Assessing conditions influencing the longitudinal distribution of exotic brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) in a mountain stream: a spatially-explicit modeling approach

Trout species often segregate along elevational gradients, yet the mechanisms driving this pattern are not fully understood. On the Logan River, Utah, USA, exotic brown trout (Salmo trutta) dominate at low elevations but are near-absent from high elevations with native Bonneville cutthroat trout (Onchorhynchus clarkii utah). We used a spatially-explicit Bayesian modeling approach to evaluate how abiotic conditions (describing mechanisms related to temperature and physical habitat) as well as propagule pressure explained the distribution of brown trout in this system. Many covariates strongly explained redd abundance based on model performance and coefficient strength, including average annual temperature, average summer temperature, gravel availability, distance from a concentrated stocking area, and anchor ice-impeded distance from a concentrated stocking area. In contrast, covariates that exhibited low performance in models and/or a weak relationship to redd abundance included reach-average water depth, stocking intensity to the reach, average winter temperature, and number of days with anchor ice. Even if climate change creates more suitable summer temperature conditions for brown trout at high elevations, our findings suggest their success may be limited by other conditions. The potential role of anchor ice in limiting movement upstream is compelling considering evidence suggesting anchor ice prevalence on the Logan River has decreased significantly over the last several decades, likely in response to climatic changes. Further experimental and field research is needed to explore the role of anchor ice, spawning gravel availability, and locations of historical stocking in structuring brown trout distributions on the Logan River and elsewhere.     

Comparison of allopatric cutthroat trout stocks with those sympatric with coho salmon and sculpins in small streams

Synopsis Juvenile stocks of allopatric (upstream of barrier falls) cutthroat troutSalmo clarki and those sympatric (downstream of barrier falls) with coho salmonOncorhynchus kisutch and sculpinsCottus spp., were sampled during the late summer period of low flows in six small coastal streams in British Columbia. The objective was to obtain and compare information on pattern of habitat use and fish size distribution of these two trout types. In most instances, density (n m^–2; g m^–2) of cutthroat trout was considerably greater in pools and glides in the allopatric than in the sympatric stocks. The sympatric salmonids were dominated by juvenile coho salmon in pools and cutthroat trout in riffles. Sympatric cutthroat trout constituted from 7 to 45 % of the salmonids present in pools and from 50 to 90% in riffles. Glides were areas of intermediate densities for both salmonids, although coho salmon was the more abundant species in most instances. The density of sculpins was high in all three habitat types, and frequently it exceeded that of coho salmon and cutthroat trout combined. Sympatric cutthroat trout consisted primarily of underyearling fish, whereas allopatric cutthroat trout consisted primarily of two or more age classes with a large proportion of them living in pools. When tested in a laboratory stream both types of cutthroat trout had similar habitat preferences and agonistic behaviours, with the exception that allopatric trout made greater use of cover and defended pools more intensely than sympatric trout when the flow was increased. The results of this study provide insight of potential impact of coho salmon juvenile transplants into stream segments supporting allopatric cutthroat trout.     

Fall and Early Winter Movements of Cutthroat Trout, Oncorhynchus clarki, in Relation to Water Temperature and Ice Conditions in Dutch Creek, Alberta

Fall and winter movement and behaviour of 28 cutthroat trout Oncorhynchus clarki was determined using radiotelemetry to evaluate the effects of water temperature and ice conditions. As water temperatures decreased, cutthroat trout moved from more solitary positions to aggregations. With few exceptions, radiotagged fish aggregated with other fish in groups varying from 5 to approximately 70 fish. The percentage of fish aggregating and the mean size of aggregation was negatively correlated with water temperature. The mean distance moved by radiotagged cutthroat trout from 1 September to 12 January was 1.0km. After forming aggregations, fish tended to stay within a 120m length of stream until the end of tracking in mid-January. Fish that were less sedentary after their initial overwintering movement usually moved when their habitat was occluded by anchor ice. These fish moved thirty times farther and six times more often than fish in stable overwintering areas. In Dutch Creek multiple freezing events caused several ice related habitat exclusions and movements associated with large decreases in air temperature. Several bull trout and mountain whitefish were observed in groups with cutthroat trout.     

