Long‐term fish assemblages of inner bends in a large river

We sampled fishes at 17 inner bend sites on the Wabash River in 2008 to compare with collections from 1977 to 1997. We used the same seine collection methods as previous years and collected a total of 37 species. Mean site Shannon‐Wiener diversity, species richness, evenness and abundance for all years were similar. We used multivariate analyses to test for patterns in fish assemblage structure among all sites and all years. The multivariate analyses resulted in distinct assemblages for each collection‐year, suggesting shifts in assemblage composition among years. We used separate multivariate analyses to examine fish assemblage variation within individual years. Variation that corresponded to an upstream–downstream pattern was present in 1977 and 2008, but not in 1997. A hydrologic analysis based on daily discharge revealed that eight large flood events occurred from 1928 to 2007, with four of these events during the recent 20 years. We quantified substrate variation at the 17 sites in 2008 and identified a longitudinal gradient in dominant substrate categories with gravel upstream and sand downstream that was correlated with the first axis of the 2008 fish assemblage ordination. We suggest that observed changes in fish assemblages in decadal periods were from hydrologic impacts of large floods on local habitats. Copyright © 2010 John Wiley & Sons, Ltd.     

The impact of intermediate‐head navigation locks on downstream fish passage

Navigation in inland waterways is increasingly important worldwide and so is inherently the construction and use of navigation locks. However, the impact of navigation locks on downstream migrating fish is rarely documented. In Belgium, the Albert Canal connecting the Meuse River to the Scheldt Estuary may offer migration opportunities for European eel (Anguilla anguilla) and Atlantic salmon (Salmo salar), two critically endangered species. During their downstream migration phase (respectively silver eels and salmon smolts), both species have to pass five intermediate‐head navigation locks before reaching the estuary. Previous research showed that silver eel escapement is largely unsuccessful and that eels are delayed extensively at the navigation lock complexes. To get a better understanding of the mechanisms behind these failures and delays, we tagged and released 62 silver eels and 44 salmon smolts in the vicinity of one navigation lock complex of the canal. This paper reports the mechanisms behind the previously perceived delay, the route choices to pass the complex, and the risks involved. Of the 65% tagged eels and 73% tagged smolts that succeeded to pass the complex, respectively, 20% and 41% needed more than one trial to pass the complex. Moreover, 52% of all trials were via intakes of the lock filling system, at least four smolts (17%) died after intake passing, and about 30% of both intake‐passing smolts and eels stopped migrating after passage. Therefore, intermediate‐head navigation locks are a potential threat to downstream migrating fish, which requires more research to fully investigate its impact.     

Impacts of a reservoir on fish assemblages of small tributaries of the Corumbá river,Brazil

Fish community surveys were conducted in five tributaries of the Corumbá River before and after damming. Electrofishing samples were collected monthly in the pre‐impoundment period (March 1996 to August 1996) and 15 in the post‐impoundment period (September 1996 to February 1999). A self‐organizing map (SOM, an Artificial Neural Network algorithm) was used to represent the patterns of fish assemblages. Samples collected in both the pre‐ and post‐impoundment periods were randomly dispersed on the SOM, and, therefore, a clear and significant pattern of separation between samples collected during these two time periods was not found. Mean and maximum water depth, which is correlated with ground water level, did not significantly separate the pre‐ and post‐impoundment samples. However, we found significant differences between the two periods for water temperature, pH, conductivity, DO and current velocity, but abundances of fish species (summarized in the clusters identified by the SOM) did not differ significantly. Instead, the validity of the clusters distinguished by the SOM was confirmed by significant differences in some biotic variables: species richness, equitability and log transformed total abundance. Indicator species values identified the most preferred cluster (and respective complex of environmental factors) for a given species. Only one cluster did not contain any significant species indicator values, but it was dominated by samples from the Furnas Stream, which was the only effluent that could be entered by fish from the main river channel after the damming owing to its location below the dam, which has no fish ladder. Copyright © 2008 John Wiley & Sons, Ltd.     

