomic approach, using the names S. rizeensis and Salmo labrax for trout from the Black Sea basin and Salmo caspius and Salmo ciscaucasicus for the fish from the Caspian basin.     

Lack of molecular genetic divergence between sea-ranched and wild sea trout (Salmo trutta)

The supportive breeding programme for sea trout (Salmo trutta) in the River Dalälven, Sweden, is based on a sea‐ranched hatchery stock of local origin that has been kept ‘closed’ to the immigration of wild genes since the late 1960s (about seven generations). In spite of an apparent potential for substantial uni directional gene flow from sea‐ranched to wild (naturally produced) trout, phenotypic differences with a presumed genetic basis have previously been observed between the two ‘stocks’. Likewise, two previous studies of allozyme and mitochondrial DNA variation based on a single year of sampling have indicated genetic differentiation. In the present study we used microsatellite and allozyme data collected over four consecutive years, and tested for the existence of overall genetic stock divergence while accounting for temporal heterogeneity. Statistical analyses of allele frequency variation (F‐statistics) and multilocus genotypes (assignment tests) revealed that wild and sea‐ranched trout were significantly different in three of four years, whereas no overall genetic divergence could be found when temporal heterogeneity among years within stocks was accounted for. On the basis of estimates of effective population size in the two stocks, and of F_ST between them, we also assessed the level of gene flow from sea‐ranched to wild trout to be ≈ 80% per generation (with a lower confidence limit of ≈ 20%). The results suggest that the reproductive success of hatchery and naturally produced trout may be quite similar in the wild, and that the genetic characteristics of the wild stock are largely determined by introgressed genes from sea‐ranched fish.     

Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa

DNA sequence data were collected and screened for single nucleotide polymorphisms (SNPs) in westslope cutthroat trout (Oncorhynchus clarki lewisi) and also for substitutions that could be used to genetically discriminate rainbow trout (O. mykiss) and cutthroat trout, as well as several cutthroat trout subspecies. In total, 260 expressed sequence tag‐derived loci were sequenced and allelic discrimination genotyping assays developed from 217 of the variable sites. Another 50 putative SNPs in westslope cutthroat trout were identified by restriction‐site‐associated DNA sequencing, and seven of these were developed into assays. Twelve O. mykiss SNP assays that were variable within westslope cutthroat trout and 12 previously published SNP assays were also included in downstream testing. A total of 241 assays were tested on six westslope cutthroat trout populations (N = 32 per population), as well as collections of four other cutthroat trout subspecies and a population of rainbow trout. All assays were evaluated for reliability and deviation from Hardy–Weinberg and linkage equilibria. Poorly performing and duplicate assays were removed from the data set, and the remaining 200 assays were used in tests of population differentiation. The remaining markers easily distinguished the various subspecies tested, as evidenced by mean G_ST of 0.74. A smaller subset of the markers (N = 86; average G_ST = 0.40) was useful for distinguishing the six populations of westslope cutthroat trout. This study increases by an order of magnitude the number of genetic markers available for the study of westslope cutthroat trout and closely related taxa and includes many markers in genes (developed from ESTs).     

Growth chronologies of white sucker, Catostomuscommersoni, and lake trout, Salvelinusnamaycush: a comparison among lakes and between trophic levels

A growth chronology index was used to determine whether changes in ecosystem structure and function in lakes could be associated with fish growth histories. Growth chronologies were compared for white suckers, Catostomus commersoni, from Little Moose (oligotrophic), Oneida (eutrophic), and Cayuga (mesotrophic) lakes (New York) from opercular bone growth increments, and for lake trout, Salvelinus namaycush, from Little Moose Lake using otolith growth. The longevity of these species allowed the development of chronologies from 17 to 33 years in length using only contemporary collections. We used these chronologies to examine whether fish growth histories could be used as an index for ecosystem-scale changes. Specifically, we examined whether zebra mussel, Dreissena polymorpha, invasion in Oneida and Cayuga lakes in the early 1990s, and treatment of sewage effluent from dwellings around Little Moose Lake beginning during the late 1980s could be detected in white sucker and lake trout growth chronologies. White sucker growth in Oneida and Cayuga Lakes did not differ before and after zebra mussel invasions. Neither white sucker nor lake trout growth chronologies from Little Moose Lake reflect changes in growth expected with reduced productivity levels associated with improved sewage treatment. Growth chronologies of these two species did not detect the ecosystem-scale changes that occurred in the study lakes.     

