A Large-scale, Hierarchical Approach for Assessing Habitat Associations of Fish Assemblages in Large Dryland Rivers

Multiple-scale assessments of fish-habitat associations are limited despite the fact that riverine fish assemblages are influenced by factors operating over a range of spatial scales. A method for assessing fish-habitat assemblages at multiple scales is proposed and tested in a large Australian dryland river, the Barwon–Darling River. Six discrete mesohabitat types (large wood, smooth bank, irregular bank, matted bank, mid-channel and deep pool) nested within 10 km long river reaches were sampled. Individual reaches were, in turn, nested within four larger geomorphological zones, previously identified along the river. Fish assemblages varied significantly between mesohabitat types and at different spatial scales. Golden perch (Macquaria ambigua), Murray cod (Maccullochella peelii peelii) and common carp (Cyprinus carpio) were strongly associated with large wood, but golden perch and Murray cod exhibited higher habitat specificity than carp. Bony herring (Nematalosa erebi) were more common in shallow edgewater habitats. At the river-scale, regional differences in the fish assemblage occurred at scales closely corresponding to geomorphological zones and these differences were associated with changes in the relative abundance of species rather than the addition or replacement of species. The proposed hierarchical framework improves the efficiency of fish surveys in large rivers by viewing meso-scale fish-habitat associations in the context of larger-scale geomorphological processes.     

Limited Effects of Large‐Scale Riparian Restoration on Seed Banks in Agriculture

I examined the effect of riparian forest restoration on plant abundance and diversity, including weed species, on agricultural lands along the Sacramento River in California (United States). Riparian forest restoration on the Sacramento River is occurring on a large‐scale, with a goal of restoring approximately 80,000 ha over 160 km of the river. In multiuse habitats, such as the Sacramento River, effects of adjoining habitat types and movement of species across these habitats can have important management implications in terms of landscape‐scale patterns of species distributions. Increased numbers of pest animals and weeds on agricultural lands associated with restored habitats could have negative economic impacts, and in turn affect support for restoration of natural areas. In order to determine the distribution and abundance of weeds associated with large‐scale restoration, I collected seed bank soil samples on orchards between 0 and 5.6 km from adjacent restored riparian, remnant riparian, and agricultural habitats. I determined the abundance, species richness, and dispersal mode of plant species in the seed bank and analyzed these variables in terms of adjacent habitat type and age of restored habitat. I found that agricultural weed species had higher densities at the edge of restored riparian habitat and that native plants had higher densities adjacent to remnant riparian habitat. Weed seed abundance increased significantly on walnut farms adjacent to restored habitat with time since restored. I supply strong empirical evidence that large areas of natural and restored habitats do not lead to a greater penetration of weed species into agricultural areas, but rather that weed penetration is both temporally and spatially limited.     

Cascading Ecological Responses to an In‐Stream Restoration Project in a Midwestern River

River restoration projects are increasingly common, but assessments of ecological responses and overall success of the vast majority of efforts are lacking. Information on potential positive ecological effects of restoration efforts can be used to justify further projects and refine methods. We examined responses of multiple trophic levels, aquatic insects and riparian birds, to a series of rock weirs installed in an Illinois river to stabilize the channel. We quantified adult insect emergence and performed weekly point counts of birds in spring at four weir and four non‐weir (control) sites. Emerging insect abundance was higher at control sites, but species richness and diversity were higher at weir sites. Total insect emergence production did not differ between site types, but emergence production of larger‐bodied taxa was higher at weir sites. Ordinations and analysis of similarity indicated differences in insect and bird assemblages between site types. Birds showed a positive numerical response to large‐bodied emerging insects, and total bird abundance was higher at weir sites. Clutch size and feeding rates of a focal bird species, Prothonotaria citrea (Prothonotary Warbler), did not differ between sites, but the number of hatchlings and fledglings was higher at control sites. Molothrus ater (cowbird) parasitism was higher at weir sites, likely because of increased edge habitat associated with weir construction activities. Results show positive ecological impacts of in‐stream restoration and provide justification for further efforts. However, forest disturbance associated with construction could offset some benefits to some species, and thus refinements to procedures may be necessary.     