Spatio‐temporal variations in fish assemblages in a tropical regulated lower river course: an environmental guild

Fish assemblage patterns were studied in the lower river reach of the Uthokawiphatprasit anti‐salt dam, 6 km upstream from the Pak Panang River mouth, Southern Thailand, where the dam was opened occasionally depending on the upstream water level. Matrix data of the presence–absence of 71 fish species in 102 surveys was used in the analysis by applying a self‐organizing map (SOM) model. The trained SOM (lattice 8 × 7) showed that after 6 years of operation, five assemblage patterns were distinguished. These patterns described the probability of the occurrence of fish in each fish environmental guild, which according to changes in flow and water geomorphology. Clusters Ia and Ib were mostly the surveys in upstream stations and occupied by fish in potamonic guilds, whereas the fish in the estuarine guild and marine guilds showed a high probability of occurring in clusters IIa, IIb and IIc, which belonged to the surveys in downstream stations. The surveys of the stations near the dam (i.e. stations 5 and 6) during the opening phase were contained in cluster IIb. The Kruskal–Wallis test showed that there was no statistical difference in the probability of occurrence among assemblages of the diadromous, catadromous and semi‐anadromous fishes but not the amphidromous fishes, which had a low probability of occurrence in clusters Ia and Ib. The fish assemblages were arrayed along a longitudinal gradient, where salinity and pH were the most important controlling variables and explained 94.0% of the total inertia. Copyright © 2009 John Wiley & Sons, Ltd.     

Aquatic habitat change in the Arkansas river after the development of a lock‐and‐dam commercial navigation system

The McClellan–Kerr Arkansas River Navigation System (MKARNS), completed in 1971, required the construction of 17 locks and dams and associated navigation works to make the Arkansas and Verdigris Rivers navigable for barge traffic from the Mississippi River to Catoosa, Oklahoma. We used a Geographic Information System to assess habitat changes in the 477‐km portion of this system within Arkansas from 1973 to 1999. Total aquatic area declined by 9% from 42 404 to 38 655 ha. Aquatic habitat losses were 1–17% among pools. Greatest habitat losses occurred in diked secondary channels (former secondary channels with flow reduced by rock dikes) and backwaters adjacent to the main channel. Most of the area of dike pools (aquatic habitat downstream of rock dikes), diked secondary channels and adjacent backwaters were <0.9 m deep. Copyright © 2008 John Wiley & Sons, Ltd.     

The influence of hydro‐climatic and anthropogenic effects on the long‐term variation of commercial fisheries in a large floodplain river

This study deals with the effects of climate fluctuations and anthropogenic impacts on fisheries of Paraná River over the last 100 years. It is the first attempt to appraise the influence of hydro‐climatic and anthropogenic variables on the population changes of the most important inland fisheries of Argentina. Datasets covering more than eight decades (1935–2016) of a number of frequent and abundant commercial species inhabiting the main channel as well as the large floodplain of Paraná River were used. Our results suggest that fish catches and structure changed over time. Long and short‐term changes and reductions were closely related to fluctuations of 18 hydro‐climatic variables. Positive effects on the ichthyofauna were recorded during humid periods (1930–1940 and 1970–2000), when the frequency of large spring–summer floods increased. An increase in anthropic impacts (accounted for with nine variables) were recorded during the last two decades. We highlight the usefulness of the approach to support the management of the resources, ensuring sustainability of commercial fish assemblages and the long‐term conservation of biodiversity in big rivers.     

Age,growth and non‐flood recruitment of two potamodromous fishes in a large semi‐arid/temperate river system

Golden perch Macquaria ambigua (Percichthyidae) and silver perch Bidyanus bidyanus (Terapontidae) are two potamodromous fish species of the Murray‐Darling river system in southeastern Australia. Ageing of these species using thin sections of the sagittal otoliths and validation with known‐age fish revealed: they live for over 26 years; male and female silver perch reach maturity at 3 and 5 years respectively; male and female golden perch reach maturity at 2 and 4 years respectively; both species exhibit sexual dimorphism with larger females; and growth varies (L_∞ silver perch 331–397 mm, golden perch 354–502 mm) among interconnected river systems. Longevity and opportunistic growth are characteristics that are well suited to the semi‐arid and temperate hydrology of this river system. A flood‐recruitment model for these two species, consistent with the ‘flood‐pulse concept’, has previously been assumed to be the main mechanism of recruitment. The model appeared appropriate for this large, low‐gradient river system with productive floodplains. However, in the middle reaches of the Murray River we found that golden perch recruitment was strong in non‐flood years and poor in flood years, and silver perch recruited in all years. These data do not preclude golden perch recruiting during floods as well, because downstream larval drift may have resulted in strong year‐classes being swept downstream of the sampling area during high flows. However, the recruitment models for these species need to be re‐evaluated to include within‐channel flows. Importantly, these flows can be manipulated by river regulation, unlike large floods, and therefore there is potential to enhance recruitment. Copyright © 2003 John Wiley & Sons, Ltd.     