Comparison of competitive ability between native and introduced salmonids: evidence from pairwise contests

Brown trout, Salmo trutta, and rainbow trout, Oncorhynchus mykiss, have been introduced to freshwaters in Hokkaido, Japan. Today, it is recognized that these introduced salmonids have negative impacts on native salmonids such as white-spotted charr, Salvelinus leucomaenis, and masu salmon, O. masou. In particular, interspecific competition may be an important mechanism that could contribute to the exclusion for native salmonids. In this study, experimental pairwise contests were conducted to compare interference competitive ability between native and introduced salmonids. We demonstrated that brown trout were competitively superior to white-spotted charr and masu salmon whereas rainbow trout were superior to white-spotted charr. We suggest that introduced brown trout negatively impact both white-spotted charr and masu salmon, and introduced rainbow trout negatively impact white-spotted charr.     

A genetic comparison of pig, cow and trout isolates of Lactococcus garvieae by PFGE analysis

Aims: Genetic comparison of Lactococcus garvieae isolated from mammals and fish. Methods and Results: One hundred and ninety‐seven L. garvieae isolates obtained from trout (n = 153), cow (n = 7) and pigs (n = 37) were genetically characterized by determining their pulsed‐field gel electrophoresis (PFGE) profiles after macrorestriction with Bsp120I. Overall, L. garvieae isolates from pigs, cow and trout exhibited distinct PFGE patterns, with a low genetic relationship between them. Isolates from trout generated two pulsotypes [Genetic diversity (GD) 0·01] showing that the fish isolates were more genetically homogenous than the others. The L. garvieae isolates from cows displayed five (GD 0·71) different pulsotypes, while the swine isolates displayed 13 different pulsotypes (GD 0·35). Twenty‐one of the 37 swine strains (56·8%) were grouped in a single cluster that included two closely related (93% similarity) pulsotypes. These pulsotypes exhibited a high frequency of isolation from different organs of the animals, and they were also broadly distributed among herds, suggesting a wide distribution across the swine population. This suggests that L. garvieae might be able to colonize different organs of the swine cardio‐respiratory system. Conclusions: Results indicate that most L. garvieae isolates from pigs and trout exhibited a distinct genetic background. Significance and Impact of the Study: The present study describes the isolation of L. garvieae from both diseased and healthy pigs for the first time, and the findings suggest that pigs could be a previously unknown reservoir of this pathogen.     

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.     

Daily energy intake and growth of piscivorous brown trout,Salmo trutta

• 1 The chief objectives were to determine the daily energy intake and growth of piscivorous brown trout (Salmo trutta), and to compare the observed values with those expected from models developed previously for brown trout feeding on freshwater invertebrates. Energy budgets for individual fish were obtained from experiments with 40 trout (initial live weight 250–318 g) bred from wild parents, and kept at five constant temperatures (5, 10, 13, 15, 18 °C) and 100% oxygen saturation. Each trout was fed to satiation on freshly killed sticklebacks (Gasterosteus aculeatus) over a period of 42 days.
• 2 Energy intake (C_IN cal day^‐1) and growth (C_G cal day^‐1) were measured directly and energy losses (C_Q cal day^‐1) were estimated by difference (C_Q = C_IN ‐ C_G). All three variables increased with temperature. A model previously used to predict the daily energy intake (C_IN(INV)) of trout feeding to satiation on invertebrates was adapted, by changing only one parameter, to provide an excellent model (R² = 0.998) for predicting the mean daily energy intake (C_IN(ST)) for the piscivorous trout. Values of C_IN(ST) were 58% (range 48–67%) higher than those for C_IN(INV). A simple model was also developed to estimate mean daily energy losses for piscivorous trout (R² = 0.999). Both models were combined to provide excellent estimates of the daily energy gain (growth) of the piscivorous trout, and this was about three times that for trout feeding on invertebrates. The optimum temperature for maximum growth in energy terms increased from 13.9 °C for trout feeding on invertebrates to 17.0 °C (range 16.6–17.4 °C) for piscivorous trout.
• 3 The models are basically an extension of those developed for trout feeding on invertebrates. They show clearly how energy intake, growth, and the optimum temperature for growth increase markedly when trout change their diet from invertebrates to fish. The implications of this are discussed and it is shown that, in theory, these increases should continue if a more energy‐rich diet was utilised by the trout.

