The complementary role of lentic and lotic habitats for Arctic grayling in a complex stream‐lake network in Arctic Alaska

Lakes can be important to stream dwelling fishes, yet how individuals exploit habitat heterogeneity across complex stream‐lake networks is poorly understood. Furthermore, despite growing awareness that intermittent streams are widely used by fish, studies documenting the use of seasonally accessible lakes remain scarce. We studied Arctic grayling (Thymallus arcticus) in a small seasonally flowing (June–October) stream‐lake network in Alaska using PIT telemetry. Overall, 70% of fish visited two lakes, 8% used a single lake, and 22% used only stream reaches. We identified five distinct behavioural patterns that differed in dominant macrohabitat used (deep lake, shallow lake or stream reaches), entry day into the network and mobility. Some juvenile fish spent the entire summer in a shallow seasonally frozen lake (average 71 days), whereas others demonstrated prospecting behaviour and only entered the stream channel briefly in September. Another group included adult and juvenile fish that were highly mobile, moving up to 27 km while in the 3‐km stream‐lake network, and used stream reaches extensively (average 59 days). Lentic and lotic habitats served differing roles for individuals, some fish occupied stream reaches as summer foraging habitat, and other individuals used them as migration corridors to access lakes. Our study emphasises the importance of considering stream‐lake connectivity in stream fish assessments, even to shallow seasonally frozen habitats not widely recognised as important. Furthermore, we demonstrate that individuals may use temporary aquatic habitats in complex and changing ways across ontogeny that are not captured by typical classifications of fish movement behaviour.     

Freshwater habitat associations between pink (Oncorhynchus gorbuscha), chum (O. keta) and Chinook salmon (O. tshawytscha) in a watershed dominated by sockeye salmon (O. nerka) abundance

To understand the interplay between habitat use and contemporary anadromous Pacific salmon, Oncorhynchus spp., distributions we explored the habitat associations of three species, pink (O. gorbuscha), chum (O. keta) and Chinook salmon (O. tshawytscha) in streams of the Wood River system of Bristol Bay, Alaska, where sockeye salmon (O. nerka) are numerically dominant. We developed models to investigate the occurrence of nondominant salmon in relation to habitat characteristics and sockeye salmon density, using four decades of salmon presence and abundance data. The frequency of occurrence and abundance of nondominant species increased with watershed drainage area and stream depth and decreased with sockeye salmon density. The range of occurrence varied from nonexistent to perennial for the other species in sockeye‐dominated streams. Increasing watershed area resulted in larger stream habitat area and deeper habitats, allowing for the sympatric occurrence and persistence of all salmon species. The relationships between habitat and the presence of these Pacific salmon help define their requirements but also remind us that the patterns of presence and absence, within the overall ranges of salmon species, have yet to be fully understood.     

Estimating size‐specific brook trout abundance in continuously sampled headwater streams using Bayesian mixed models with zero inflation and overdispersion

Abstract – We examined habitat factors related to reach‐scale brook trout Salvelinus fontinalis counts of four size classes in two headwater stream networks within two contrasting summers in Connecticut, USA. Two study stream networks (7.7 and 4.4 km) were surveyed in a spatially continuous manner in their entirety, and a set of Bayesian generalised linear mixed models was compared. Trout abundance was best described by a zero‐inflated overdispersed Poisson model. The effect of habitat covariates was not always consistent among size classes and years. There were nonlinear relationships between trout counts and stream temperature in both years. Colder reaches harboured higher trout counts in the warmer summer of 2008, but this pattern was not observed in the cooler and very wet summer of 2009. Amount of pool habitat was nearly consistently important across size classes and years, and counts of the largest size class were correlated positively with maximum depth and negatively with stream gradient. Spatial mapping of trout distributions showed that reaches with high trout counts may differ among size classes, particularly between the smallest and largest size classes, suggesting that movement may allow the largest trout to exploit spatially patchy habitats in these small headwaters.     

