Riparian ecotones and spatial variation of fish assemblages in Portuguese lowland streams

The first results of a long-term study on the role of riparian ecotones on the population and community dynamics of Iberian stream fish are presented and discussed. Riparian and macrophyte cover, bank slope and depth were among the most important variables affecting fish distribution. In general small fish favoured shallow areas with high macrophyte cover, whereas large fish dominated in deep areas with a high riparian cover. Slight spatial changes in terrestrial prey use were found suggesting a minor role for this resource during autumn. Finally, no significant spatial differences were found for linear growth, although some differences were obtained for the condition factor.     

Beta diversity of stream fish assemblages: partitioning variation between spatial and environmental factors

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BIODIVERSITY RESEARCH: Native and introduced fish species richness in Mediterranean streams: the role of multiple landscape influences

Aim To examine the role of multiple landscape factors on the species richness patterns of native and introduced freshwater fish. Location Mediterranean streams, south‐western Iberian Peninsula, Europe (c. 87,000 km²). Methods We used a dataset of fish occurrences from 436 stream sites. We quantified the incremental explanatory power of multiple landscape factors in native, introduced, and overall local species richness using regression analysis. First, we related variation in local species richness across river basins to regional species richness (here, the basin species pool), area and factors of climate and topography. Second, we related within‐river basin local species richness to site’s climate and topography, and spatial structure derived from Principal Coordinates of Neighbour Matrices approach, after testing for species richness spatial autocorrelation; predicted local richness was mapped. Results Patterns of local species richness across river basins were strongly associated with regional species richness for overall, native and introduced species; annual rainfall showed a significant incremental contribution to variation in introduced species richness only. Within river basins, environmental factors were associated with local richness for the three species groups, though their contributions to the total explained variation were inferior to those of spatial factors; rainfall seasonality and stream slope were the most consistent environmental correlates for all species groups, while the influence of spatial factors was most prevalent for native species. Main conclusions Landscape factors operating among and within river basins seem to play a relevant role in shaping local species richness of both native and introduced species, and may be contingent on basin‐specific contexts. Nevertheless, local factors, such as habitat characteristics and biotic interactions and human‐induced disturbances may also be at play. Multiscale approaches incorporating a multitude of factors are strongly encouraged to facilitate a deeper understanding of the biodiversity patterns of Mediterranean streams, and to promote more effective conservation and management strategies.     

Contrasted impacts of climate change on stream fish assemblages along an environmental gradient

Aim To investigate the potential impacts of climate change on stream fish assemblages in terms of species and biological trait diversity, composition and similarity. Location One‐thousand one‐hundred and ten stream sections in France. Methods We predicted the future potential distribution of 35 common stream fish species facing changes in temperature and precipitation regime. Seven different species distribution models were applied and a consensus forecast was produced to limit uncertainty between single‐models. The potential impacts of climate change on fish assemblages were assessed using both species and biological trait approaches. We then addressed the spatial distribution of potential impacts along the upstream–downstream gradient. Results Overall, climate change was predicted to result in an increase in species and trait diversity. Species and trait composition of the fish assemblages were also projected to be highly modified. Changes in assemblages’ diversity and composition differed strongly along the upstream–downstream gradient, with upstream and midstream assemblages more modified than downstream assemblages. We also predicted a global increase in species and trait similarity between pairwise assemblages indicating a future species and trait homogenization of fish assemblages. Nevertheless, we found that upstream assemblages would differentiate, whereas midstream and downstream assemblages would homogenize. Our results suggested that colonization could be the main driver of the predicted homogenization, while local extinctions could result in assemblage differentiation. Main conclusions This study demonstrated that climate change could lead to contrasted impacts on fish assemblage structure and diversity depending on the position along the upstream–downstream gradient. These results could have important implications in terms of ecosystem monitoring as they could be useful in establishing areas that would need conservation prioritization.     