Diet and feeding habits of predatory fishes upstream and downstream of a low-level weir

A study investigating the influence of a low-level weir on the diets of three migratory percithyid species was undertaken on the Murrumbidgee River, Australia. A combination of fish community sampling and stomach flushing determined that Yanco Weir substantially impacted upon the abundance and feeding habits of golden perch Macquaria ambigua , Murray cod Maccullochella peelii peelii and trout cod Maccullochella macquariensis . The relative abundance of all three species was significantly greater downstream of the weir, where individuals attempting upstream migrations were obstructed. In areas of fish aggregations, some species displayed altered feeding strategies and exploited different prey taxa upstream and downstream of the weir. Diet overlap, and the proportion of individuals with empty stomachs, was also substantially greater from downstream zones. These results suggest that competition among species may be greater in areas of increased predator abundance and some species could be partitioning resources to minimize competitive interactions. Reducing accumulations of predatory species, by providing suitable fish passage facilities, would be an effective means to prevent such trophic interactions occurring at other low-level weirs.     

High‐resolution riparian vegetation mapping to prioritize conservation and restoration in an impaired desert river

In highly impaired watersheds, it is critical to identify both areas with desirable habitat as conservation zones and impaired areas with the highest likelihood of improvement as restoration zones. We present how detailed riparian vegetation mapping can be used to prioritize conservation and restoration sites within a riparian and instream habitat restoration program targeting 3 native fish species on the San Rafael River, a desert river in southeastern Utah, United States. We classified vegetation using a combination of object‐based image analysis (OBIA) on high‐resolution (0.5 m), multispectral, satellite imagery with oblique aerial photography and field‐based data collection. The OBIA approach is objective, repeatable, and applicable to large areas. The overall accuracy of the classification was 80% (Cohen's κ = 0.77). We used this high‐resolution vegetation classification alongside existing data on habitat condition and aquatic species' distributions to identify reaches' conservation value and restoration potential to guide management actions. Specifically, cottonwood (Populus fremontii) and tamarisk (Tamarix ramosissima) density layers helped to establish broad restoration and conservation reach classes. The high‐resolution vegetation mapping precisely identified individual cottonwood trees and tamarisk thickets, which were used to determine specific locations for restoration activities such as beaver dam analogue structures in cottonwood restoration areas, or strategic tamarisk removal in high‐density tamarisk sites. The site prioritization method presented here is effective for planning large‐scale river restoration and is transferable to other desert river systems elsewhere in the world.     

Habitat use,movement and activity of two large-bodied native riverine fishes in a regulated lowland weir pool

The construction of dams and weirs, and associated changes to hydrological and hydraulic (e.g., water level and velocity) characteristics of rivers is a key environmental threat for fish. These multiple stressors potentially can affect fish in a variety of ways, including by causing changes in their movement, habitat use and activity. Understanding how and why these changes occur can inform management efforts to ameliorate these threats. In this context, we used acoustic telemetry to examine habitat use, longitudinal movement and activity of two lowland river fishes, Murray cod Maccullochella peelii and golden perch Macquaria ambigua, in a weir pool environment in south-eastern Australia. We compared our results to published studies on riverine populations to determine if their behaviours are similar (or not). We show that M. peelii and M. ambigua in a weir pool exhibited some similar behaviours to conspecific riverine populations, such as strong site fidelity and use of woody habitat for M. ambigua. However, some behaviours, such as large-scale (tens–hundreds of kilometres) movements documented for riverine populations, were rarely observed. These differences potentially reflect flow regulation (e.g., stable water levels, loss of hydraulic cues) in the weir pool. The two species also exhibited contrasting responses to dissolved oxygen conditions in the weir pool, which may reflect differences in their life history. Overall, this study shows that although some aspects of these two native fishes' life history can continue despite flow regulation, other aspects may change in weir pools, potentially impacting on long-term population persistence.     