Census and effective population sizes of white‐spotted charr (Salvelinus leucomaenis) in a fragmented landscape

Several habitat models have been proposed to predict population size for stream fishes and to guide habitat assessment and monitoring techniques. However, most models do not incorporate the potential advantage of molecular genetic markers. We conducted a field survey and microsatellite DNA analyses to quantify the relationships among genetic diversity, census/effective population size and habitat variables in fragmented populations of white‐spotted charr (Salvelinus leucomaenis). The census population size significantly increased with the stream length, the number of pools and a pool‐riffle sequence index, a proxy for channel‐unit habitat type complexity within reaches. Population density was correlated with the pool‐riffle sequence index only. Genetic diversity and effective population size were not correlated with the habitat variables or census population size. There was a lack of isolation‐by‐distance population structure in the studied populations. Our results suggest that stream length and the number of pools within reaches associated with habitat complexity are the habitat variables that explain the majority of variation in population size of white‐spotted charr. Our findings provide further evidence that census population size per se is a poor indicator of the inclusive genetic diversity within populations in a fragmented landscape.     

Explaining spatial variability in stream habitats using both natural and management‐influenced landscape predictors

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High‐resolution modelling of ocean circulation can reveal retention spots important for biodiversity conservation

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Polymorphic mountain whitefish (Prosopium williamsoni) in a coastal riverscape: size class assemblages,distribution, and habitat associations

We compared the assemblage structure, spatial distributions, and habitat associations of mountain whitefish (Prosopium williamsoni) morphotypes and size classes. We hypothesised that morphotypes would have different spatial distributions and would be associated with different habitat features based on feeding behaviour and diet. Spatially continuous sampling was conducted over a broad extent (29 km) in the Calawah River, WA (USA). Whitefish were enumerated via snorkelling in three size classes: small (10–29 cm), medium (30–49 cm), and large (≥50 cm). We identified morphotypes based on head and snout morphology: a pinocchio form that had an elongated snout and a normal form with a blunted snout. Large size classes of both morphotypes were distributed downstream of small and medium size classes, and normal whitefish were distributed downstream of pinocchio whitefish. Ordination of whitefish assemblages with nonmetric multidimensional scaling revealed that normal whitefish size classes were associated with higher gradient and depth, whereas pinocchio whitefish size classes were positively associated with pool area, distance upstream, and depth. Reach‐scale generalised additive models indicated that normal whitefish relative density was associated with larger substrate size in downstream reaches (R² = 0.64), and pinocchio whitefish were associated with greater stream depth in the reaches farther upstream (R² = 0.87). These results suggest broad‐scale spatial segregation (1–10 km), particularly between larger and more phenotypically extreme individuals. These results provide the first perspective on spatial distributions and habitat relationships of polymorphic mountain whitefish.     

Ecological factors influencing movement of creek chub in an intermittent stream of the Ozark Mountains,Arkansas

Increasing our understanding of the traits and adaptations that promote the survival and persistence of organisms in highly dynamic environments will aid in the conservation of populations and communities. Projected effects of climate change and land alterations suggest headwater streams may become more intermittent and less predictable, consequently altering biological processes (i.e. dispersal or movement) that govern population dynamics. Few studies have provided insight into movement dynamics of nongame fishes in small headwater streams that commonly experience intermittent conditions. The purpose of this study was to investigate movement of a fish species adapted to intermittent stream conditions. Our objectives were to (i) describe the general movement patterns of creek chub, Semotilus atromaculatus, in an intermittent stream and (ii) investigate which ecological factors may influence movement in patchy environments. Creek chub displayed some of the longest distances moved compared to many other stream fishes in perennial streams (179–1069 m seasonal averages; 4678 m maximum distance). Directional movement was significant only in May with more individuals moving upstream. The probability of creek chub movement was inversely related to habitat complexity and pool area. Creek chub adapted to intermittent stream conditions not only exhibited increases in the frequency and distance of movement compared to other nongame fishes, but also exhibited movements in relation to local habitat metrics. These results demonstrate some of the potential adaptations that are likely to promote the survival and persistence of populations in highly dynamic environments such as intermittent streams.     