Assessing effects of water abstraction on fish assemblages in Mediterranean streams

1. Water abstraction strongly affects streams in arid and semiarid ecosystems, particularly where there is a Mediterranean climate. Excessive abstraction reduces the availability of water for human uses downstream and impairs the capacity of streams to support native biota. 2. We investigated the flow regime and related variables in six river basins of the Iberian Peninsula and show that they have been strongly altered, with declining flows (autoregressive models) and groundwater levels during the 20th century. These streams had lower flows and more frequent droughts than predicted by the official hydrological model used in this region. Three of these rivers were sometimes dry, whereas there were predicted by the model to be permanently flowing. Meanwhile, there has been no decrease in annual precipitation. 3. We also investigated the fish assemblage of a stream in one of these river basins (Tordera) for 6 years and show that sites more affected by water abstraction display significant differences in four fish metrics (catch per unit effort, number of benthic species, number of intolerant species and proportional abundance of intolerant individuals) commonly used to assess the biotic condition of streams. 4. We discuss the utility of these metrics in assessing impacts of water abstraction and point out the need for detailed characterisation of the natural flow regime (and hence drought events) prior to the application of biotic indices in streams severely affected by water abstraction. In particular, in cases of artificially dry streams, it is more appropriate for regulatory agencies to assign index scores that reflect biotic degradation than to assign ‘missing’ scores, as is presently customary in assessments of Iberian streams.     

Habitat structure and invertebrate assemblages on stream stones: A multivariate view from the riffle

Abstract Highly structured habitats, those with complex or heterogeneous physical structure, commonly contain more species than simply structured ones. However, tests of this relationship have been hampered by habitat-specific definitions and measurements of habitat structure and, in stream studies, by insufficient information on spatial variation in faunal abundances. We sampled the fauna of 90 stones collected from an order 4 section of the Taggerty and Steavenson Rivers, southeastern Australia. The spatially nested sampling design encompassed three spatial scales (sites within the same stream order, riffles at the same site and groups of stones within the same riffle) but no temporal replication, as we were only able to sample once. Habitat structure of stones was quantified by measuring the amount and type of epilithon on stones, together with stone shapes, sizes, textures and surface complexities. For the latter two attributes, we used a new method, involving image analysis, which can be used to quantify habitat structure in comparable ways in other systems. Species richness (S) was related to some measures of habitat structure, being higher on stones with a rough texture and weakly related to the amount of epilithon present. Total numbers of individuals (N) were also higher on rough stones, and faunal composition (as quantified by hybrid multidimensional scaling) was related to abundance of epilithon. However, flow environments, as quantified by water velocities and depths, were also related to faunal composition. Riffles varied in both faunal densities and near-bed flow environment, but not in any consistent way. Such variability means that individual riffles cannot be reasonably used to ‘represent’ stream sections or orders, an assumption commonly made in stream studies. Neglect of such issues has also resulted in poor conceptual integration between large- and small-scale studies in stream ecology.     

Climate change hastens the turnover of stream fish assemblages

Stream fish are expected to be significantly influenced by climate change, as they are ectothermic animals whose dispersal is limited within hydrographic networks. Nonetheless, they are also controlled by other physical factors that may prevent them moving to new thermally suitable sites. Using presence–absence records in 655 sites widespread throughout nine French river units, we predicted the potential future distribution of 30 common stream fish species facing temperature warming and change in precipitation regime. We also assessed the potential impacts on fish assemblages' structure and diversity. Only cold-water species, whose diversity is very low in French streams, were predicted to experience a strong reduction in the number of suitable sites. In contrast, most cool-water and warm-water fish species were projected to colonize many newly suitable sites. Considering that cold headwater streams are the most numerous on the Earth's surface, our results suggested that headwater species would undergo a deleterious effect of climate change, whereas downstream species would expand their range by migrating to sites located in intermediate streams or upstream. As a result, local species richness was forecasted to increase greatly and high turnover rates indicated future fundamental changes in assemblages' structure. Changes in assemblage composition were also positively related to the intensity of warming. Overall, these results (1) stressed the importance of accounting for both climatic and topographic factors when assessing the future distribution of riverine fish species and (2) may be viewed as a first estimation of climate change impacts on European freshwater fish assemblages.     