Habitat preferences and habitat restoration options for small‐bodied and juvenile fish species in the northern Murray–Darling Basin

Degradation of instream habitats in the northern Murray–Darling Basin has occurred through numerous stressors, including siltation, clearing of bankside vegetation, intrusion of livestock and impacts of pest species. A better understanding of habitat preferences of native fish species could help guide future instream habitat restoration actions. The habitat choices of seven native fish species, juvenile Murray Cod (Maccullochella peelii), juvenile Golden Perch (Macquaria ambigua ambigua), juvenile Silver Perch (Bidyanus bidyanus), adult Murray–Darling Rainbowfish (Melanotaenia fluviatilis), adult Olive Perchlet (Ambassis agassizii), adult Un‐specked Hardyhead (Craterocephalus stercusmuscarum fulvus) and adult carp gudgeons (Hypseleotris spp.) were tested in preference troughs to help inform potential habitat restoration actions in the Condamine catchment. Each species was given a choice between pair combinations of open sandy habitat, submerged macrophytes, emergent plants and rocky rubble. Habitat preferences varied between species. Murray Cod, Golden Perch, carp gudgeons and Olive Perchlets preferred structure over open sandy habitat, whilst juvenile Silver Perch, Un‐specked Hardyhead and Murray–Darling Rainbowfish did not avoid open sandy habitats. Juvenile Murray Cod preferred rocky rubble habitat over all other habitat choices. Use of complex rock piles to provide nursery habitat for Murray Cod populations is a potential restoration option. Introduction of rock could also benefit Golden Perch and carp gudgeons. Use of emergent plants, submerged macrophytes and rocky rubble for habitat restoration all appear to have merit for one or more species of small‐bodied fishes or juvenile stages of larger sized fishes. Rocky rubble or floating attached macrophytes could be viable restoration options in areas too turbid to establish submerged macrophytes. These habitat interventions would complement existing actions such as re‐snagging and provision of fish passage to assist with sustainable management of native fish populations.     

Ontogenetic patterns of habitat use by fishes within the main channel of an Australian floodplain river

The ontogenetic patterns of habitat use by a community of fishes in the main channel of the Broken River, an Australian lowland river, was investigated. Stratified sampling was conducted fortnightly across six habitat types throughout the spring‐summer period within the main channel. As predicted by the 'low flow recruitment hypothesis', backwaters and still littoral habitats were important nursery habitats for most species. These habitats were found to be used by some species throughout all stages of their life cycle, while other species showed clear ontogenetic shifts in habitat preference. Only one species, Murray cod Maccullochella peelii peelii , was never found in backwaters. This study confirms the significance of main channel habitats in the rearing of larvae of some riverine fish species, and emphasizes the importance of considering the habitat requirements of all stages of a fish's life cycle in the management and restoration of rivers and streams.     

Influence of habitat heterogeneity on the distribution of larval Pacific lamprey (Lampetra tridentata) at two spatial scales

1. Spatial patterns in channel morphology and substratum composition at small (1–10 metres) and large scales (1–10 kilometres) were analysed to determine the influence of habitat heterogeneity on the distribution and abundance of larval lamprey. 2. We used a nested sampling design and multiple logistic regression to evaluate spatial heterogeneity in the abundance of larval Pacific lamprey, Lampetra tridentata, and habitat in 30 sites (each composed of twelve 1‐m² quadrat samples) distributed throughout a 55‐km section of the Middle Fork John Day River, OR, U.SA. Statistical models predicting the relative abundance of larvae both among sites (large scale) and among samples (small scale) were ranked using Akaike's Information Criterion (AIC) to identify the ‘best approximating’ models from a set of a priori candidate models determined from the literature on larval lamprey habitat associations. 3. Stream habitat variables predicted patterns in larval abundance but played different roles at different spatial scales. The abundance of larvae at large scales was positively associated with water depth and open riparian canopy, whereas patchiness in larval occurrence at small scales was associated with low water velocity, channel‐unit morphology (pool habitats), and the availability of habitat suitable for burrowing. 4. Habitat variables explained variation in larval abundance at large and small scales, but locational factors, such as longitudinal position (river km) and sample location within the channel unit, explained additional variation in the logistic regression model. The results emphasise the need for spatially explicit analysis, both in examining fish habitat relationships and in developing conservation plans for declining fish populations.     