Discovery and characterization of novel genetic markers for use in the management of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi)

The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) is threatened by habitat destruction, over‐harvest and hybridization with nonnative trout. Currently, three Geographic Management Units (GMUs) are recognized within the taxon. Here, we describe a suite of 68 single‐nucleotide polymorphism (SNP) genetic markers for use in the study and management of Lahontan cutthroat trout and a closely related subspecies, the Paiute cutthroat trout (O. c. seleneris). These include markers variable within the two subspecies (n = 35), diagnostic for the two subspecies (n = 23) and diagnostic for Yellowstone cutthroat trout (O. c. bouvieri) and other closely related subspecies (n = 10). Sixty‐three markers were discovered by Sanger sequencing of 171 EST loci in an ascertainment panel including Lahontan cutthroat trout from four populations representing all GMUs. Five markers were identified in a secondary sequencing effort with a single population of Lahontan cutthroat trout. TaqMan assays were validated on six Lahontan cutthroat trout populations and a diverse panel of other trout. Over 90% of the markers variable in Lahontan cutthroat trout were polymorphic in at least two populations, and 66% were variable within all three GMUs. All Lahontan diagnostic markers were also fixed for the Lahontan allele in Paiute cutthroat trout. Most of the Yellowstone diagnostic markers can also be used for this purpose in other cutthroat trout subspecies. This is the first set of SNP markers to be developed for Lahontan cutthroat trout, and will be an important tool for conservation and management.     

A mechanistic assessment of seasonal microhabitat selection by drift-feeding rainbow trout <Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis> in a Southwestern headwater stream

The positioning of fishes within a riverscape is dependent on the proximity of complementary habitats. In this study, foraging and non-foraging habitat were quantified monthly over an entire year for a rainbow trout (Oncorhynchus mykiss) population in an isolated, headwater stream in southcentral New Mexico. The stream follows a seasonal thermal and hydrologic pattern typical for a Southwestern stream and was deemed suitable for re-introduction of the native and close relative, Rio Grande cutthroat trout (O. clarkii virginalis). However, uncertainty associated with limited habitat needed to be resolved if repatriation of the native fish was to be successful. Habitat was evaluated using resource selection functions with a mechanistic drift-foraging model to explain trout distributions. Macroinvertebrate drift was strongly season- and temperature-dependent (lower in winter and spring, higher in summer and fall). Models identified stream depth as the most limiting factor for habitat selection across seasons and size-classes. Additionally, positions closer to cover were selected during the winter by smaller size-classes (0, 1, 2), while net energy intake was important during the spring for most size-classes (0, 1, 2, 3). Drift-foraging models identified that 81% of observed trout selected positions that could meet maintenance levels throughout the year. Moreover, 40% of selected habitats could sustain maximum growth. Stream positions occupied by rainbow trout were more energetically profitable than random sites regardless of season or size-class. Larger size-classes (3, 4+) were energetically more limited throughout the year than were smaller size-classes. This research suggests that habitat in the form of deep pools is of paramount importance for rainbow trout or native cutthroat trout.     

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.     

Challenging convention: the winter ecology of brown trout (Salmo trutta) in a productive and stable environment

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Habitat use of Atlantic salmon Salmo salar parr in a dynamic winter environment: the influence of anchor‐ice dams

The effect of anchor‐ice dams on the physical habitat and behavioural responses of Atlantic salmon Salmo salar parr in a small, steep stream was investigated. Anchor‐ice dams formed periodically, leading to a dynamic winter environment as the study reach alternated between riffle and walk dominated habitat. Parr demonstrated large individual variation in habitat use, utilizing most of the wetted stream width, and were generally unaffected by diel changes in the mesohabitat composition. Furthermore, parr displayed high site fidelity in areas with low embedded substrata, and demonstrated few large movements between the three mesohabitat classes present: shallow riffle, walk and pool. Findings from this study question the importance of hydraulic variables such as water depth, flow velocity and dynamic ice formation as single habitat features for juvenile stream salmonids during winter and emphasize the importance of access to substratum cover.     

Effects of biotic and abiotic factors on the distribution of trout and salmon along a longitudinal stream gradient

Synopsis We examined the influence of biotic and abiotic factors on the distribution, abundance, and condition of salmonid fishes along a stream gradient. We observed a longitudinal change in fish distribution with native cutthroat trout, Oncorhynchus clarki utah, and introduced brown trout, Salmo trutta, demonstrating a distinct pattern of allopatry. Cutthroat trout dominated high elevation reaches, while reaches at lower elevations were dominated by brown trout. A transition zone between these populations was associated with lower total trout abundance, consistent changes in temperature and discharge, and differences in dietary preference. Variation in cutthroat trout abundance was best explained by a model including the abundance of brown trout and diel temperature, whereas variation in brown trout abundance was best explained by a model including the abundance of cutthroat trout and discharge. These results suggest the potential for condition-mediated competition between the two species. The results from our study can aid biologists in prioritizing conservation activities and in developing robust management strategies for cutthroat trout.     