Effects of dams in river networks on fish assemblages in non‐impoundment sections of rivers in Michigan and Wisconsin,USA

Regional assessment of cumulative impacts of dams on riverine fish assemblages provides resource managers essential information for dam operation, potential dam removal, river health assessment and overall ecosystem management. Such an assessment is challenging because characteristics of fish assemblages are not only affected by dams, but also influenced by natural variation and human‐induced modification (in addition to dams) in thermal and flow regimes, physicochemical habitats and biological assemblages. This study evaluated the impacts of dams on river fish assemblages in the non‐impoundment sections of rivers in the states of Michigan and Wisconsin using multiple fish assemblage indicators and multiple approaches to distinguish the influences of dams from those of other natural and human‐induced factors. We found that environmental factors that influence fish assemblages in addition to dams should be incorporated when evaluating regional effects of dams on fish assemblages. Without considering such co‐influential factors, the evaluation is inadequate and potentially misleading. The role of dams alone in determining fish assemblages at a regional spatial scale is relatively small (explained less than 20% of variance) compared with the other environmental factors, such as river size, flow and thermal regimes and land uses jointly. However, our results do demonstrate that downstream and upstream dams can substantially modify fish assemblages in the non‐impoundment sections of rivers. After excluding river size and land‐use influences, our results clearly demonstrate that dams have significant impacts on fish biotic‐integrity and habitat‐and‐social‐preference indicators. The influences of the upstream dams, downstream dams, distance to dams, and dam density differ among the fish indicators, which have different implications for maintaining river biotic integrity, protecting biodiversity and managing fisheries. Copyright © 2010 John Wiley & Sons, Ltd.     

An assessment of the effectiveness of a vertical‐slot fishway for non‐salmonid fish at a tidal barrier on a large tropical/subtropical river

Fishways for salmon in temperate rivers have often been successful, but salmonid‐type fishways for non‐salmonid species in tropical and subtropical rivers have frequently failed. This study assessed the effectiveness of modifying a salmonid‐type pool‐and‐weir fishway into a vertical‐slot design on a tidal barrage on the subtropical Fitzroy River, in Queensland, north‐eastern Australia. In 38 paired samples of the top and bottom of the fishway, over 16 months, 29 fish species and over 23 000 fish were collected at a maximum rate of 3400 per day. This study shows much greater potential for success with a vertical‐slot fishway as relatively few fish negotiated the original pool‐and‐weir design. Common species using the vertical‐slot fishway included blue‐catfish (Arius graeffei [Ariidae]), bony herring (Nematalosa erebi [Clupeidae]), striped mullet (Mugil cephalus [Mugilidae]), barramundi (Lates calcarifer [Centropomidae]), and long‐finned eels (Anguilla reinhardtii [Anguillidae]). Freshwater shrimp (Macrobrachium australiense [Palaemonidae]), juvenile crabs (Varuna litterata [Grapsidae]) and long‐finned elvers did not ascend the full length of the fishway and specific fishways for these species are recommended. Fish between 25 and 640 mm in length ascended the fishway, although the passage of smaller size classes of immature fish was restricted and this may be important for the sustainability of these migratory populations. The barramundi (200–640 mm) which ascended the fishway were all immature fish. However, during a period of low river flows enlarging the width of the vertical‐slot from 0.15 to 0.45 m only encouraged a small number of larger fish (890 mm maximum length) to enter. The strong diel movement patterns of many species will need to be considered in future fishway design. Blue‐catfish could ascend the fishway in 2 h, but many fish remained in the fishway and this behaviour may cause crowding and a reduction in fishway capacity. Further work is needed to assess the proportion of fish finding the fishway entrance. However, the findings suggest that vertical‐slot fishways with lower water velocities and turbulence than salmonid fishways have great potential to pass the diverse migratory fish fauna of subtropical and tropical rivers. Copyright © 1999 John Wiley & Sons, Ltd.     

