Investigating a major assumption of predictive instream habitat models: is water velocity preference of juvenile Atlantic salmon independent of discharge?

The mean column velocity preference of juvenile Atlantic salmon Salmo salar (LF 30–55 mm) was investigated by observing their spatial pattern of habitat use in a laboratory flume while varying discharge (Q) over a 18‐fold range (Q=2·6–46·8l s^‐1). Based on 341 fish observations at three discharges (Q=2·6, 15·0 and 46·8l s^‐1), three separate velocity preference curves were developed using standard procedures. The mean column velocities measured at 0·6 depth for the fish positions at the set low, medium and high discharges had medians of 7, 10 and 24 cm s^‐1, respectively, and varied significantly between the discharges. Across the range of flows, the fish utilized mean column velocities between 0 and 56 cm s^‐1, but the three velocity preference curves differed. Differences between juvenile Atlantic salmon use of habitat, defined according to mean column velocities at different discharges, were greatest at the lower end of the available range of velocities (<20 cm s^‐1). Weighted usable area (WUA), the output of the instream flow model PHABSIM that is used to describe the available habitat at a given discharge, was calculated for the flume using the preference curves built at the three set discharges. The model was highly sensitive to differences between the three preference curves and WUA varied by up to a two‐fold difference. Furthermore, habitat‐discharge relationships derived from the three preference curves were very different. Predicted habitat losses across the modelled range of discharges varied by up to 150% depending upon which velocity preference curve was used in the model. Thus, the assumption that a single preference curve can be applied across a range of discharges is not valid and is likely to result in large errors when employing PHABSIM and other models that use similar principles.     

Influence of lateral gradients of hydrologic connectivity on trophic positions of fishes in the Upper Mississippi River

1. Riverscapes consist of the main channel and lateral slackwater habitats along a gradient of hydrological connectivity from maximum connection in main channel habitats to minimum connection in backwaters. Spatiotemporal differences in water currents along this gradient produce dynamic habitat conditions that influence species diversity, population densities and trophic interactions of fishes. 2. We examined the importance of lateral connectivity gradients for food web dynamics in the Upper Mississippi River during spring (high flow, moderately low temperatures) and summer (low flow, higher temperatures). We used literature information and gut contents analyses to determine feeding guilds and stable isotope analysis to estimate mean trophic position of local fish assemblages. During June and August 2006, we collected over 1000 tissue samples from four habitats (main channel, secondary channels, tertiary channels and backwaters) distributed within four hydrologic connectivity gradients. 3. Mean trophic position differed among feeding guilds and seasons, with highest values in spring. Mean trophic position of fish assemblages, variability in trophic position and food chain length (maximum trophic position) of the two dominant piscivore species (Micropterus salmoides and M. dolomieu) in both seasons were significantly associated with habitat along the lateral connectivity gradient. Food chain length peaked in tertiary channels in both seasons, probably due to higher species diversity of prey at these habitats. We infer that food chain length and trophic position of fish assemblages were lower in backwater habitats in the summer mainly because of the use of alternative food sources in these habitats. 4. A greater number of conspecifics exhibited significant among‐habitat variation in trophic position during the summer, indicating that low river stages can constrain fish movements in the Upper Mississippi River. 5. Results of this study should provide a better understanding of the fundamental structure of large river ecosystems and an improved basis for river rehabilitation and management through knowledge of the importance of lateral complexity in rivers.     

Comparative use of side and main channels by small‐bodied fish in a large,unimpounded river

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Comparisons of habitat availability and habitat use by an allopatric cohort of juvenile Atlantic salmon Salmo salar under conditions of low competition in a Norwegian stream

Allopatric Atlantic salmon parr occupied a wider and lower range of mean water velocities than have been previously reported for parr in sympatry. With regard to depth, substrate and cover no substantial differences were found. Different fish sizes did not affect habitat use by parr significantly, neither did habitat use change during the season. Habitat availability strongly influenced observed habitat use thus, invalidating use of habitat suitability curves based on observations of habitat occupancy by fish only. The allopatric parr consistently selected habitats different from the available habitat, i.e. had preferences also in the absence of intraspecific interactions between age classes. Habitat conditions not used by the fish were more readily identifiable than habitats used. The parr rarely used shallow (≤ 10 cm) and deep (> 60 cm) stream areas, low mean water velocities (< 10 cm s^-1), fine substrate (sand and finer) and stream areas without cover. However, the calculated habitat preferences were also affected by habitat availability. Multivariate analysis did not identify any of the habitat variables as substantially more important than the others, but suggested that the importance of variables may vary with type of habitat studied.     