Seasonal and temperature‐related movement of Colorado River cutthroat trout in a low‐elevation,Rocky Mountain stream

Mobile species will migrate considerable distances to find habitats suitable for meeting life history requirements, and stream‐dwelling salmonids are no exception. In April–October 2014, we used radio‐telemetry to examine habitat use and movement of 36 Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus (CRCT) in a 14.9‐km fragment of Milk Creek, a relatively low‐elevation stream in the Rocky Mountains (Colorado). We also used a network of data loggers to track stream temperature across time and space. Our objectives were to (1) characterize distribution and movement of CRCT, (2) evaluate seasonal differences in distribution and movement of CRCT, and (3) explore the relationship between stream temperature and distribution and movement of CRCT. During the course of our study, median range of CRCT was 4.81 km (range = 0.14–10.94) and median total movement was 5.94 km (range = 0.14–26.02). Median location of CRCT was significantly further upstream in summer than in spring, whereas range and movement of CRCT were greater in spring than in summer. Twenty‐six of the 27 CRCT tracked through mid‐June displayed a potamodromous (freshwater migratory) life history, migrating 1.8–8.0 km upstream during the spring spawning season. Four of the seven CRCT tracked through July migrated >1.4 km in summer. CRCT selected relatively cool reaches during summer months, and early‐summer movement was positively correlated with mean stream temperature. Study fish occupied stream segments in spring and fall that were thermally unsuitable, if not lethal, to the species in summer. Although transmitter loss limited the scope of inference, our findings suggest that preferred habitat is a moving target in Milk Creek, and that CRCT move to occupy that target. Because mobile organisms move among complementary habitats and exploit seasonally‐unsuitable reaches, we recommend that spatial and temporal variability be accounted for in delineations of distributional boundaries.     

A suite of twelve single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trout

A suite of 12 subspecies and species-specific single nucleotide polymorphism (species-specific SNP) markers was developed to distinguish rainbow trout (RT) Oncorhynchus mykiss from the four major subspecies of cutthroat trout: westslope cutthroat trout (WCT) Oncorhynchus clarki lewisi, Yellowstone cutthroat trout (YCT) Oncorhynchus clarki bouvieri, coastal cutthroat trout (CCT) Oncorhynchus clarki clarki, Lahontan cutthroat trout (LCT) Oncorhynchus clarki henshawi, and their hybrids. Several of the markers were linked to help strengthen hybrid determinations, and sex-specific species-specific SNP assays were also developed.     

Y chromosome phylogeny for cutthroat trout (Oncorhynchus clarkii) subspecies is generally concordant with those of other markers

Sequence divergence was evaluated in the non-recombining, male-specific OmyY1 region of the Y chromosome among the subspecies of cutthroat trout (Oncorhynchus clarkii) in the western United States. This evaluation identified subspecies-discriminating OmyY1-haplotypes within a ～1200 bp region of the OmyY1 locus and localized the region to the end of the Y chromosome by FISH analysis. OmyY1 sequences were aligned and used to reconstruct a phylogeny of the cutthroat trout subspecies and related species via maximum-parsimony and Bayesian analyses. In the Y-haplotype phylogeny, clade distributions generally corresponded to the geographic distributions of the recognized subspecies. This phylogeny generally corresponded to a mitochondrial tree obtained for these subspecies in a previous study. Both support a clade of trout vs. Pacific salmon, of rainbow trout, and of a Yellowstone cutthroat group within the cutthroat trout. In our OmyY1 tree, however, the cutthroat “clade”, although present topologically, was not statistically significant. Some key differences were found between trees obtained from the paternally-inherited OmyY1 vs. maternally-inherited mitochondrial haplotypes in cutthroat trout compared to rainbow trout. Other findings are: The trout OmyY1 region evolves between 3 and 13 times slower than the trout mitochondrial regions that have been studied. The Lahontan cutthroat trout had a fixed OmyY1 sequence throughout ten separate populations, suggesting this subspecies underwent a severe population bottleneck prior to its current dispersal throughout the Great Basin during the pluvial phase of the last ice age. The Yellowstone group is the most derived among the cutthroat trout and consists of the Yellowstone, Bonneville, Colorado, Rio Grande and greenback subspecies. Identification of subspecies and sex with this Y-chromosome marker may prove useful in conservation efforts.     