Critical landscape attributes that influence fish population dynamics in headwater streams

Three landscape attributes are likely to have strong effects on the rate-dependent processes determining fish population dynamics in headwater streams: (1) functional interactions at terrestrial-aquatic ecotones and their influence on temporal and spatial variation in resource supply and predator-prey interactions, (2) large-scale spatial habitat relationships and their effect on resource use and fish movement, and (3) presence of refugia from harsh environmental conditions and their influence on fish survival and emigration/immigration rates. Elucidating how these factors interact over a range of temporal and spatial scales should be a major goal of lotic fish ecologists.     

Temporal variability in the spatial and environmental determinants of functional metacommunity organization – stream fish in a human‐modified landscape

1. Quantifying the relative importance of environmental filtering versus regional spatial structuring has become an intensively studied area in the context of metacommunity ecology. However, most studies have evaluated the role of environmental and spatial processes using taxonomic data sets of single snapshot surveys. 2. Here, we examined temporal changes in patterns and possible processes behind the functional metacommunity organization of stream fishes in a human‐modified landscape. Specifically, we (i) studied general changes in the functional composition of fish assemblages among 40 wadeable stream sites during a 3‐year study period in the catchment area of Lake Balaton, Hungary, (ii) quantified the relative importance of spatial and environmental factors as determinants of metacommunity structure and (iii) examined temporal variability in the relative role of spatial and environmental processes for this metacommunity. 3. Partial triadic analysis showed that assemblages could be effectively ordered along a functional gradient from invertebrate consuming species dominated by the opportunistic life‐history strategy, to assemblages with a diverse array of functional attributes. The analysis also revealed that functional fish assemblage structure was moderately stable among the sites between the sampling periods. 4. Despite moderate stability, variance partitioning using redundancy analyses (RDA) showed considerable temporal variability in the contribution of environmental and spatial factors to this pattern. The analyses also showed that environmental variables were, in general, more important than spatial ones in determining metacommunity structure. Of these, natural environmental variables (e.g. altitude, velocity) proved to be more influential than human‐related effects (e.g. pond area, % inhabited area above the site, nutrient enrichment), even in this landscape with relatively low variation in altitude and stream size. 5. Pond area was, however, the most important human stressor variable that was positively associated with the abundance of non‐native species with diverse functional attributes. The temporal variability in the relative importance of environmental and spatial factors was probably shaped by the release of non‐native fish from fish ponds to the stream system during flood events. 6. To conclude, both spatial processes and environmental control shape the functional metacommunity organization of stream fish assemblages in human‐modified landscapes, but their importance can vary in time. We argue, therefore, that metacommunity studies should better consider temporal variability in the ecological mechanisms (e.g. dispersal limitation, species sorting) that determine the dynamics of landscape‐level community organization.     

Assessment of fish communities using environmental DNA: Effect of spatial sampling design in lentic systems of different sizes

