Genetic structure and management of the Neotropical migratory fish Megaleporinus obtusidens on a highly impacted river basin

Habitat fragmentation caused by hydroelectric dams has depleted fish populations worldwide. Restocking actions are usually adopted to recover those populations, but hatchery management protocols rarely guarantee the maintenance of genetic diversity and a balanced contribution among captive breeders each generation. Here, a set of 10 microsatellite markers was used to assess the genetic diversity (average allelic richness A_R?=?10.87 and expected heterozygosity H_E?=?0.742, respectively) and structuring of Megaleporinus obtusidens, a migratory freshwater fish inhabiting over 2500 km of the São Francisco River in Brazil. Three main genetic clusters were identified in this species across the river basin that could be related to the sharply different climatic and hydrologic regimes from the Upper to the Lower course. A significant reduction (> 50%) in genetic diversity was observed in the broodstock when compared to their wild conspecifics, especially in the allelic richness. The information here presented will aid for management of genetic resources of this species in the São Francisco River taking as reference the genetic clusters identified. Furthermore, the results indicated that restocking is not necessary unless signals of population depletion occurs and, if so, hatchery reproductive protocols should rely on artificial fertilization rather than mass spawning.

     

Longitudinal patterns of fish assemblages in a large tropical river in southeastern Brazil: evaluating environmental influences and some concepts in river ecology

This study aimed to evaluate environmental influences on fish distribution and to assess the extent to which concepts in river ecology accommodate levels of spatio-temporal heterogeneity of fish assemblages in a 1,080-km long tropical river. A total of 25 sites were sampled between November 2002 and March 2003 in two seasons (summer/wet versus winter/dry). A thermal gradient separating the upper reaches from the lower reaches was detected. The middle-upper reaches showed higher conductivity and lower dissolved oxygen and pH levels compared with the other reaches. Although some significant associations were found between some fish abundance and environmental variables, the most abundant species (Tilapia rendalli, Geophagus brasiliensis, and Oligosarcus hepsetus) occurred in most sites and under most environmental conditions. Fish community structure varied more in space (longitudinal) than through time (seasonal). The community in the lower reach species was more diverse in comparison with the other reaches. Differences in the fish assemblage structure among the longitudinal river sections appear to have been influenced by the effects of damming, and seem to be partially consistent with the Serial Discontinuity Concept, which views dams as discontinuities within the river continuum. Only the lower river reach showed seasonal differences in the fish community structure, attributable to the influence of flooding. Management plans and biodiversity conservation will benefit by considering the effects of dam disruption and flood increased connectivity to the lotic systems. Handling editor: J. Trexler     

Factors influencing fish distribution and community structure in a small coastal river in southwestern Costa Rica

We evaluated the relative importance of habitat size and diversity and distance from the ocean in explaining longitudinal patterns of fish distribution and community structure (species richness, evenness, and diversity) in the lower 5 km of the Rio Claro. The Rio Claro is a small coastal river in Corcovado National Park, southwestern Costa Rica, with a depauperate freshwater fish fauna. We observed 22 species in pools, 19 of which occured during quantitative sampling. Most of these species probably spent part of their lives in the Pacific Ocean. We observed no species in riffles, although these habitats were common and several taxa (e.g., Gobiesocidae, Gobiidae) were adapted for life in fast turbulent water. Fish abundance, and species richness, evenness, and diversity were highest near the ocean, where high tides influenced river levels and salinity. Eight species were not observed further than 2900 m from the ocean, whereas 6 species were not encountered in samples nearest the ocean; the remaining 8 species were present throughout the study area. Distance from the ocean was a better predictor of fish abundance and community structure than were pool width, pool depth, pool surface area, pool volume, amount of cover present, substrate diversity, or depth diversity. Based in qualitative comparisons of our data with previously published data from 1980–1986, the fish assemblage of the Rio Claro is persistent in both species composition and relative abundance.     

Geomorphology and fish assemblages in a Piedmont river basin, U.S.A.