Evaluating the efficacy of seasonal grazing and livestock exclusion as restoration tools for birds in riparian habitat of the Okanagan Valley,British Columbia,Canada

Riparian habitat supports the highest density and diversity of songbirds in Western North America despite covering less than 1% of the land area. Widespread destruction and degradation of riparian habitat, especially by livestock grazing, has led to habitat restoration efforts. In 2000, restoration activities in the form of permanent and seasonal exclusion of livestock from riparian areas were initiated to improve habitat for the endangered Western Yellow‐breasted Chat (Icteria virens auricollis) population, which is dependent on early successional shrub habitat for nesting, in the Okanagan Valley of British Columbia, Canada. We assessed the effectiveness of livestock exclusion by examining temporal changes in the abundance, richness, and breeding performance of birds in restoration and reference sites. The abundance of W. Yellow‐breasted Chats significantly increased between 2002 and 2013 in areas where restoration activities occurred. However, restoration did not have significant effects on the abundance, richness, or breeding performance of other riparian birds at the restoration sites independent of temporal changes that occurred at reference sites. Our results provide evidence that limiting livestock grazing in temperate riparian areas can lead to recovery of endangered riparian songbirds that rely on early successional shrub habitat but may have limited effects on common species that are not strictly reliant on this habitat.     

Comparative movements of four large fish species in a lowland river

A multi‐year radio‐telemetry data set was used to comparatively examine the concurrent movements of the adults of three large‐bodied Australian native freshwater fishes (Murray cod Maccullochella peelii, trout cod Maccullochella macquariensis and golden perch Macquaria ambigua) and the introduced carp Cyprinus carpio. The study was conducted over a reach scale in the regulated Murray River in south‐eastern Australia. Differences were identified in the movements among these species. The predominant behaviour was the use of small movements (<1 km) for all species, and although larger‐scale movements (>1 km) did occur, the frequency varied considerably among species. Large‐scale movements were least evident for M. macquariensis and more common for M. ambigua and C. carpio with these two species also having a greater propensity to change locations. Macquaria ambigua displayed the largest movements and more M. ambigua moved on a ‘continual’ basis. Although a degree of site fidelity was evident for all species, the highest levels were exhibited by M. macquariensis and M. peelii. Homing was also evident to some degree in all species, but was greatest for M. peelii.     

The presence of anadromous twaite shad (Alosa fallax) in the Ebro River (western Mediterranean,Spain): an indicator of the population's recovery?

Although the Ebro River is one of the largest Mediterranean rivers, the presence of anadromous fish species was near to complete extirpation since the second half of the 20th century. However, many mature twaite shads (Alosa fallax) were captured at the lower reaches of this river (Xerta's weir site, 63 river km) in spring 2005, suggesting a natural recovery of this population. In this study, the first biological data on twaite shad from the Ebro River are presented, and their significance for the species conservation and recovery are discussed. The historical reasons for the decline of this species are reviewed, and data supports the proposal for urgent construction of a proper fish passage for anadromous species at the Xerta's weir. This action would allow fish access to a further 60 km of river upstream of the weir, representing a 200% increase in the amount of freshwater habitat and potential spawning areas. Improved access together with restrictive fishery regulations will assist with renewed interest in the fishery and conservation of the species.     

Influence of Landscape Geomorphology on Large Wood Jams and Salmonids in an Old-growth River of Upper Michigan

We investigated the structure of large wood jams (LWJ) and their use by brook trout (Salvelinus fontinalis, Mitchill) and other fish in four geomorphically-distinct sections of the Little Carp River, a small river flowing through an uncut, old-growth, northern hardwood-conifer forest along the south shore of Lake Superior, Upper Michigan. We characterized nine LWJ per section and then electroshocked fish at three randomly selected LWJ per section. Structural characteristics of LWJ (e.g., total volume of wood, number of logs) varied with geomorphology at the scale of approximately one km. Differences in the abundance of fish associated with LWJ were not statistically significant among LWJ and non-LWJ portions of stream across all study reaches. Factors that explained most variability in the proportion of salmonids at LWJ (valley constraint, volume and number of pieces in the jam) reflected both large-scale geomorphology and characteristics of LWJ. If emulating an old-growth system is the goal for restoring habitat, attention should be given to the correlation of LWJ with larger-scale geomorphology of the reference river. However, it cannot be assumed that LWJ restoration will necessarily increase brook trout abundance near LWJ in a system similar to the Little Carp River as we observed low overall correlation between brook trout abundance and LWJ.     