Effects of ice and floods on vegetation in streams in cold regions: implications for climate change

Riparian zones support some of the most dynamic and species‐rich plant communities in cold regions. A common conception among plant ecologists is that flooding during the season when plants are dormant generally has little effect on the survival and production of riparian vegetation. We show that winter floods may also be of fundamental importance for the composition of riverine vegetation. We investigated the effects of ice formation on riparian and in‐stream vegetation in northern Sweden using a combination of experiments and observations in 25 reaches, spanning a gradient from ice‐free to ice‐rich reaches. The ice‐rich reaches were characterized by high production of frazil and anchor ice. In a couple of experiments, we exposed riparian vegetation to experimentally induced winter flooding, which reduced the dominant dwarf‐shrub cover and led to colonization of a species‐rich forb‐dominated vegetation. In another experiment, natural winter floods caused by anchor‐ice formation removed plant mimics both in the in‐stream and in the riparian zone, further supporting the result that anchor ice maintains dynamic plant communities. With a warmer winter climate, ice‐induced winter floods may first increase in frequency because of more frequent shifts between freezing and thawing during winter, but further warming and shortening of the winter might make them less common than today. If ice‐induced winter floods become reduced in number because of a warming climate, an important disturbance agent for riparian and in‐stream vegetation will be removed, leading to reduced species richness in streams and rivers in cold regions. Given that such regions are expected to have more plant species in the future because of immigration from the south, the distribution of species richness among habitats can be expected to show novel patterns.     

Seasonal habitat selection by lake trout (<Emphasis Type="Italic">Salvelinus namaycush</Emphasis>) in a small Canadian shield lake: constraints imposed by winter conditions

The need for cold, well-oxygenated waters significantly reduces the habitat available for lake trout (Salvelinus namaycush) during stratification of small temperate lakes. We examined the spatial and pelagic distribution of lake trout over two consecutive summers and winters and tested whether winter increased habitat availability and access to littoral regions in a boreal shield lake in which pelagic prey fish are absent. In winter, lake trout had a narrowly defined pelagic distribution that was skewed to the upper 3 m of the water column and spatially situated in the central region of the lake. Individual core areas of use (50% Kernel utilization distributions) in winter were much reduced (75%) and spatially non-overlapping compared to summer areas, but activity levels were similar between seasons. Winter habitat selection is in contrast to observations from the stratified season, when lake trout were consistently located in much deeper waters (>6 m) and widely distributed throughout the lake. Winter distribution of lake trout appeared to be strongly influenced by ambient light levels; snow depth and day length accounted for up to 69% of the variation in daily median fish depth. More restricted habitat use during winter than summer was in contrast to our original prediction and illustrates that a different suite of factors influence lake trout distribution between these seasons.     

Winter bird communities in the northern Negev: species dispersal patterns, habitat use and implications for habitat conservation

Bird habitat conservation may require different management strategies for different seasonal bird assemblages. We studied habitat use by winter birds in forest and scrubland habitat patches in the northern Negev, Israel. Our goal was to assess whether differences in responses to landscape and habitat structure between breeding and non-breeding seasons require changes in future conservation plans that have been suggested for the Negev breeding bird community. We evaluated habitat and area effects on bird abundance and distribution and tested whether species habitat use during winter involves niche shifts. Compared with breeding birds, a larger proportion of winter bird species occupied both scrubland and forest. As in summer, forest bird species responded to habitat structure, whereas scrubland species were associated with both habitat structure and area. Resident birds disperse into habitats in which they were not present during summer. Consequently, for several species, the correlation between bird densities and environmental factors showed a better fit at the landscape rather than at the habitat scale. In addition, rather than niche shift, birds actually extended their niche breadth. Nest site selection may constrain bird distribution into a realized niche, smaller than their fundamental niche. Despite the scale differences in habitat use, the similar species diversity patterns between seasons suggest that both winter and summer birds would benefit from conservation of scrub patches larger than 50 ha, and enrichment of foliage layers within the planted forests.     

Asymmetric competition drives lake use of coexisting salmonids

To what degree are population differences in resource use caused by competition and the occupation of adjacent positions along environmental gradients evidence of competition? Habitat use may be the result of a competitive lottery, or restricted by competition. We tested to what extent population differences in habitat use of two salmonids, cutthroat trout (Oncorhynchus clarki) and Dolly Varden charr (Salvelinus malma) were influenced by interspecific competition. We hypothesized that the depth distribution of Dolly Varden charr would be affected by competition from the more littoral and surface-oriented cutthroat trout, and that the depth distribution of cutthroat trout would be little affected by competition from Dolly Varden charr. Sympatric populations of cutthroat trout and Dolly Varden charr were created by reciprocal transfers of previously allopatric populations in two experimental lakes. We found evidence of asymmetric competition, as Dolly Varden charr were displaced from littoral habitats when sympatric with cutthroat trout, whereas cutthroat trout remained unaffected by the presence of Dolly Varden charr. Evolved differences between the species, and differences between experimental lakes, also contributed to population differences in habitat use, but asymmetric competition remained as the main driver of different depth distributions in sympatry.     