1. We investigated linkages between fishes and fluvial geomorphology in 31 wadeable streams in the Etowah River basin in northern Georgia, U.S.A. Streams were stratified into three catchment sizes of approximately 15, 50 and 100 km², and fishes and geomorphology were sampled at the reach scale (i.e. 20–40 times stream width). 2. Non‐metric multidimensional scaling (NMDS) identified 85% of the among‐site variation in fish assemblage structure and identified strong patterns in species composition across sites. Assemblages shifted from domination by centrarchids, and other pool species that spawn in fine sediments and have generalised food preferences, to darter‐cyprinid‐redhorse sucker complexes that inhabit riffles and runs, feed primarily on invertebrates, and spawn on coarser stream beds. 3. Richness and density were correlated with basin area, a measure of stream size, but species composition was best predicted (i.e. |r| between 0.60–0.82) by reach‐level geomorphic variables (stream slope, bed texture, bed mobility and tractive force) that were unrelated to stream size. Stream slope was the dominant factor controlling stream habitat. Low slope streams had smaller bed particles, more fines in riffles, lower tractive force and greater bed mobility compared with high slope streams. 4. Our results contrast with the ‘River Continuum Concept’ which argues that stream assemblages vary predictably along stream size gradients. Our findings support the ‘Process Domains Concept’, which argues that local‐scale geomorphic processes determine the stream habitat and disturbance regimes that influence stream communities.     

Spatio-temporal patterns of fish assemblages in a large regulated alluvial river

1. The River Durance, the last alpine tributary of the River Rhône, is a large, braided alluvial hydrosystem. Following large-scale regulation, flow downstream of the Serre-Ponçon dam has been maintained at 1/40th of previous annual mean discharge. To assess the effects of historical disturbances, fish assemblages and habitat use were analysed during five summers in a representative reach of the middle Durance.
2. Habitat availability and use were assessed with a multi-scale approach including the variables water depth, current velocity, roughness height of substratum, amount of woody debris and lateral/longitudinal location. Eighteen fish species were sampled by electrofishing in 289 habitat sample units.
3. Partial least square (PLS) regression showed that taxa were mainly distributed according to relationships between their total length and water depth/velocity variables. Fish assemblage composition was also related to roughness height as well as distance from the bank or to the nearest large woody debris. However, PLS regression revealed no significant differences in habitat selection between two periods of varying hydromorphological stability.
4. Fish distribution patterns and density were related to proximity to the bank and cover, indicating that local scale variables need to be considered in conservation and restoration programmes.     

The longitudinal distribution and community dynamics of zooplankton in a regulated large river: a case study of the Nakdong River (Korea)

The longitudinal distribution and seasonal dynamics of zooplankton were examined along a 200-km section of the middle to lower Nakdong River, Korea. Zooplankton was sampled twice a month from January 1995 to December 1997 at five sites in the main river channel. There was considerable longitudinal variation in total zooplankton abundance (ANOVA, p < 0.001). All major zooplankton groups (rotifers, cladocerans, copepodids and nauplii) increased significantly with distance downstream along the river. There also were statistically significant seasonal differences in zooplankton abundance at the sampling sites (ANOVA, p < 0.01). Zooplankton abundance was high in spring and fall and low in summer and winter. The seasonal pattern of rotifers was similar to that of total zooplankton. This reflected the fact that rotifers (Brachionus calyciflorus, B. rubens, Keratella cochlearis and Polyarthra spp.) strongly dominated the zooplankton community at all locations. Among the macrozooplankton, small-bodied cladocerans (e.g. Bosmina spp.) dominated; the abundance of large-bodied cladocerans (e.g. Daphnia) was negligible (0–5 ind. l^–1). Among the environmental variables considered, partial residence time seemed to play the most important role in determining characteristics of the river zooplankton community.     

Inverse sampling of controls in a matched case control study

A method of inverse sampling of controls in a matched case-control study is described in which, for each case, controls are sampled until a discordant set is achieved. For a binary exposure, inverse sampling is used to determine the number of controls for each case. When most individuals in a population have the same exposure, standard case-control sampling may result in many case-control sets being concordant with respect to exposure and thus uninformative in the conditional logistic analysis. The method using inverse control sampling is proposed as a solution to this problem in situations when it is practically feasible. In many circumstances, inverse control sampling is found to offer improved statistical efficiency relative to a comparable study with a fixed number of controls per case.     