Distribution of migratory fishes and shrimps along multivariate gradients in tropical island streams

Among the 16 species of fishes and shrimps studied at 51 sites along several small streams at Basse Terre, Guadeloupe, Lesser Antilles, more than 60% showed a spatial distribution significantly influenced by environmental conditions. These included altitude, basin size, terrestrial vegetation and land use. However, the range of the species habitat was generally high, except for three species limited to the downstream stretches (two fishes and one shrimp). The habitat characteristics of fish and shrimp species tended to differ, but the difference was not significant (P<0·05). On the contrary, the habitat characteristics of amphidromous and catadromous species clearly differed, with a lower occurrence at the most elevated sites of catadromous species than amphidromous species.     

Effects of discharge and local density on the growth of juvenile Atlantic salmon Salmo salar

The study explored the combined effects of density, physical habitat and different discharge levels on the growth of juvenile Atlantic salmon Salmo salar in artificial streams, by manipulating flow during both summer and winter conditions. Growth was high during all four summer trials and increased linearly with discharge and mean velocity. Differences in fish densities (fish m^?3) due to differences in stream volume explained a similar proportion of the variation in mean growth among discharge treatments. Within streams, the fish aggregated in areas of larger sediment size, where shelters were probably abundant, while growth decreased with increasing densities. Fish appeared to favour the availability of shelter over maximization of growth. Mean growth was negative during all winter trials and did not vary among discharge treatments. These results suggest that increased fish densities are a major cause of reduced summer growth at low discharge, and that habitat‐mediated density differences explain the majority of the growth variation across habitat conditions both during summer and winter.     

Seasonal and spatial microhabitat selection and segregation in young Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L., in a Norwegian river

Seasonal microhabitat selection by sympatric young Atlantic salmon and brown trout was studied by diving. Both species, especially Atlantic salmon, showed seasonal variation with respect to surface and mean water velocities and depth. This variation is partly attributed to varying water flows and water temperatures. In winter the fish sought shelter in the substratum. A spatial variation in habitat use along the river due to different habitat availabilities was observed. Both species occupied habitats within the ranges of the microhabitat variables, rather than selecting narrow optima. It is hypothesized that the genetic basis allows a certain range to the behavioural response. Microhabitat segregation between the two species was pronounced, with brown trout inhabiting the more slow-flowing and partly more shallow stream areas. Atlantic salmon tolerated a wider range of water velocities and depths. Habitat suitability curves were produced from both species. It is suggested that habitat suitability curves that are based on observations of fish occupancy of habitat at median or base flow may not be suitable in habitat simulation models, where available habitat is projected at substantially greater water flows.     

Shifts in drag and swimming potential during grayling ontogenesis: relations with habitat use

The drag coefficient (C_d) of grayling Thymallus thymallus was dependent on body surface conditions and rigidity. At comparable flow conditions, C_d values of a fish preserved in formalin (high body rigidity) were 15–30% lower than those obtained on a freshly-killed fish (medium rigidity); the presence of skin mucus on fish could reduce C_d by 10%. The hydrodynamic potential of grayling increased during ontogenesis, because C_d values decreased (except for yolk sac larvae, which had a particular morphology) and the swimming capacities (in terms of relative muscular mass) increased. Grayling morphology evolves towards hydrodynamically efficient shape at high velocities, and there is a relationship between these shifts in hydrodynamic abilities and the different habitats (in terms of current velocity) used by five morphological groups. Therefore, the concept of hydrodynamic potential (i.e. hydrodynamics of shape and swimming capacities) could be a useful tool in fish ecomorphology and predictions of habitat use.     

Water flow dynamics in the respiratory tract of the carp (Cyprinus carpio L.).

Simultaneous measurements of water velocity in the buccal chamber, and buccal and opercular hydrostatic pressure of carp have revealed surprisingly high water velocities. The high flow velocities mean that, at times, the kinetic energy of flow makes a substantial contribution to the total fluid energy. This suggests that there may be unequal distribution of hydrostatic pressures within the buccal chamber. Anatomical examinations showed that fluid channels in the buccal chamber and gill raker sieve are complex and can be expected to vary spatially and temporally throughout the respiratory cycle. It appears that there is a potential for error in many of the previous analyses of 'gill resistance and energetics of fish breathing based solely on hydrostatic pressure measurements and the simplifying assumption of steady-state conditions.     