Freshwater fish biodiversity is quickly decreasing and requires effective monitoring and conservation. Environmental DNA (eDNA)‐based methods have been shown to be highly sensitive and cost‐efficient for aquatic biodiversity surveys, but few studies have systematically investigated how spatial sampling design affects eDNA‐detected fish communities across lentic systems of different sizes. We compared the spatial patterns of fish diversity determined using eDNA in three lakes of small (SL; 3 ha), medium (ML; 122 ha) and large (LL; 4,343 ha) size using a spatially explicit grid sampling method. A total of 100 water samples (including nine, 17 and 18 shoreline samples and six, 14 and 36 interior samples from SL, ML and LL, respectively) were collected, and fish communities were analysed using eDNA metabarcoding of the mitochondrial 12S region. Together, 30, 35 and 41 fish taxa were detected in samples from SL, ML, and LL, respectively. We observed that eDNA from shoreline samples effectively captured the majority of the fish diversity of entire waterbodies, and pooled samples recovered fewer species than individually processed samples. Significant spatial autocorrelations between fish communities within 250 m and 2 km of each other were detected in ML and LL, respectively. Additionally, the relative sequence abundances of many fish species exhibited spatial distribution patterns that correlated with their typical habitat occupation. Overall, our results support the validity of a shoreline sampling strategy for eDNA‐based fish community surveys in lentic systems but also suggest that a spatially comprehensive sampling design can reveal finer distribution patterns of individual species.     

Temporal dynamics of stream fish assemblages and the role of spatial scale in quantifying change

1. Spatial grain of studies of communities is often based on arbitrary convention. Few studies have examined how spatial scaling of grain size affects estimates of compositional change over time, despite its broad implications.
2. Fish assemblage structure was compared between 1974 and 2014 at 33 sampling locations in the Muddy Boggy River drainage, USA. The two main objectives for this comparison were to quantify change in assemblage structure and to test for a relationship between compositional change and spatial scale. Spatial scale was manipulated by pooling assemblage data into a continuous range of groups, which increased in size from K = 33 pairs (i.e., local scale) to K = 1 pair (i.e., global scale), via clustering algorithm based on pair‐wise fluvial distance.
3. Local assemblages (stream reaches) varied in the degree of assemblage change over time (range = 0.10–0.99 dissimilarity; mean = 0.66). The global assemblage (drainage), however, remained relatively similar. A discontinuity in the relationship between compositional change and spatial scale occurred at K = 15 (mean dissimilarity = 0.56; p = .062), and this grouping is roughly the size of the headwater/tributary drainages (i.e., stream order ≤ 3) in the study system.
4. Spatial scale can impact estimates of biodiversity change over time. These results suggest assemblages are more dynamic at individual stream reaches than at the scale of the entire drainage. The decline in assemblage change at the spatial scale of K = 15 deserves further attention given the marginal significance, despite a small sample size (n = 15). This pattern could suggest regional and meta‐community processes become more important in shaping assemblage dynamics at the scale of headwater drainages, whereas the factors responsible for driving individual stream reach dynamics (e.g., stochasticity) become less important. Defining assemblages at a larger scale will result in different estimates of species persistence. Biodiversity monitoring efforts must take the effect of spatial scaling into consideration.

     

EcoGenetics: An R package for the management and exploratory analysis of spatial data in landscape genetics

The integration of ecology and genetics has become established in recent decades, in hand with the development of new technologies, whose implementation is allowing an improvement of the tools used for data analysis. In a landscape genetics context, integrative management of population information from different sources can make spatial studies involving phenotypic, genotypic and environmental data simpler, more accessible and faster. Tools for exploratory analysis of autocorrelation can help to uncover the spatial genetic structure of populations and generate appropriate hypotheses in searching for possible causes and consequences of their spatial processes. This study presents EcoGenetics, an R package with tools for multisource management and exploratory analysis in landscape genetics.     

Geographic variation in patterns of nestedness among local stream fish assemblages in Virginia