Diel distribution patterns of fishes in a temperate large lowland river

During the day, juveniles and typical inshore species in the lower Oder River, Germany, inhabited the littoral (0·05–1·50 m deep) while potamal species inhabited the mid‐channel (40–100 m from the banks). During the night, two behavioural groups were distinguished: 1) potamal species and large individuals of other species, moved from offshore to the littoral, and 2) nocturnal foraging species, became active and increased in inshore and offshore habitats. Inshore, the most significant differences at night was the increasing density of silver bream Blicca bjoerkna increasing both total biomass and total length of fishes caught. Offshore, the increasing density of whitefin gudgeon Gobio albipinnatus at night was most significant. Additional night electrofishing improved the assessment of the abundance, age and size structure of typical potamal fish species. It should be incorporated in large river fish monitoring programmes.     

Ecological impact of introduced fish in high altitude lakes: a case of study from the European Alps

Fish introduction is a major threat to alpine lake biota leading to the loss of native species and to the degeneration of natural food-webs. This study provides an extensive investigation on the impact of the introduced fish Salvelinus fontinalis on the native communities of alpine lakes in the Gran Paradiso National Park. We compared the macroinvertebrate and zooplankton communities of six stocked and nine fishless lakes with a repeated sampling approach during the summers 2006–2009. The impact of fish presence on alpine lake fauna is often mediated by the strong seasonality governing these ecosystems, and it dramatically affects the faunal assemblage of littoral macroinvertebrates and the size, structure, and composition of the pelagic zooplankton community with a strong selective predation of the more visible taxa. Direct ecological impacts include a decrease or extinction of non-burrower macroinvertebrates and of large zooplankton species, while small zooplankton species and burrower macroinvertebrates were indirectly advantaged by fish presence. Due to the existence of a compensation between rotifers and crustaceans, fish presence does not affect total zooplankton biomass and diversity even if fish are a factor of ecological exclusion for large crustaceans. These compensatory mechanisms are a key process surrounding the impact of introduced fish in alpine lakes.     

Habitat structural complexity and morphological diversity of fish assemblages in a Neotropical floodplain river

High species richness and evenness in structurally complex habitats has been hypothesized to be associated with niche partitioning. To test this idea, relationships between habitat structural complexity in river littoral-zone habitats and morphological diversity of tropical fishes were examined in the Cinaruco River, Venezuela. Six habitat attributes were quantified in 45 sites spanning a range of structural complexity. Fishes were collected during day and night to estimate species density and relative abundances at each site. Twenty-two morphological variables were measured for each species. Principal components analysis (PCA) of physical habitat data yielded two axes that modeled >80% of variation across sites. The first two axes from PCA of fish morphological variables modeled >70% of variation. Species density during both day and night was negatively associated with flow velocity and positively associated with habitat complexity. Similarity of day and night samples from the same site was significantly greater for sites with high habitat complexity and low flow. In general, mean local assemblage morphological PC scores were not significantly associated with habitat PC scores. Average, maximum, and standard deviation of morphological Euclidean distances of local assemblages revealed positive associations with structural complexity and negative associations with flow. These relationships held even when the positive relationship of species density was statistically removed from assemblage morphological patterns. Findings suggest that both species niche compression and assemblage niche space increase when habitat complexity is greater and flow velocity is lower in this tropical lowland river.Electronic Supplementary Material Supplementary material is available for this article at     

A comparison of modeling techniques to predict juvenile 0+ fish species occurrences in a large river system

Even if European river management and restoration are largely supported by the use of reliable tools, these tools are most often “generalist” and provide only initial leads of alteration sources. Acknowledging that young-of-the-year (YOY) fish assemblages are highly dependent on riverine habitat conditions, the development of a YOY-based tool might be very useful or even essential in the design and implementation of conservation or restoration plan of large rivers, in measuring more straight-forward the losses and gains of hydro-ecological functionalities. In the past 20 years, new modeling techniques have emerged from a growing sophistication of statistical model applied to ecology. “Machine learning methods” (ML) are now recognized as holding great promise for the advancement of understanding and prediction of ecological phenomena. The aim of this work was to select the appropriate statistical technique to model YOY assemblages according to different meso-scale habitat variables that are meaningful to planners. To do this, two “Machine Learning” methods, Classification and Regression Trees (CART) and Boosted Regression Trees (BRT), were compared to Generalized Linear Models (GLM). We modeled the occurrence of 9 species from the Seine River basin (France) in order to compare models abilities to accurately predict the presence and absence of each species. BRT appeared to be the best technique for modeling 0+ fish occurrences in our dataset.     