Ontogeny of Diel Pattern of Stream-Margin Habitat Use by Emerging Brown Trout, Salmo Trutta, in Experimental Channels: Influence of Food and Predator Presence

Age-0 brown trout, Salmo trutta, inhabit shallow and slow-flowing habitats where they can easily maintain stationary swimming positions. However, recent results have shown that they use deeper and faster habitats during daylight than at night, suggesting the occurrence of a nocturnal movement toward stream-margin habitats. Experiments were conducted to describe precisely when this diel pattern of habitat use appears during ontogeny. In two indoor channels, free-embryo brown trout were deposited under the gravel. When emerging, alevins were free to choose between margin (2 cm deep, 0-2 cm s^-1) or deep habitat (12 cm, 2-4 cm s^-1), or to leave the channel (upstream or downstream). During the week of emergence, upstream and downstream catches, fish habitat use (deep habitat or margin), and fish behavior (resting or swimming) were measured by direct observations and trap counts. Three treatments were performed: (1) fish artificially fed on drifting invertebrates, (2) fish exposed to predators (bullhead, Cottus gobio), and (3) control channels (no food, no predator). In control and food channels, a diel pattern of habitat use was observed 1-2 days after the emergence started. Most fish rested in the margin at night, whereas they moved towards the deep habitat during daylight to hold stationary swimming positions. In the presence of bullhead, most trout were cryptic, and visible fish stood in the margin during both daylight and at night. The importance of predation risk and foraging behavior on the ontogeny of the diel pattern of habitat use is discussed. Results support the direct development without larva from free-embryo via alevin in brown trout.     

Niche partitioning and the effect of interspecific competition on microhabitat use by two sympatric galaxiid stream fishes

1. Numerous interacting abiotic and biotic factors influence niche use and assemblage structure of freshwater fishes, but the strength of each factor changes with spatial scale. Few studies have examined the role of interspecific competition in structuring stream fish assemblages across spatial scales. We used field and laboratory approaches to examine microhabitat partitioning and the effect of interspecific competition on microhabitat use in two sympatric stream fishes (Galaxias‘southern’ and Galaxias gollumoides) at large (among streams and among sites within streams) and small (within artificial stream channels) spatial scales. 2. Diurnal microhabitat partitioning and interspecific competition at large spatial scales were analysed among three sympatry streams (streams with allotopic and syntopic sites; three separate catchments) and four allopatry streams (streams with only allotopic sites; two separate catchments). Electro‐fishing was used to sample habitat use of fishes at 30 random points within each site by quantifying four variables for each individual: water velocity, depth, distance to nearest cover and substratum size. Habitat availability was then quantified for each site by measuring those variables at each of 50 random points. Diet and stable isotope partitioning was analysed from syntopic sites only. Diel cycles of microhabitat use and interspecific competition at small spatial scales were examined by monitoring water velocity use over 48 h in artificial stream channels for three treatments: (i) allopatric G. ‘southern’ (10 G. ‘southern’); (ii) allopatric G. gollumoides (10 G. gollumoides) and (iii) sympatry (five individuals of each species). 3. One hundred and ninety‐four G. ‘southern’ and 239 G. gollumoides were sampled across all seven streams, and habitat availability between the two species was similar among all sites. Galaxias‘southern’ utilised faster water velocities than G. gollumoides in both the field and in channel experiments. Both species utilised faster water velocities in channels at night than during the day. Diet differences were observed and were supported by isotopic differences (two of three sites). No interspecific differences were observed for the other three microhabitat variables in the field, and multivariate habitat selection did not differ between species. Interspecific competition had no effect on microhabitat use of either species against any variable either in the field (large scale) or in channels (small scale). 4. The results suggest that niche partitioning occurs along a subset of microhabitat variables (water velocity use and diet). Interspecific competition does not appear to be a major biotic factor controlling microhabitat use by these sympatric taxa at any spatial scale. The results further suggest that stream fish assemblages are not primarily structured by biotic factors, reinforcing other studies de‐emphasising interspecific competition.     