Nestedness of faunal assemblages is a multi-scale phenomenon, potentially influenced by a variety of factors. Prior small-scale studies have found freshwater fish species assemblages to be nested along stream courses as a result of either selective colonization or extinction. However, within-stream gradients in temperature and other factors are correlated with the distributions of many fish species and may also contribute to nestedness. At a regional level, strongly nested patterns would require a consistent set of structuring mechanisms across streams, and correlation among species tolerances of the environmental factors that influence distribution. Thus, nestedness should be negatively associated with the spatial extent of the region analyzed and positively associated with elevational gradients (a correlate of temperature and other environmental factors). We examined these relationships for the freshwater fishes of Virginia. Regions were defined within a spatial hierarchy and included whole river drainages, portions of drainages within physiographic provinces, and smaller subdrainages. In most cases, nestedness was significantly stronger in regions of smaller spatial extent and in regions characterized by greater topographic relief. Analysis of hydrologic variability and patterns of faunal turnover provided no evidence that inter-annual colonization/extinction dynamics contributed to elevational differences in nestedness. These results suggest that, at regional scales, nestedness is influenced by interactions between biotic and abiotic factors, and that the strongest nestedness is likely to occur where a small number of organizational processes predominate, i.e., over small spatial extents and regions exhibiting strong environmental gradients.The Virginia Cooperate Fish and Wildlife Research Unit is jointly sponsored by United States Geological Survey, Virginia Polytechnic Institute and State University, and Virginia Department of Game and Inland Fisheries.     

Associations between fish assemblages and environmental factors for Mediterranean-type rivers during summer

The structure of summer fish assemblages was examined along longitudinal gradients in 31 Mediterranean-type rivers of the middle Guadiana basin (south-west Iberian Peninsula), using data from 157 sites including small streams to deep rivers. An ordination analysis, based on 16 variables, was applied to species presence, using principal component and canonical correspondence analysis. The results for the habitat data were compared with those for the biological data using a Mantel analysis, and the agreement was highly significant. Spatial structure was considered by partitioning the total variability among the environmental and geographical variables. The fish assemblages showed longitudinal zoning during the summer, with species distributed over gradients of habitat size (depth), water quality (current and physico-chemical variables), and cover (substratum and vegetation), according to their adult size and life history. The size of the habitat that remained available in summer had the greatest biological effect, being the most important factor explaining fish species distribution and assemblage structure during this stressing season. Strictly spatial variation was low, but there was still a high residual variation. Habitat associations and life-history strategies are discussed for native and exotic species.     

Concordance among stream assemblages and spatial autocorrelation along a fragmented gradient

Patterns of spatial autocorrelation of biota and distributional similarity (concordance) between assemblages of different organism groups have important implications in both theoretical ecology and biodiversity conservation. Here we report environmental gradients and spatial distribution patterns of taxonomic composition among stream fish, benthic macroinvertebrate, and diatom assemblages along a fragmented stream in south‐western France. We quantified spatial patterns of lotic assemblage structure along this stream, and we tested for concordance in distribution patterns among the three taxonomic groups. Our results showed that both environmental characteristics and stream assemblages were spatially autocorrelated. For stream fish and diatom assemblages, these patterns reflected assemblage changes along the longitudinal stream gradient, whereas environmental variables and benthic macroinvertebrates exhibited a more patchy spatial pattern. Cross‐taxa concordance was significant between stream fish and diatoms, and between stream fish and benthic macroinvertebrates. The assemblage concordance between stream fish and diatoms could be attributed to similar responses along the longitudinal gradient, whereas those between stream fish and benthic macroinvertebrates may result from biotic interactions. Based on potential dispersal capacities of taxa, our results validated the hypotheses that weakly dispersing taxa exhibit greater concordance than highly dispersing ones and that dispersal capacities affect how taxonomic groups respond to their local environment. Both diatoms and highly dispersing stream fish were affected by stream fragmentation (i.e. the number of dams between sites), while the effect of fragmentation was not significant for invertebrates that fly well in their adult stage, thus emphasizing the importance of the way of dispersal. These results suggest that addressing the effects of dispersal capacity on stream assemblage patterns is crucial to identifying mechanisms behind patterns and to better understanding the determinants of stream biodiversity.     