Spatial variation in composition and richness of fish communities in a southwestern Australian river system

Thirteen species of fish were recorded from the non-tidal reaches of the Murray River system, southwestern Australia. Of these, nine were indigenous species. Although this system occurs in a zone of moderate to high rainfall, the species richness of this system is comparable to that of much harsher environments, such as the Canadian boreal zone or the Nevada desert. Species richness tends to increase in a downstream direction, and most changes in species composition are due to addition, rather than replacement of species. Stream order was strongly and significantly positively correlated with species richness (P < 0.001), but was in effect functioning as a composite variable. Stepwise multiple regression analysis showed that stream width, pH range, distance from the main stream, distance from the estuary, barriers and stream gradient together explained more than 80% of the variation in species richness. The variables, barriers, distance from the main stream and distance from the estuary, support island biogeography type explanations for variations in species richness, while the variable, stream width complies with the river continuum concept. A predictive model for species richness of any given reach of a lower west coastal stream in Australia was tried using variables that can be gathered almost entirely from detailed topographic maps and aerial photographs.     

Monitoring fish passes using infrared beaming: a case study in an Iberian river

An application of a new automated fish counting device – the Riverwatcher System (RW) – was used to monitor upstream fish movements in a pool‐and‐weir fish pass in the River Zêzere, Portugal, for 141 days from June 2002 to May 2003. Fish populations were also collected downstream using multimesh gillnets (5 different mesh sizes ranging from 30 mm to 85 mm knot to knot; ratio between mesh sizes of about 1.30) and electrofishing for comparison with fish records produced by the RW. More than 3000 individual Iberian nase Chondrostoma polylepis ascended the fish pass and moved through the RW during the study period. However, only 18% of the records produced by the RW contained silhouettes similar to fish; no individual smaller than 15 cm TL was recorded by the counter. Most seasonal movements (73.9%) occurred in spring and were associated with reproduction. Displacements seemed to occur independently of time of day. Water temperature (range: 12–22°C) was the only significant environmental variable (P < 0.01) influencing upstream movements of this species. Further development of hardware and software will be necessary to improve performance of the counter, particularly in Mediterranean rivers, where more turbid waters and a greater proportion of small‐size species are present.     

Metacommunity of a host metapopulation: explaining patterns and structures of a fish parasite metacommunity in a Neotropical floodplain basin

Host-parasite metacommunities are influenced by a myriad of factors, although little is known about which processes affect this relationship at different scales. Here, we tested how local habitat characteristics and host traits explained the parasite metacommunity of a migratory fish in a large Brazilian river floodplain. The parasite metacommunity structure showed a Clementsian pattern, which indicates a more deterministic assembly pattern, in accordance with partial Redundancy Analysis results. Results indicated that species filtering is the predominant mechanism driving community assembly. Patterns were clearer in the dry season of the floodplain. Environmental determinism seems to explain ectoparasite metacommunities in the dry season, in contrast with endoparasites that were more correlated to host traits. Overall, our results indicated that ectoparasitism is an interaction marked by opportunity, whereas endoparasitism is likely related to host features. Thus, we argue that metacommunity structuring of parasites depends on the infection strategy. Our results show that floodplain dynamics are central not only for free-living animal organizations but also for symbiotic interactions. Here, we highlight the importance of understanding the factors influencing the distribution of parasites to predict their transmission, as well as the importance of floodplain dynamics and its hydrological regime on the maintenance of ecological interactions.