Interactive effects of abiotic,hydrological and anthropogenic factors on fish abundance and distribution in natural run‐of‐the‐river shallow lakes

Ecological processes in lowland rivers are mostly dominated by hydrology and its interactions with other environmental factors. Fish–habitat relationships in rivers are also influenced by human impacts. In this study, we describe patterns of abundance and distribution of fish species in a group of natural lowland river lakes along spatial anthropogenic and abiotic gradients when four hydrologically different summers are compared. We also describe the proportion of the total variances in fish species abundances that can be accounted for by selected abiotic (water conductivity), hydrological (water residence time) and human activity‐derived (total phosphorus (TP) concentration and NO₃:NH₄) variables. Consequently, our main purpose is to explore how abiotic and anthropogenic factors interact to affect fish abundance and distribution together with consistent results across different hydrological conditions. We conclude with a briefly discussion of some management implications. The anthropogenic impacts on water quality, the extreme hydrological variability and the fluctuating abiotic environment affected fish abundance and distribution. Pampa inland silverside Odontesthes bonariensis was benefited from a less human disturbed environment with higher water residence time and total salinity, whereas species as Cyphocharax voga, Parapimelodus valenciennis and Cyprinus carpio found these conditions largely disadvantageous. On the other hand, while most species showed stronger—either negative or positive—response to anthropogenic, hydrological or abiotic factors Oligosarcus jenynsii was only slightly affected. This paper identified the ecological function of a lowland river under its natural flow regime. There are not many opportunities to study unmodified rivers worldwide. Therefore, our findings may help in assessment programmes of fish communities in flow altered and human disturbed aquatic ecosystems. Copyright © 2008 John Wiley & Sons, Ltd.     

Development of a standardized large river bioassessment protocol (LR‐BP) for macroinvertebrate assemblages

Efforts to develop benthic macroinvertebrate sampling protocols for the bioassessment of lotic ecosystems have been focused largely on wadeable systems. As these methods became increasingly refined and accepted, a growing number of monitoring agencies expanded their work and are now developing sampling protocols for non‐wadeable large rivers. Large rivers can differ from wadeable streams in many ways that preclude the use of some wadeable stream sampling protocols. Hence, resource managers need clear and consistent large river bioassessment protocols for measuring ecological integrity that are cost effective, logistically feasible, and meet or are adaptable to the multi‐purpose sampling needs of researchers and managers. We conducted a study using an experimental macroinvertebrate sampling method that was designed to overcome limitations of several methods currently in use. Our objectives were to: (1) determine the appropriate number of sampling points needed; (2) determine an appropriate laboratory subsample size to use and (3) examine how varying reach length affects assemblage characteristics. For six reaches in each of two large rivers, we sampled the macroinvertebrates of both banks at 12 transects separated by increasingly larger distances using a multi‐habitat, semi‐quantitative technique. Interpretation of results relied on the values attained for nine benthic macroinvertebrate assemblage metrics. Results from Monte Carlo methods indicated that, using the sampling methods described herein, a representative sample of the assemblage was collected by sampling both banks on 6 transects. Across all sites, we did not observe a consistent relationship between transect spacing (i.e. total reach length) and metric values, indicating that our sampling protocol was relatively robust with respect to variation in reach length. Therefore, flexibility exists that permits the study reach length to be dictated by the spatial scale (e.g. repeating geomorphic units) in question. For those preferring to use a fixed reach length, we recommend that transects be spaced at a minimum of 100 m intervals over a 500 m distance. We recommend that the field method be coupled with a fixed laboratory subsample size of 300 organisms for bioassessment purposes, with the recognition that a subsample size of 500 organisms may be needed to meet the objectives of more rigorous studies. It is likely this approach will over‐sample sites of uniform composition, but the goal was to develop a robust sampling protocol that would perform well across sites of differing habitat composition. Possible modifications to the method to streamline its future application in the field are provided. Published in 2006 by John Wiley & Sons, Ltd.     