Multi-scale habitat selection by Murray cod Maccullochella peelii peelii in two lowland rivers

This study provides information on habitat selection by the threatened Murray cod Maccullochella peelii peelii at two spatial scales in the Ovens and Murray Rivers in south-eastern Australia. Both adult (>450 mm total length, L _T) and age 0 year (<150 mm L _T) M. p. peelii selected macro and microhabitats based on structural variables. At the macrohabitat scale, adults selected channel habitats in the river, floodplain channels at high floods and within Lake Mulwala, whereas the floodplain proper was avoided. Adult and age 0 year fish selected similar microhabitats regardless of site or hydrologic conditions, and selection was primarily influenced by the presence of higher loadings of structural woody habitat, higher c.v. in depth, more overhanging vegetation, shallower comparative depths and lower water velocities, closer to the bank. Age 0 year M. p. peelii appeared to select shallower habitats with greater amounts of structural woody habitat, closer to the river bank than adult fish.     

Spatial and temporal variation in fish assemblage structure in the Mary River,south-eastern Queensland: the influence of habitat structure

Synopsis Fish assemblages at eleven sites within the Mary River were sampled over a 15 month period by back-pack electrofishing. The study took place during a period of abnormally low flows but included two high flow events one of which approached record levels. Spatial and temporal variation in fish assemblage structure was pronounced. Spatial variation was related to position within the catchment and correlated with habitat attributes related to substrate composition and water depth. The absence of a strong effect due to water velocity was probably due to overall low water flows throughout the study period. Temporal variation at some sites, particularly headwater sites, was correlated with changes in the amount and type of cover available to fishes. Cover was significantly correlated with the mean species richness of each site. Flooding had very little effect on both fish assemblage structure and the physical structure of the habitat but resulted in substantial reduction in the amount and type of cover available to fishes. The flow regime of the Mary River was highly variable and consequently both the timing and duration of high and low flows was unpredictable.     

Why do Foraging Stream Salmonids Move During Summer?

We hypothesize that foraging stream salmonids move during summer because (1) they monitor habitat conditions at a reach scale (100s of m), and (2) dominant fish move when conditions in their present foraging location become sub-optimal relative to conditions at other locations in the reach. To test these ideas, we quantified temporal variation in foraging habitat quality between late spring and early fall in a reach of a small Rocky Mountain brook charr, Salvelinus fontinalis, stream, predicted optimal-foraging fish distributions within the reach, and experimentally manipulated access to foraging sites and measured fish responses. Our results show that high-quality foraging sites were located at certain places in the reach during one period, but at different places during others, consistent with the hypothesis that fish movement is required if dominant fish are to occupy high-quality foraging sites throughout summer. The optimal foraging model was able to predict foraging locations within study pools, but not the exact location of individual fish within the pools or the reach. However, empirical evidence suggests that fish were distributed in order to maximize energy intake at the reach scale. Finally, dominant fish excluded from their preferred foraging location either left the pools (three of six cases), or began to occupy focal points of the next largest fish which, in turn, exited the pool (two of six cases). If habitat selection was occurring only within habitat units, then large fish, when excluded from their preferred locations, would select the next best locations within the pool. Taken together, these results suggest that charr use summertime movements to both monitor habitat conditions at a large spatial scale, and to gain access to optimal foraging locations even as conditions change temporally.     

Use of three types of stream-margin habitat by age-0 brown trout late in the growing season

The use of stream-margin habitat by age-0 salmonids has been studied, but differences in use among various types of habitat along stream margins has not been addressed. We described the nighttime use of habitat features by age-0 brown trout (Salmo trutta) among three types of stream-margin habitat late in the growing season (August–September) and assessed the extent to which use of habitat features within each type differed over the sampling period. Differences in water depths, water velocities, distances from shore, and substrate at the locations of fish along the margins of pools, the margins of riffles, and in backwaters were studied. Variation in habitat use also was observed during the study period as fish increased in length. Our observations are important considerations when developing habitat suitability criteria for assessment of instream-flow needs of age-0 brown trout.     