Ecology of a saline stream: community responses to spatial gradients of environmental conditions

Spatial changes in structural and functional characteristics of fish and macroinvertebrate communities in eastern Kentucky were investigated in a drainage system chronically exposed to high levels of chloride salts from nearby oilfield operations. Salinity levels at biological monitoring stations ranged from 0.12–31.3‰. Lotic regions with salinities greater than 10‰ were dominated by larvae of the dipterans Ephydra and Culicoides. In regions with salinities less than 10‰ species richness increased more or less linearly with decreasing levels of chloride salts. Ephemeropterans appeared to be one of the major invertebrate groups least tolerant of elevated NaCl levels and were absent in regions with salinities greater than 2‰ Availability of food resources, such as periphyton and particulate organic matter, did not appear to be grossly altered in disturbed regions, and it is suggested that the observed distribution of macroinvertebrate fauna was largely in response to taxonomic differences in salt tolerance. Fish seemed to be more tolerant of highly saline conditions, and several species were observed in regions experiencing salinities as high as 15‰. Accordingly, assemblages of fish taxa along the salinity gradient may have been influenced by trophic factors, such as spatial limitations in availability of invertebrate prey.     

A probabilistic model characterizing fish assemblages of French rivers: a framework for environmental assessment

1. Management of running waters and assessment of water quality trends require the use of biological methods. Among potential indicators, fish assemblages are of particular interest because of their ability to integrate environmental variability at different spatial scales. 2. The French Water Agencies and the Ministry of the Environment initiated a research programme to develop a fish-based index that would be applicable nation-wide. Such an index should encompass the relative importance of geographic, ecoregional and local factors influencing the distribution of riverine fishes. 3. An effective way of using the information available from fish assemblages to establish such an index is through the use of the 'reference condition approach' which involves testing a fish assemblage exposed to a potential stress against a reference condition that is unexposed to such a stress. 4. Logistic regression procedures were applied, using a fish data set of 650 reference sites fairly evenly distributed across French rivers and defined by some easily measured regional and local characteristics, to elaborate the simplest possible response model that adequately explains the observed patterns of occurrence for each species of a fish assemblage at a given site of any given river. This allows us to predict a 'theoretical' assemblage at a site. 5. The models were validated using a second independent data set of 88 reference sites. Using a third data set of 88 disturbed sites, the observed assemblages were then compared against the reference condition as defined by the 'theoretical' assemblages. The amount of deviation between the expected and observed assemblages within these sites is used as a measure of degradation. 6. This approach could be used as a framework for adapting and calibrating a multimetric index, thereby serving as a practical technical reference for conducting cost-effective biological assessments of lotic systems.     

Spatial autocorrelation patterns of stream invertebrates: exogenous and endogenous factors

Aim To investigate spatial autocorrelation of taxonomic stream invertebrate groups (richness and composition) at a large geographical scale and to analyse the importance of exogenous and endogenous factors. Location The Mediterranean Basin. Methods For exogenous factors, we used large‐scale factors related to climate, geology and river zonation; for endogenous factors, we used the dispersal mode of each taxonomic group. After describing and analysing spatial patterns of genus richness and genus composition of stream invertebrate groups in the Mediterranean Basin, we computed Moran’s I before and after accounting for the exogenous factors and related it to the endogenous factors. Results In relation to genus richness, most of the taxonomic groups did not show significant spatial autocorrelation, suggesting that no main large‐scale exogenous or endogenous factors were important and that local‐scale factors were probably controlling taxonomic richness. In contrast, for genus composition, all taxonomic groups except Odonata had significant spatial autocorrelation before accounting for the environment. After accounting for the environment, most taxonomic groups still had a significant spatial autocorrelation, but it decreased with their increasing dispersal ability (from Crustacea to Coleoptera). Thus, spatial taxonomic composition of groups with the strongest dispersal potential is mainly related to exogenous factors, whereas that of groups with weaker dispersal potential is related to a combination of exogenous and endogenous factors. Main conclusions Our results illustrate the importance of dispersal as an endogenous factor causing spatial autocorrelation and suggest that ignoring endogenous factors can lead to misunderstandings when explaining large‐scale community patterns.