Spatial modelling of freshwater fish in semi‐arid river systems: a tool for conservation

This paper examines the feasibility of using multivariate statistics to model fish species distribution and habitat requirements for intermittent streams in semi‐arid regions, many of which are coming under increasing pressure from water resource development schemes. The assessment was based on the geographical distribution of six endemic fish species in the Guadiana river, a semi‐arid river system in southern Iberia. Their presence was related to 20 environmental variables linked to climate, geomorphology, riparian vegetation and location in the drainage basin. These variables were collected in the field or from topographical maps to evaluate habitat suitability and to predict the presence of the species according to season. Multivariate logistic regression in a geographic information system (GIS) environment was performed to identify regions with high probability of occurrence for each species. The variables that best explained the occurrence of the species were the sample location in the drainage basin, the geomorphology and the riparian vegetation. The models presented have a high predictive power and can be used in monitoring and predicting temporal changes caused by human activities. This modelling approach can be used to predict the areas that need to be conserved to protect or rehabilitate the endangered species. Armed with this information, managers can formulate conservation measures to prevent further degradation of the stocks and possibly enhance the populations. Copyright © 2002 John Wiley & Sons, Ltd.     

Implications of an invasive fish barrier for the long‐term recovery of native fish assemblages in a previously degraded northeastern Illinois River system

Barriers to fish movement have been used to prevent the spread of invasive fishes but may also limit the movements of native fishes. We evaluated the potential consequences of a proposed barrier on the Illinois River Waterway, meant to inhibit the spread of silver and bighead carps, to the continued recovery of native fishes in the Des Plaines River following water quality improvements. We compared changes in upstream cumulative species richness and community structure from 1983 to 2013 in the DuPage River, an adjacent tributary with an impassable dam, to the area upstream of a newly proposed barrier on the Des Plaines River where fish can currently pass through a navigational lock. Fewer species displayed truncated distributions upstream of the passable lock and dam (n = 18) compared with the impassable dam (n = 23). Due to water quality improvements in the Illinois River as a whole, cumulative species richness downstream of both dams steadily increased over time. Richness also increased upstream of the passable dam but plateaued upstream of the impassable dam. Fifteen to 18 species accounted for differences in community structure between areas downstream and upstream of either dam. Most species (78–100%) were found in greater relative abundance downstream of the impassable dam, and only 53% were found in greater relative abundance downstream of the passable dam. The truncation in species richness and abundance at the impassable dam foreshadows the potential consequences of an indiscriminate barrier on native fishes and the continued recovery of native assemblages.     

Spatial patterns of fish communities in the Upper Mississippi River System: assessing fragmentation by low‐head dams

We assessed the similarity of fish communities among river reaches to assess community‐level fragmentation by low‐head dams in the Upper Mississippi River System (UMRS). The spatial coverage of standardized electrofishing sampling used in the Long Term Resource Monitoring Program (LTRMP) was extended for three of the six regional trend areas (RTA; pools 4, 13, and the Open River Reach) to include river reaches (outpools) immediately upstream and downstream from the standard RTA from 15 June to 31 October 2000. Additionally, pools 19 and 20 were sampled in September 2000. Cluster analysis and non‐metric multidimensional scaling of community composition and structure data revealed two major groups, upper and lower reaches, and four (for composition) or five (for structure) sub‐groupings of river reaches. In general, all outpools grouped with the nearest RTA for both community composition (no exception) and community structure (one exception). This suggests that fragmentation of fish communities from low‐head dams is minimal. Mantel correlations demonstrated strong inverse association between the similarity of fish communities with the distance between reaches. Habitat variables measured during electrofishing collections were significantly correlated with spatial variation of fish composition and community structure, but provided only marginal improvements to correlations with distance between reaches alone. Furthermore, habitat variability among river reaches also was related to distance between reaches. Determining the extent to which variation of fish communities is related to habitat or demographic processes (e.g. migration, larval drift, source‐sink dynamics) will be challenging for this system. Although low‐head dams on the UMRS may restrict movements for individuals and populations of certain fish species, we found little evidence that these effects have led to substantial, community‐level fragmentation. Copyright © 2006 John Wiley & Sons, Ltd.     