Projected impacts of climate change on stream salmonids with implications for resilience‐based management

The sustainability of freshwater fisheries is increasingly affected by climate warming, habitat alteration, invasive species and other drivers of global change. The State of Michigan, USA, contains ecologically, socioeconomically valuable coldwater stream salmonid fisheries that are highly susceptible to these ecological alterations. Thus, there is a need for future management approaches that promote resilient stream ecosystems that absorb change amidst disturbances. Fisheries professionals in Michigan are responding to this need by designing a comprehensive management plan for stream brook charr (Salvelinus fontinalis), brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) populations. To assist in developing such a plan, we used stream‐specific regression models to forecast thermal habitat suitability in streams throughout Michigan from 2006 to 2056 under different predicted climate change scenarios. As baseflow index (i.e., relative groundwater input) increased, stream thermal sensitivity (i.e., relative susceptibility to temperature change) decreased. Thus, the magnitude of temperature warming and frequency of thermal habitat degradation were lowest in streams with the highest baseflow indices. Thermal habitats were most suitable in rainbow trout streams as this species has a wider temperature range for growth (12.0–22.5 °C) compared to brook charr (11.0–20.5 °C) and brown trout (12.0–20.0 °C). Our study promotes resilience‐based salmonid management by providing a methodology for stream temperature and thermal habitat suitability prediction. Fisheries professionals can use this approach to protect coldwater habitats and drivers of stream cooling and ultimately conserve resilient salmonid populations amidst global change.     

Objective classification of Navarro River salmon habitat: a watershed‐based critical habitat case study

• 1. Prevailing freshwater conservation approaches in the USA stem from policy‐based ecosystem management directives, science‐based gap analyses, and legal interpretations of critical habitats. In California, there has been no systematic prioritization of freshwater habitats critical to the persistence of anadromous salmonid populations.
• 2. Anadromous salmonids provide an optimal focal species for conservation prioritization of freshwater habitats in California owing to their flagship, umbrella and keystone status.
• 3. The Navarro River is a key watershed for both Endangered Species Act and Clean Water Act recovery efforts in the state of California. This watershed serves as a case study in the use of iterative discriminant analysis to objectively classify freshwater habitats critical to the persistence of two species of threatened anadromous salmonids, steelhead (Oncorhynchus mykiss) and coho (Oncorhynchus kisutch).
• 4. Riverscape parameters were used initially to define suitable habitat for focal species; subsequent refinement accounted for human disturbance within the watershed. Results from this study identify 22.1 km of riverine habitat critical to the persistence of coho salmon in the Navarro River watershed, which need active conservation or restoration; it also identified an additional 269.4 km of riverine habitat in need of protection for its aquatic habitat values.

Copyright © 2007 John Wiley & Sons, Ltd.     

Cohort‐specific variation in juvenile coho salmon habitat use

In this study, we examined summer and fall freshwater rearing habitat use by juvenile coho salmon (Oncorhynchus kisutch) in the quickly urbanising Big Lake drainage in south‐central Alaska. Habitat use was assessed by regressing fish count data against habitat survey information across thirty study sites using generalised linear mixed models. Habitat associations were examined by age‐0 and age‐1+ cohorts separately, providing an opportunity to compare habitat use across different juvenile coho salmon life stages during freshwater rearing. Regression results indicated that the age‐0 cohorts were strongly associated with shallow, wide stream reaches with in‐stream vegetation, whereas age‐1+ cohorts were associated with deeper stream reaches. Furthermore, associations between fork length and habitat characteristics suggest cohort‐specific habitat use patterns are distinct from those attributable to fish size. Habitat use information generated from this study is being used to guide optimal fish passage restoration planning in the Big Lake drainage. Evidence for habitat use partitioning by age cohort during freshwater juvenile rearing indicates that pooling age cohorts into a single “juvenile” stage for the purposes of watershed management may mask important habitat use dynamics.     

Integration of ecology,demography and genetics to reveal population structure and persistence: a mini review and case study of stream‐dwelling Dolly Varden