Efficacy of a nature-like bypass channel in a Portuguese lowland river

Throughout Europe in the last decade there has been a steady shift away from more technical fish pass designs to more nature‐like passes, such as nature‐like bypass channels. Upstream fish passage in a nature‐like bypass channel was investigated in a lowland river, the Lima River, for 117 days from March 2000 to May 2002. Fish passage was recorded using an automatic video recording system. Electrofishing samples within the bypass and below the weir were compared with species abundance found on the tape recordings. More than 7500 individuals of eight species passed through the bypass channel. Species composition was dominated by striped mullet (65.3%) and potamodromous species (34.3%), which used the bypass mainly at night. Of the environmental variables considered, bypass discharge explained most of the variation in the number of cyprinids, whereas water temperature was more important for diadromous species. Comparing species composition below the weir using passage recordings provided a useful tool to assess species efficacy of the bypass, although biological requirements should also be taken into account. This study proved the efficacy of the bypass for passage of almost all occurring species and life stages and also for providing suitable habitat for fish fauna, highlighting the use of these facilities for river restoration schemes.     

Influence of fine‐scale habitat requirements and riparian degradation on the distribution of the purple‐crowned fairy‐wren (Malurus coronatus coronatus) in northern Australia

Species distributions are influenced by variation in environmental conditions across many scales. Knowledge of fine‐scale habitat requirements is important for predicting species occurrence and identifying suitable habitat for target species. Here we investigate the perplexing distribution of a riparian habitat specialist, the western subspecies of the purple‐crowned fairy‐wren (Malurus coronatus coronatus), in relation to fine‐scale habitat associations and patterns of riparian degradation. Surveys of vegetation attributes, river structure and disturbance indicators that are likely to be causal determinants of the species occurrence were undertaken at 635 sites across 14 catchments. Generalized Linear Mixed Modelling demonstrated that the probability of purple‐crowned fairy‐wren occurrence increased with Pandanus aquaticus crown cover, shrub density and height of emergent trees, while riparian structure and signs of cattle were indirect predictors of occurrence. As our study area predominantly contained Pandanus type habitat, we failed to identify river grass as an important component of habitat. Predictions from a cross‐validated model of purple‐crowned fairy‐wren occurrence suggested distribution is constrained by three factors: (i) low quality of local habitat within catchments where the species occurs; (ii) broad‐scale reduction in habitat quality that has resulted in extinction of the species from parts of its range; and (iii) unmeasured variables that limit the exploitation of suitable habitat. The reliance of the species on dense shrubby understorey suggests conservation efforts should aim to maintain the complexity of understorey structure by managing fire and grazing intensity. Efforts to halt the continuing decline of riparian condition and maintain connectivity between areas of quality habitat will help to ensure persistence of riparian habitat specialists in northern Australia.     

Fish habitat rehabilitation using wood in the world

To provide river managers and researchers with practical knowledge about fish rehabilitation, various studies of fish habitat rehabilitation that used wood were reviewed. The review focuses on fish responses, wood installation methods, and geomorphic features of the rehabilitation sites. Most studies were conducted in moderately sized (small and medium) streams with relatively high bed gradients and aimed to improve the habitats of salmonid species. In this stream type, structures spanning the full (log dam) and partial (log deflector) width of the river were most common, and wood structures that created pools and covers were successful in improving fish habitat. Some projects were conducted in moderately sized low-gradient streams, in which wooden devices used to create instream cover were effective for fish assemblages. There were few studies in other aquatic ecosystems. However, well-designed large wood structures, known as engineered log jams, were used in rehabilitation projects for large rivers. In slack-water or lentic systems such as side-channels, estuaries, and reservoirs, small and large wood structures that created cover were used to improve habitat for many fish species. For successful fish habitat rehabilitation projects, the hydrogeomorphic conditions of rehabilitation sites should be carefully examined to avoid physical failure of wood structures. Although artificial wood structures can be used to improve fish habitat in various aquatic ecosystems, they should be considered to be a complementary or interim habitat enhancement technique. The recovery of natural dynamic processes at the watershed scale is the ultimate target of restoration programs.     