     

Non-additive and non-stationary properties in the spatial distribution of a large marine fish population

Density-independent and density-dependent variables both affect the spatial distributions of species. However, their effects are often separately addressed using different analytical techniques. We apply a spatially explicit regression framework that incorporates localized, interactive and threshold effects of both density-independent (water temperature) and density-dependent (population abundance) variables, to study the spatial distribution of a well-monitored flatfish population in the eastern Bering Sea. Results indicate that when population biomass was beyond a threshold a further increase in biomass-promoted habitat expansion in a non-additive fashion with water temperature. In contrast, during years of low population size, habitat occupancy was affected positively only by water temperature. These results reveal the spatial signature of intraspecific abundance distribution relationships as well as the non-additive and non-stationary responses of species spatial dynamics. Furthermore, these results underscore the importance of implementing analytical techniques that can simultaneously account for density-dependent and density-independent sources of variability when studying geographical distribution patterns.     

An analysis of the distribution of fish species in a large prairie lake

The distribution of fishes in Dauphin Lake, a large, shallow, turbid, prairie lake in west-central Manitoba, was examined using gillnets. Catch per unit effort was used to assess differences in distribution thai may be attributed lo year, season, lake zone (inshore, offshore), substratum, water depth, water temperature, turbidity and presence of other fish species. Although 13 species were caught, only the distributions of the six most abundant was analysed. Variation in number of species caught was attributed mainly to lake zone, water depth and water temperature. White sucker (Catastomus commersoni) distribution can be explained by zone and temperature. Shorthead redhorse (Moxostoma macrolepidotum) catches were related to depth and temperature. Cisco (Coregonus artedii) catches varied with year, zone and temperature. Variances in northern pike (Esox Indus) distribution reflected year and zone. Walleye (Stizostedkm vitreum) varied with year, depth and temperature and differences in the catches of yellow perch (Pertaflurescens) were attributed to year, depth, temperature and turbidity. They were also positively correlated to the numbers of northern pike caught.     

Geographical distribution and habitat occurrence of the Water Shrew (Neomys fodiens) in the Weald of South-East England

A survey of 96 sites in a range of riparian habitats in the catchments of five rivers during June–August 1998 used the bait tube method to investigate the geographical distribution and habitat occurrence of Water Shrews (Neomys fodiens) in the Weald of South‐East England. Water Shrews were found at 42% of sites, and were widely distributed in all river catchments except the Mole. They occurred in many riparian habitats, including rivers, streams, canals and ditches, with a range of physical and biotic characteristics. There were no signs of habitat avoidance in response to human disturbance but Water Shrews were absent from the river catchment with lowest water quality. Logistic regression analysis was used to model the effect of habitat variables on the presence of Water Shrews, with current speed, water depth, bank incline and bank‐side vegetation identified as important variables. Fast‐flowing shallow waters had a significant positive effect on their presence, whereas scarce herbaceous vegetation and a bank of low incline had a significant negative effect. These habitat variables appear to be reliable indicators of the probability of finding Water Shrews at a particular site, and have implications for habitat management and conservation.     

Spatio-temporal distribution patterns and conservation of fish assemblages in a Chilean coastal river

River environments are characterized by extreme spatial and temporal variation in the physical environment. The relationship of fish assemblages to environmental variation is poorly understood in many systems. In Chile zonation patterns of fish assemblages have been documented in several Andean river drainages. Coastal river drainages are comparatively small, but inordinately important because of their highly endemic flora and fauna and their proximity to major human populations. For conservation purposes it is important to understand what environmental factors affect assemblage structure of fishes especially in the comparatively high diversity coastal drainages. We studied patterns of fish distribution and abundance in three rivers of the coastal, Andalien drainage near Concepción, Chile. We used multi-dimensional scaling analyses to compare patterns among zones (rithron, transition and potamon) and high and low flow seasons. Species assemblages differed by zone, but not with season. Assemblages consisted of nested subsets of species characterized by their range of distribution among zones. One species group was composed of widespread species that occurred in all three zones, another species group consisted of species found only in transitional and potamal zones, and a final group was comprised of species found only in the potamal zone. The potamal zone contained the most diverse and abundant fish assemblage. Fish assemblages were related to both water quality and habitat structure variables. This study suggests that the key to conserving the diversity of native fish communities in coastal Chilean rivers is in the conservation of potamal regions. Unfortunately, most protected areas in Chile are in the depauperate headwaters of drainages. Protection of only headwaters is clearly inadequate and will not contribute to the conservation of this unique freshwater fish fauna.