Abstract – Spatial structures can drive population dynamics and persistence. The roles of space and dispersal on dynamics, however, remain largely unknown in wild populations, mainly because of the difficulty in extensive/intensive field surveys at multiple locations. Here, I integrate results of ecological, demographic and genetic studies to elucidate detailed population structure and to identify the mechanisms of population persistence in a stream fish. Spatial structures, such as habitat size and connectivity, are particularly important in river and freshwater networks because such ecosystems are highly vulnerable to human activities. These issues are explored by examining results from a decadal research on the stream‐dwelling Dolly Varden charr in the Sorachi River basin, Japan. More than 100 local habitats (i.e. tributaries) were examined for spatial structure of populations by, such as, species presence, population census, redd counts, analysis of population synchrony and microsatellite DNA analysis. The results indicate that (i) population demography is largely independent in each tributary, (ii) some large tributaries support self‐sustaining populations, (iii) despite small population sizes in most tributaries (<30 spawning females), local extinction is rare, except in human‐influenced areas and (iv) probabilities of extinction are likely reduced by immigration of fish from neighbouring tributaries. The evidence suggests that Dolly Varden in this river system function as a source‐sink or mainland‐island metapopulation structure and that processes influencing these structures vary within the stream network. Overall, local populations may be highly persistent as long as local populations are well connected. I also discuss the vulnerability of stream fishes to habitat alterations.     

Need for speed: Preference for fast‐flowing water by the endangered semi‐aquatic Pyrenean desman (Galemys pyrenaicus) in two contrasting streams

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Far-reaching blues: Long-distance migration of the invasive Atlantic blue crab

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Contextualizing the relative importance of habitat connectivity for metapopulation persistence: A case study of a critically endangered fish

1. Local population characteristics and habitat connectivity both have important influences on metapopulation persistence; however, the relative importance of each can vary depending on the ecological context, making it difficult to apply general ‘rules-of-thumb’ for conservation actions. This is particularly true in dendritic networks, where habitat connections are constrained.
2. By constructing a metapopulation model that specifically accounts for the unique characteristics and ecological system of a target species, the relative influence of local population characteristics and habitat connectivity on metapopulation persistence can be assessed more accurately.
3. This modelling approach was used to improve conservation outcomes for the Canterbury mudfish (kо̄waro Neochanna burrowsius), a critically endangered and poorly understood species that is endemic to the Canterbury Plains of Aotearoa/New Zealand. A spatially structured metapopulation model of N. burrowsius was used to investigate the relationship between habitat patch connectivity, rate of population growth as limited by habitat quality (r_conditional), and metapopulation persistence.
4. N. burrowsius metapopulation persistence increased most strongly under increases in r_conditional, but increases in habitat connectivity also had positive effects (94% metapopulation persistence for highly connected networks vs. 39% metapopulation persistence for poorly connected networks where r_conditional = 1.3).
5. Although rates of population growth were more influential than increases in habitat connectivity in this case study, both will be important to consider for effectively allocating conservation resources for metapopulations in dendritic networks, depending on what managers could effectively manipulate to enhance metapopulation persistence.

     

Extensive dispersal of Roanoke logperch (Percina rex) inferred from genetic marker data

The dispersal ecology of most stream fishes is poorly characterised, complicating conservation efforts for these species. We used microsatellite DNA marker data to characterise dispersal patterns and effective population size (N_e) for a population of Roanoke logperch Percina rex, an endangered darter (Percidae). Juveniles and candidate parents were sampled for 2 years at sites throughout the Roanoke River watershed. Dispersal was inferred via genetic assignment tests (ATs), pedigree reconstruction (PR) and estimation of lifetime dispersal distance under a genetic isolation‐by‐distance model. Estimates of N_e varied from 105 to 1218 individuals, depending on the estimation method. Based on PR, polygamy was frequent in parents of both sexes, with individuals spawning with an average of 2.4 mates. The sample contained 61 half‐sibling pairs, but only one parent–offspring pair and no full‐sib pairs, which limited our ability to discriminate natal dispersal of juveniles from breeding dispersal of their parents between spawning events. Nonetheless, all methods indicated extensive dispersal. The AT indicated unrestricted dispersal among sites ≤15 km apart, while siblings inferred by the PR were captured an average of 14 km and up to 55 km apart. Model‐based estimates of median lifetime dispersal distance (6–24 km, depending on assumptions) bracketed AT and PR estimates, indicating that widely dispersed individuals do, on average, contribute to gene flow. Extensive dispersal of P. rex suggests that darters and other small benthic stream fishes may be unexpectedly mobile. Monitoring and management activities for such populations should encompass entire watersheds to fully capture population dynamics.     