Macrohabitat associations of fishes in shallow waters of the Detroit River

Seasonal variation in large‐scale habitat selection by fishes in shallow, Canadian waters of the Detroit River was examined. Fish communities were compared among three river segments (upstream, middle and downstream) consisting of areas of shallow water habitat separated by wide hydrologic barriers of deep, flowing water and between inshore and offshore areas. In spring, the most unique, diverse and abundant fish assemblages were found at inshore sites in the middle segment where the largest remaining wetland habitats are located. Fishes used inshore habitat to spawn and probably avoided offshore areas because macrophyte cover was not available in spring. In summer, juvenile gizzard shad Dorosoma cepedianum and white bass Morone chrysops were observed in high densities in the upstream segment, probably migrating downstream from Lake St Clair. There was little difference in the fish assemblage among macrohabitats in autumn. The upstream segment appeared to be the most degraded, because it contained no species that were not found in the other segments, had a paucity of uncommon species and had significantly more non‐native species. This state was attributed to the infilling of coastal wetlands by urban land use and a resulting loss of habitat heterogeneity. The middle segment, with the only remaining wetland habitats, had the greatest occurrence of uncommon species and the only species at risk found in this study. Conservation and restoration efforts should be greatest for wetlands; however, shallow offshore areas provide important fish habitat in summer and autumn.     

Distribution of native and introduced fish in the Seven Creeks River system,Victoria

The distribution offish within the Seven Creeks River system, a tributary of the Goulburn River in the Murray–Darling basin, was determined primarily by a survey carried out during the summer of 1975–76. Information on the past occurrence of fish in the system was obtained from historical records. Seventeen species offish, eleven native and six exotic, have been recorded from the system. Habitat characteristics, cohabiting species and food habits are presented for each species recorded during the survey, and factors affecting present distributions are discussed. Siltation appears to have had adverse effects on native Murray cod, Maccullochella peeli, and Macquarie perch, Macquaria australasica, both of which were once common in the lower reaches of the system. The presence of Macquarie perch and the rare native trout cod, Maccullochella macquariensis, in the upper reaches of the system is traced to fish released in 1921 and 1922. A nother native species, the western carp gudgeon, Hypseleotris klunzingeri, was first observed in the system only after it had been introduced into farm dams in the area in the mid 1960s. Relationships between native and introduced fish are complex. Although the food requirements of some native and introduced species overlap and some native fish have been found in the stomachs of introduced species, the only evidence of a substantial effect of an introduced species on a native species is the apparent fragmentation of the range of common mountain galaxiids, Galaxias olidus, by brown trout, Salmo trutta, whose numbers in the system were, until recently, augmented by continual releases of hatchery-reared fish.     

Impacts of an invasive willow (Salix × rubens) on riparian bird assemblages in south‐eastern Australia

We explored how a woody plant invader affected riparian bird assemblages. We surveyed 15 200‐m‐long transects in riparian zones in a much‐changed landscape of eastern Victoria, Australia. Abundance, species‐richness, foraging‐guild richness and composition of birds were compared in transects in three habitat types: (i) riparian zones dominated by the invasive willow Salix × rubens; (ii) riparian zones lined with native woody species; and (iii) riparian zones cleared of almost all woody vegetation. We also measured abundance and richness of arthropods and habitat structure to explore further the effects of food resources and habitat on the avifauna. We observed 67 bird species from 14 foraging guilds. Native riparian transects had more birds, bird species and foraging guilds than willow‐invaded or cleared transects. Habitat complexity increased from cleared to willow‐invaded to native riparian transects, as did abundance of native and woodland‐dependent birds. Native shrub and trees species had more foliage and branch‐associated arthropods than did willows, consistent with a greater abundance and variety of foraging guilds of birds dependent on this resource. Willow spread into cleared areas is unlikely to facilitate greatly native bird abundance and diversity even though habitat complexity is increased. Willow invasion into the native riparian zone, by decreasing food resources and altering habitat, is likely to reduce native bird biodiversity and further disrupt connectivity of the riparian zone.