Short-term cues used by foraging trout in a California stream

Stream salmonids choose foraging locations to maximize the energy benefit of foraging within the constraints of size-mediated dominance hierarchies and predation risk. But, because stream habitats are temporally variable, fish must use a search process to monitor changing habitat conditions as a means of locating potentially-better foraging locations. I explored the cues used by the cutthroat trout, Oncorhynchus clarki clarki, when searching for food at the pool scale by artificially increasing prey availability at different locations by using special feeders and by manipulating pool velocities. Behavior of individually marked fish was monitored from stream bank platforms under unmanipulated control conditions and under seven experimental sets of conditions involving different combinations of feeder location and velocity manipulation. Under natural conditions fish elected to forage in the deepest (>50 cm), fastest (0.10–0.25 m s⁻¹) locations and within 1 m of structure cover, but would readily move to shallower (<30 cm) water away from cover if velocities were manipulated to be highest there. Although fish did not locate feeders unless they were placed in high-velocity areas, when high velocity was provided fish would move into very shallow water (<20 cm) if prey were delivered there. Responses of individual trout to manipulations indicated that water velocity was the main physical cue used by fish to decide where to forage, and that fish could also learn about new food sources by observing conspecifics. Overall, results indicated fish were not “perfect searchers” that could quickly locate new food resources over short time scales, even when the new resources were within a few meters of the fish’s normal foraging location. When given the correct cues, however, fish could detect new food sources and defend them against subordinate fish. Movement of new fish into and out of the study pools during the ten-day observation period was common, consistent with the idea that trout used movement as a means of exploring and learning about habitat conditions at the reach scale.     

Shifts in morphometrics and their relation to hydrodynamic potential and habitat use during grayling ontogenesis

The theory of saltatory ontogeny predicts sudden morphological shifts during fish development which often occur simultaneously with physiological, anatomical or behavioural shifts. Therefore, our objectives were to identify potential sudden morphological shifts during grayling Thymallus thymallus ontogenesis and to check if these shifts affected the hydrodynamic potential of grayling in periods of known shifts in habitat use. In the 144 grayling studied (total length: 14·9–142·7 mm), three of 28 morphological variables considered revealed saltatory events during ontogenesis: position of maximal body height, position of maximal body width, and length to pelvic fin insertion. Using all variables (except total and standard length), five morphological groups were separated by multivariate analysis and each group had a particular hydrodynamic potential related to the drag of flow. Between these five different morphological groups, differences in the physical habitat use were observed. Basically, the saltatory pattern during grayling ontogenesis corresponded to a sequential habitat use that increased flow exposure and, simultaneously, to a stepwise improvement (at each habitat shift) of the hydrodynamic potential until the body had a shape that minimized drag of flow. The study confirms the theory of saltatory ontogeny for grayling in a context of flow physics and hydrodynamic adaptations.     

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

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

Response of fishes and aquatic habitats to sand-bed stream restoration using large woody debris

Effects of habitat rehabilitation of Little Topashaw Creek, a sinuous, sand-bed stream draining 37 km² in northwest Mississippi are described. The rehabilitation project consisted of placing 72 large woody debris structures along eroding concave banks and planting 4000 willow cuttings in sandbars. Response was measured by monitoring flow, channel geometry, physical aquatic habitat, and fish populations. Initially, debris structures reduced high flow velocities at concave bank toes, preventing further erosion and inducing deposition. Physical response during the first year following construction included creation of sand berms along eroding banks and slight increases in base flow water width and depth. Fish collections showed assemblages typical of incising streams within the region, but minor initial responses to debris addition were evident. Progressive failure of the structures and renewed erosion were observed during the second year after construction.     

Seasonal variation in diel activity and microhabitat use of an endemic New Zealand stream-dwelling galaxiid fish

1. Seasonal variation in microhabitat use and activity of 14 giant kokopu Galaxias argenteus, a drift‐feeding galaxiid fish, was compared using radiotelemetry. 2. During winter giant kokopu predominantly used low velocities and intermediate depths by night and day. Activity recorded during 24 and 72 h periods indicated that fish were consistently active at night and inactive during the day. Activity data corresponded with point‐in‐time habitat use data, both of which indicated that fish were concealed amongst cover during the day and used open water habitats at night. 3. During summer, giant kokopu used higher water velocities, shallower depths and coarser substrata, particularly at night but also occasionally during the day relative to winter. Giant kokopu were active by both day and night in summer, although periods of activity were less defined and less predictable than during winter. 4. Adults used predictable home reaches at base‐flow, with most individuals repeatedly using of one or two cover locations within their ‘home’ reach. Reaches used by fish were relatively short (rarely exceeding 26 m) irrespective of season and always included a single pool‐riffle sequence. 5. Diel and seasonal behaviour of giant kokopu was generally comparable with that exhibited by other drift feeding fish species in small temperate streams. However, the nocturnal activity of giant kokopu contrasts with activity patterns in various salmonids, indicating that the impact of predation by different drift feeding fish may vary considerably.