Habitat requirements of weasels <Emphasis Type="Italic">Mustela nivalis</Emphasis> constrain their impact on prey populations in complex ecosystems of the temperate zone

Differences in habitat use by prey and predator may lead to a shift of occupied niches and affect dynamics of their populations. The weasel Mustela nivalis specializes in hunting rodents, therefore habitat preferences of this predator may have important consequences for the population dynamics of its prey. We investigated habitat selection by weasels in the Bia?owie?a Forest in different seasons at the landscape and local scales, and evaluated possible consequences for the population dynamics of their prey. At the landscape scale, weasels preferred open habitats (both dry and wet) and avoided forest. In open areas they selected habitats with higher prey abundance, except during the low-density phase of the vole cycle, when the distribution of these predators was more uniform. Also in winter, the distribution of weasels at the landscape scale was proportional to available resources. In summer, within open dry and wet habitats, weasels preferred areas characterised by dense vegetation, but avoided poor plant cover. In winter, weasels used wet open areas proportionally to availability of habitats when hunting, but in contrast to summer, they rested only in habitats characterized by a lower water level, which offered better thermal conditions. At the local scale, the abundance of voles was a less important factor affecting the distribution of these predators. Although we were not able to provide direct evidence for the existence of refuges for voles, our results show that they may be located within habitat patches, where availability of dense plant cover and physiological constraints limit the activity of weasels. Our results indicate that in complex ecosystems of the temperate zone, characterized by a mosaic pattern of vegetation types and habitat specific dynamics of rodents, impact of weasels on prey populations might be limited.     

The importance of seasonal macrophyte cover for the behaviour and performance of brown trout (Salmo trutta) in a groundwater‐fed river

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The effects of intra- and inter-specific competition on the distribution of stocked juvenile Atlantic salmon, Salmo salar L., in relation to depth and gradient in an upland trout, Salmo trutta L., stream

The relative effects of inter- and intra-specific competition on the distribution of stocked salmon in relation to depth and gradient were investigated in an upland stream during two summer sampling periods. The stream was divided into two areas by an impassable fish barrier, and trout were removed from the upstream section prior to 2 years of salmon stocking. A small amount of trout re-immigration to the cleared area occurred. Under sympatric conditions in the downstream section the fry of both species were significantly more abundant in shallow water, whereas the yearling and older fish tended to inhabit the deeper, slow-flowing areas. Under near allopatric conditions in the cleared section salmon fry changed their distribution to include deeper areas, with shallow, fast-flowing water becoming the least preferred habitat. This trend for a wide distribution of salmon fry over all the available habitat in the upstream section was maintained in the second year when parr were present but trout remained at very low densities. It was therefore concluded that high inter-specific competition from trout was responsible for restricting the distribution of salmon fry to shallow habitat in the control area. Intra-specific competition from older salmon apparently only affected the growth and survival of salmon fry. The regulating mechanisms involved in these inter- and intra-specific effects are discussed in terms of competition for stream resources and predation. Recommendations based on the findings are made for stocking and habitat management of salmonid waters.     

The influence of small-scale variation in habitat on winter trout distribution and diet in an afforested catchment

(1) Habitat influences on trout distribution and diet at a reach scale were analysed over a single winter in a conifer-afforested catchment in Ireland, in an area subject to very low levels of atmospheric pollution. (2) A total of 234 salmonids were sampled from which 1194 individual prey items were recovered. Salmonids were sampled at eleven sites over a 2 km stretch of the river Douglas, a third order stream of the river Araglin in the Munster Blackwater, Co. Cork, Ireland. (3) In this winter study, water depth and flow primarily influenced trout distribution. (4) Stepwise multiple regression was used to identify the most influential environmental factors on trout metrics. Trout biomass was positively correlated to maximum depth and the percentage of pool area within sites, but density and condition were not significantly influenced by habitat variation at the reach scale. (5) The results from diet analysis suggest that trout are heterogeneous generalist feeders in winter, preying mainly on Trichoptera and Ephemeroptera species. Prey diversity in the diet of individuals throughout the study was positively correlated to the percentage of deciduous vegetation, undercut banks and coniferous vegetation, whilst the prey sub-population diversity at site scale was not related to any of the habitat variables measured.