     

Biomarkers in fish from dioxin-contaminated fjords

Abstract

The Grenland fjords, southern Norway, have been heavily contaminated by dibenzo-p-dioxins and dibenzofurans (dioxins) over decades through inputs from a magnesium smelter. Despite radically decreased inputs since 1990, there are still high levels of dioxins in both biotic and abiotic components of the fjords. The aim of the study was to establish whether biomarkers’ responses in three fish species, Atlantic cod (Gadus morhua L.), sea-trout (anadromous brown trout, Salmo trutta L.) and flounder (Platichthys flesus L.), could be used to discern the effects in the most contaminated ecosystem, Frierfjord, from the effects in the adjacent, less-contaminated ecosystem, Eidangerfjord. Biomarker responses clearly indicated that the three fish species were affected by dioxin exposure. Phase I responses in cod and trout could be used to differentiate exposure in the two fjord ecosystems. Phase II responses (glutathione S-transferase) in cod and trout similarly indicated a higher dioxin exposure in Frierfjord compared with Eidangerfjord. Results for glutathione S-transferase and glutathione reductase indicated different exposure levels in the two fjords, but also showed seasonal variability, and the results highlighted the need for baseline data for these biomarkers.     

Characterization of sex chromosomes in rainbow trout and coho salmon using fluorescence in situ hybridization (FISH)

With the aim of characterizing the sex chromosomes of rainbow trout (Oncorhynchus mykiss) and to identify the sex chromosomes of coho salmon (O. kisutch), we used molecular markers OmyP9, 5S rDNA, and a growth hormone gene fragment (GH2), as FISH probes. Metaphase chromosomes were obtained from lymphocyte cultures from farm specimens of rainbow trout and coho salmon. Rainbow trout sex marker OmyP9 hybridizes on the sex chromosomes of rainbow trout, while in coho salmon, fluorescent signals were localized in the medial region of the long arm of one subtelocentric chromosome pair. This hybridization pattern together with the hybridization of a GH2 intron probe on a chromosome pair having the same morphology, suggests that a subtelocentric pair could be the sex chromosomes in this species. We confirm that in rainbow trout, one of the two loci for 5S rDNA genes is on the X chromosome. In males of this species that lack a heteromorphic sex pair (XX males), the 5S rDNA probe hybridized to both subtelocentrics This finding is discussed in relation to the hypothesis of intraspecific polymorphism of sex chromosomes in rainbow trout.     

Localization of monoamines in the forebrain of two salmonid species,with special reference to the hypothalamo-hypophysial system

Summary In the salmon and trout aminergic cell bodies were found in the nucleus recessus lateraralis (NRL) and the nucleus recessus posterioris (NRP), both of which are situated near the third ventricle. Three cell types could be distinguished. Type 1 produces a green and type 2 a yellow fluorescence. The former type probably contains dopamine and the latter 5-hydroxytryptamine. Both types possess intraventricular protrusions in contact with the cerebrospinal fluid. The third cell type produces a less intense blue-green fluorescence; relatively few cells of this type have thick processes in contact with the ventricle. In addition, large fluorescent cells were found in the salmon, dorsal from the caudal part of the NRL. The various parts of the NRL and NRP are interconnected by thick bundles of nerve fibers; tracts leaving the nuclei could be traced for short distances only. The cells of the nucleus praeopticus (NPO), those of the medial part and to a much lesser extent also of the lateral part of the nucleus lateralis tuberis (NLT) have an aminergic innervation which probably originates from the NRL and/or NRP. All parts of the neurohypophysis contain many monoaminergic fibers, with aminergic material concentrated at the neuro-adenohypophysial interface. Fibers were not observed to penetrate the basal lamina. In the salmon and trout the fibers have a similar distribution, but differ in the intensity of fluorescence, being high in the salmon and low in the trout. Only in the trout have fluorescent cells been found in the adenohypophysis and very occasionally in the neurohypophysis. A number of these cells are basophilic and show a PAS-positive reaction.     

The effects of dredging and fish stocking on the trophic status of shallow,peaty ditches

Size selective predation on molluscs was apparent for lake trout (Salvelinus namaycush) and round whitefish (Prosopium cylindraceum), but not for arctic grayling (Thymallus arcticus), in the Toolik Lake region of arctic Alaska during the summer of 1986. Lake trout consumed significantly larger molluscs of all taxa than did round whitefish, and selected larger molluscs than were available on either rocky or soft-sediment habitats. Round whitefish were not size-selective on the snail Lymnaea, but were size-selective on the snail Valvata and on clams from the soft sediments. Round whitefish consumed fewer and smaller Lymnaea compared to lake trout. Because lake trout ate more Lymnaea and also tended to select larger, reproductive-sized individuals, this fish could potentially have a more detrimental impact on the Lymnaea population. Finally, differences in Lymnaea densities and size distributions between lakes with and without lake trout suggest that these fish may be responsible for the pattern of distribution, size, and density observed for Lymnaea in Toolik Lake and other area lakes.     