Linking a spatially explicit watershed model (SWAT) with an in‐stream fish habitat model (PHABSIM): A case study of setting minimum flows and levels in a low gradient,sub‐tropical river

As changes in landuse and the demand for water accelerate, regulators and resource managers are increasingly asked to evaluate water allocation against the need for protection of in‐stream habitat. In the United States, only a small number of river basins have the long‐term hydrograph data needed to make these assessments. This paper presents an example of how to bridge the conceptual and physical divide between GIS‐based watershed modelling of basin‐discharge and in‐stream hydraulic habitat models. Specifically, we used a Soil and Water Assessment Tool (SWAT) model for the Hillsborough River to produce data for use in a Physical HABitat SIMulation (PHABSIM) model of the same river. This coupling of models allowed us to develop long‐term discharge data in ungauged river systems based on watershed characteristics and precipitation records. However this approach is not without important limitations. Results confirm that accuracy of the SWAT‐predicted hydrograph declines significantly when either the DEM resolution becomes too coarse or if DEM data are resampled to a coarser or finer resolution. This is due to both changes in the size and shape of the river basin with the varying DEMs and subsequent shifts in the proportions of land use, soils and elevation. Results show the use of 30 m DEMs produced hydrographic patterns amenable for using in‐stream habitat protocols like PHABSIM model, especially where little or no hydrographic and land use information exists. Copyright © 2010 John Wiley & Sons, Ltd.     

Modelling the effects of climate and flow regulation on ice‐affected backwater staging in a large northern river

In cold region environments, ice‐jam floods (IJFs) pose a severe risk to local communities, economies, and ecosystems. Previous studies have shown that both climate and regulation affect IJF probabilities, but their relative impacts are poorly understood. This study presents a probabilistic modelling framework that couples hydrologic and hydraulic models to assess the relative role of regulated and naturalized flows on ice‐affected backwater staging. The framework is evaluated at an IJF‐prone town on the Peace River in western Canada, which has been regulated since 1972. Naturalized flows were generated for the comparison, and ice‐affected backwater profiles were calculated along jams of varying length and location and for different combinations of model parameters and boundary conditions. Results show significant differences in backwater staging (~2 m for a return period of T = 1:10 year) between two study time periods (1973–1992 vs 1993–2012) as compared with two different hydraulic flow conditions (regulated vs naturalized), suggesting a larger role of climate than regulation in backwater staging. However, regulation was found to offset flood risk during the 1973–1992 period and exacerbate flood risk during the 1993–2012 period.     

Monitoring of environmental flow outcomes in a large river basin: The Commonwealth Environmental Water Holder's long‐term intervention in the Murray–Darling Basin,Australia

The Murray–Darling Basin in south‐eastern Australia contains over 70,000 km² of wetlands and floodplains, many of which are in poor condition. In response, Australian governments have committed to a major restoration program, the Murray–Darling Basin Plan that includes management of 2,750 Gl of environmental water to protect and restore aquatic ecosystems. The restoration is being undertaken within an adaptive management framework that includes monitoring the outcomes of environmental flows in seven river valleys. This paper provides an overview of the 5‐year monitoring project and some preliminary results. Monitoring design considered the Basin Plan's environmental objectives, conceptual models of ecosystem responses to flow, and an outcomes framework linking flow responses to the environmental objectives. Monitoring indicators includes ecosystem type, vegetation, river metabolism, and fish. Responses are evaluated to identify the contribution of environmental flows to Basin Plan environmental objectives and continual improvements in management. The program is unique in that it seeks to monitor long‐term outcomes of environmental flows at the river basin scale. Despite many challenges, the monitoring has become a key part of the adaptive management of environmental flows in the Murray–Darling Basin.     