Seasonal effects of macrophyte growth on rainbow trout habitat availability and selection in a low‐gradient,groundwater‐dominated river

Rainbow trout habitat use is often described in high‐gradient, runoff‐driven, heterotrophic streams where geomorphic features and overhanging riparian vegetation provide channel complexity and cover. However, many rainbow trout populations thrive in rivers with contrasting aquatic habitat. We describe rainbow trout habitat use in a low‐gradient, groundwater‐dominated tailwater river where river flow management and macrophyte growth and senescence largely govern available trout habitat. In the summers of 2013 and 2014, available aquatic habitat (depth, velocity, macrophyte cover, substrate size) was quantified, while individual trout location was determined by radio telemetry and linked to environmental variables. Detailed habitat surveys indicate that macrophyte cover increases throughout the summer and is a strong determinant of in‐stream habitat characteristics. Paired logistic regression shows that adult rainbow trout prefer greater depths. Water depth increases with macrophyte abundance at both reach and local scales as plants restrict flow, and available trout habitat is linked to this seasonal pattern. When macrophyte abundance is high, adult trout show secondary preference for localised areas of lower macrophyte cover but otherwise show no selectivity for macrophyte cover, velocity or substrate size. Results suggest that submerged aquatic plants increased the quantity and quality of rainbow trout habitat as a source of channel complexity and cover. Macrophytes may play a similar role in other low‐gradient streams and should not be overlooked by fisheries managers considering habitat suitability.     

Broad‐scale habitat classification variables predict maximum local abundance for native but not non‐native trout in New York streams

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Large‐scale,seasonal habitat use and movements of yellow American eels in the St. Lawrence River revealed by acoustic telemetry

Large‐scale habitat use and movements of yellow American eels (Anguilla rostrata) from the St. Lawrence River were examined using acoustic telemetry from early summer to late fall in 2010 and 2011. Sixty‐seven eels were tagged, and their passage or presence was recorded using fixed acoustic arrays covering a 400 km distance along the St. Lawrence River and Estuary. Sixty‐four per cent of the 67 tagged eels were detected. Most eels were detected at only one array; the closest to their release location and at several occasions during the tracking period, suggesting a high proportion of freshwater residency in the upstream part of the St. Lawrence River. Downstream movements towards the brackish estuary (63–418 km distance) were demonstrated for 16.4% of the eels, particularly for those caught at the most downstream site that is close to the brackish estuary. Our results strongly suggest a lower activity of freshwater resident yellow eels during summer, a behaviour that may be related to day length, which defines time available for their nocturnal foraging. Indeed, yellow eels were detected primarily at night; no effect of moon phase was revealed. Movements in the vicinity of arrays (up to 116 km in the fluvial estuary) were suggested and smaller‐scale movements within Lac St. Louis were demonstrated, highlighting a yellow‐eel home range far more extensive than previously reported in smaller systems. Evidence for within‐season homing and site fidelity is also reported.     

Oceanographic habitat suitability is positively correlated with the body condition of a coastal‐pelagic fish

Species distribution models are commonly used to determine a species’ probability of occurrence but have not been used to examine the effect of environmental habitat suitability on fish condition, which is considered to be an integrated measure of physiological status. Here, we test for a relationship between oceanographic habitat suitability and the body condition of kingfish (Seriola lalandi) from eastern Australia. We (a) test whether individuals sampled from areas of high‐quality habitat were in better condition than individuals sampled from areas of low‐quality habitat, and (b) assess whether the condition of kingfish responded to oceanographic habitat suitability predicted at varying time‐before‐capture periods. Kingfish habitat was modelled as a function of sea surface temperature, sea‐level anomaly and eddy kinetic energy in a generalized additive modelling framework. Model predictions were made over one‐ to six‐week time‐before‐capture periods and compared to field‐derived kingfish condition data measured using bioelectrical impedance analysis. Oceanographic habitat suitability was significantly correlated with kingfish condition at time‐before‐capture periods ranging from one to four weeks and became increasingly correlated at shorter lead‐times. Our results highlight that (a) fish condition can respond sensitively to environmental variability and this response can be detected using oceanographic habitat suitability models, and (b) climate change may drive extensions in species range limits through spatial shifts in oceanographic habitat quality that allow individuals to persist beyond historical range boundaries without their body condition being compromised.