Predator effects on prey population dynamics in open systems

Animal population dynamics in open systems are affected not only by agents of mortality and the influence of species interactions on behavior and life histories, but also by dispersal and recruitment. We used an extensive data set to compare natural loss rates of two mayfly species that co-occur in high-elevation streams varying in predation risk, and experience different abiotic conditions during larval development. Our goals were to generate hypotheses relating predation to variation in prey population dynamics and to evaluate alternative mechanisms to explain such variation. While neither loss rates nor abundance of the species that develops during snowmelt (Baetis bicaudatus) varied systematically with fish, loss rates of the species that develops during baseflow (Baetis B) were higher in streams containing brook trout than streams without fish; and surprisingly, larvae of this species were most abundant in trout streams. This counter-intuitive pattern could not be explained by a trophic cascade, because densities of intermediate predators (stoneflies) did not differ between fish and fishless streams and predation by trout on stoneflies was negligible. A statistical model estimated that higher recruitment and accelerated development enables Baetis B to maintain larger populations in trout streams despite higher mortality from predation. Experimental estimates suggested that predation by trout potentially accounts for natural losses of Baetis B, but not Baetis bicaudatus. Predation by stoneflies on Baetis is negligible in fish streams, but could make an important contribution to observed losses of both species in fishless streams. Non-predatory sources of loss were higher for B. bicaudatus in trout streams, and for Baetis B in fishless streams. We conclude that predation alone cannot explain variation in population dynamics of either species; and the relative importance of predation is species- and environment-specific compared to non-predatory losses, such as other agents of mortality and non-consumptive effects of predators. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Non‐native trout limit native brook trout access to space and thermal refugia in a restored large‐river system

We used direct observation via snorkeling surveys to quantify microhabitat use by native brook (Salvelinus fontinalis) and non‐native brown (Salmo trutta) and rainbow (Onchorynchus mykiss) trout occupying natural and restored pool habitats within a large, high‐elevation Appalachian river, United States. Permutational multivariate analysis of variance (PERMANOVA) and subsequent two‐way analysis of variance (ANOVA) indicated a significant difference in microhabitat use by brook and non‐native trout within restored pools. We also detected a significant difference in microhabitat use by brook trout occupying pools in allopatry versus those occupying pools in sympatry with non‐native trout—a pattern that appears to be modulated by size. Smaller brook trout often occupied pools in the absence of non‐native species, where they used shallower and faster focal habitats. Larger brook trout occupied pools with, and utilized similar focal habitats (i.e. deeper, slower velocity) as, non‐native trout. Non‐native trout consistently occupied more thermally suitable microhabitats closer to cover as compared to brook trout, including the use of thermal refugia (i.e. ambient–focal temperature >2°C). These results suggest that non‐native trout influence brook trout use of restored habitats by: (1) displacing smaller brook trout from restored pools, and (2) displacing small and large brook trout from optimal microhabitats (cooler, deeper, and lower velocity). Consequently, benefits of habitat restoration in large rivers may only be fully realized by brook trout in the absence of non‐native species. Future research within this and other large river systems should characterize brook trout response to stream restoration following removal of non‐native species.     

Summer and fall microhabitat utilization of juvenile bull trout and cutthroat trout in a wilderness stream, Idaho

Microhabitat use and availability were evaluated and compared between different size classes of juvenile resident bull trout (Salvelinus confluentus) and cutthroat trout (Oncorhynchus clarki) in a small wilderness stream within the South Fork Clearwater River basin, Idaho. The objective was to determine if utilization of measured habitat characteristics changed from summer to late fall. Sampling of fish was conducted with night snorkeling. During the summer, smaller juvenile bull trout (<66 mm) total length (TL) were associated with shallow stream margins over coarse substrates. In the fall, they moved to significantly deeper, lower velocity water, and closer to cover (p<0.05), but maintained their association with coarse substrates. During the summer, larger juvenile bull trout and larger juvenile cutthroat trout (66–130 mm TL) occupied significantly deeper water than smaller juvenile bull trout (p<0.05). Generally, larger juvenile bull trout were found closer to the bottom and in lower velocity water than larger juvenile cutthroat trout (p<0.05). In the fall, larger juvenile bull trout and larger juvenile cutthroat trout were associated with significantly deeper, lower velocity water located closer to cover than in summer (p<0.05). However, cutthroat trout occupied slightly deeper water over finer substrates than bull trout. Deep water with low velocities evidently provide important rearing areas for large bull trout and large cutthroat trout in the fall. Land management practices that maintain such environments will benefit these species.