Consumer‐diet discrimination of δ13C and δ15N: Source‐ and feeding‐oriented patterns based on gut content analysis in a large subtropical river of China

Understanding the trophic discrimination (?¹³C and ?¹⁵N) between consumers and diets in fluvial systems remains difficult because of the variable food sources and complex predator–prey interactions from headwaters to the estuaries. Here, stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotopes in fish and invertebrates from a large subtropical river in southern China were determined to explore trophic discrimination in conjunction with a gut content analysis. The ?¹³C values showed significant differences (p < .05) among functional feeding groups, with fish, shrimp, and insect scrapers presenting higher ?¹³C values (1.20 ± 0.23‰ to 1.51 ± 0.31‰) than other groups. The ?¹⁵N values varied significantly between invertebrates (0.64 ± 0.17‰ of insect collector‐gatherers to 1.63 ± 0.36‰ of shrimp predators) and fish (1.98 ± 0.19‰ of detritivores to 2.71 ± 0.43‰ of crustaceavores) and exhibited an increasing tendency from primary to secondary consumers. A linear regression analysis revealed that the longitudinal changes in ?¹³C and ?¹⁵N were closely associated with the δ¹³C of periphyton, the δ¹⁵N of particulate organic matter (POM) in water, and the relative contribution (%) of periphyton and organic detritus to the diet composition of consumers. These results indicated that discrimination factors might not only be influenced by the isotope signatures of basal food sources but also downstream shifts in dominant food items utilized by consumers. In particular, trophic discrimination between periphyton– and detritus–based food chains, such as “epilithic diatoms–shrimp scrapers–crustaceavorous fish” and “POM–bivalves–molluscivorous fish,” displayed regionally specific patterns. When back‐calculating to the diet assimilation and trophic position in subtropical streams and rivers, we suggest using the basin‐scale ?¹³C value of 0.96 ± 0.26‰ for all consumers and ?¹⁵N values of 1.07 ± 0.32‰ for invertebrates and 2.38 ± 0.37‰ for fish.     

Evaluation of single and two‐stage adaptive sampling designs for estimation of density and abundance of freshwater mussels in a large river

Reliable estimates of abundance are needed to assess consequences of proposed habitat restoration and enhancement projects on freshwater mussels in the Upper Mississippi River (UMR). Although there is general guidance on sampling techniques for population assessment of freshwater mussels, the actual performance of sampling designs can depend critically on the population density and spatial distribution at the project site. To evaluate various sampling designs, we simulated sampling of populations, which varied in density and degree of spatial clustering. Because of logistics and costs of large river sampling and spatial clustering of freshwater mussels, we focused on adaptive and non‐adaptive versions of single and two‐stage sampling. The candidate designs performed similarly in terms of precision (CV) and probability of species detection for fixed sample size. Both CV and species detection were determined largely by density, spatial distribution and sample size. However, designs did differ in the rate that occupied quadrats were encountered. Occupied units had a higher probability of selection using adaptive designs than conventional designs. We used two measures of cost: sample size (i.e. number of quadrats) and distance travelled between the quadrats. Adaptive and two‐stage designs tended to reduce distance between sampling units, and thus performed better when distance travelled was considered. Based on the comparisons, we provide general recommendations on the sampling designs for the freshwater mussels in the UMR, and presumably other large rivers. Published in 2009 by John Wiley & Sons, Ltd.     

Reference databases,primer choice,and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Biodiversity monitoring via environmental DNA, particularly metabarcoding, is evolving into a powerful assessment tool for riverine systems. However, for metabarcoding to be fully integrated into standardized monitoring programmes, some current challenges concerning sampling design, laboratory workflow, and data analysis need to be overcome. Here, we review some of these major challenges and potential solutions. We further illustrate three potential pitfalls, namely the choice of suitable metabarcoding primers, the necessity of complete reference databases, and varying assay sensitivities, by a reappraisal of our‐own recently carried out metabarcoding study in the Volga headwaters. TaqMan qPCRs had detected catfish (Silurus glanis) and European eel (Anguilla anguilla), whereas metabarcoding had not, in the same samples. Furthermore, after extending the genetic reference database by 12 additional species and re‐analysing the metabarcoding data, we additionally detected the Siberian spiny loach (Cobitis sibirica) and Ukrainian brook lamprey (Eudontomyzon mariae) and reassigned the operational taxonomic units previously assigned to Misgurnus fossilis to Cobitis sibirica. In silico analysis of metabarcoding primer efficiencies revealed considerable variability among primer pairs and among target species, which could lead to strong primer bias and potential false‐negatives in metabarcoding studies if not properly compensated for. These results highlight some of the pitfalls of eDNA‐metabarcoding as a means of monitoring fish biodiversity in large rivers, which need to be considered in order to fully unleash the full potential of these approaches for freshwater biodiversity monitoring.