Young-of-the-year fish assemblages as indicators of anthropogenic disturbances in large tributaries of the Seine River Basin (France)

A variety of indices targeting a number of different biological assemblages have been developed to assess aquatic ecosystem condition, identify the drivers of alteration and provide information on possible restoration measures. Fish-based indices, commonly focused on adult assemblages, are capable of indicating declines in condition, but often provide limited information on the ultimate causes for the observed changes. Using young-of-the-year (YOY) fish assemblages has been suggested as a means of improving the sensitivity of fish-based indicators. To verify this assumption, we first model, using boosted regression trees, the occurrence of 16 YOY fish species as a function of twenty two environmental factors in 227 reference (i.e., least disturbed) habitats located in the river Seine (France) and its two main tributaries (i.e., Oise and Marne rivers). We then validate the species models using an independent dataset of 74 reference habitats. Finally, using three independent data sets reflecting different categories of disturbances (i.e., physico-chemical disturbances, physical disturbances induced by navigation and a mix of both disturbances), we measure the deviation between expected and observed species occurrences to evaluate our species models ability in detecting these disturbances. The models are ecologically meaningful and overall perform well in discriminating between reference and disturbed habitats, showing a stable response for all unimpaired habitats and highlighting the main habitat disturbances tested.     

Multi-scale approach for predicting fish species distributions across coral reef seascapes

Two of the major limitations to effective management of coral reef ecosystems are a lack of information on the spatial distribution of marine species and a paucity of data on the interacting environmental variables that drive distributional patterns. Advances in marine remote sensing, together with the novel integration of landscape ecology and advanced niche modelling techniques provide an unprecedented opportunity to reliably model and map marine species distributions across many kilometres of coral reef ecosystems. We developed a multi-scale approach using three-dimensional seafloor morphology and across-shelf location to predict spatial distributions for five common Caribbean fish species. Seascape topography was quantified from high resolution bathymetry at five spatial scales (5–300 m radii) surrounding fish survey sites. Model performance and map accuracy was assessed for two high performing machine-learning algorithms: Boosted Regression Trees (BRT) and Maximum Entropy Species Distribution Modelling (MaxEnt). The three most important predictors were geographical location across the shelf, followed by a measure of topographic complexity. Predictor contribution differed among species, yet rarely changed across spatial scales. BRT provided ‘outstanding’ model predictions (AUC = >0.9) for three of five fish species. MaxEnt provided ‘outstanding’ model predictions for two of five species, with the remaining three models considered ‘excellent’ (AUC = 0.8–0.9). In contrast, MaxEnt spatial predictions were markedly more accurate (92% map accuracy) than BRT (68% map accuracy). We demonstrate that reliable spatial predictions for a range of key fish species can be achieved by modelling the interaction between the geographical location across the shelf and the topographic heterogeneity of seafloor structure. This multi-scale, analytic approach is an important new cost-effective tool to accurately delineate essential fish habitat and support conservation prioritization in marine protected area design, zoning in marine spatial planning, and ecosystem-based fisheries management.     

美国大陆外来入侵物种斑马纹贻贝(Dreissena polymorpha)潜在生境预测模型

防止外来生物入侵造成危害的重要手段是阻止可能造成入侵的物种进入适合其生存的地区.论文以1864个美国外来入侵物种斑马纹贻贝定点发生数据和开放式基础地理信息数据库Daymet的34个环境变量为主要信息源,采用逻辑斯蒂回归(LR)、分类与回归树模型(CART)、基于规则的遗传算法(GARP)、最大熵法(Maxent)4种途径,建立美国大陆部分潜在生境预测模型,从接受者运行特征曲线下面积(AUC)、Pearson相关系数、Kappa值3个方面来检验模型预测精度,在此基础上分析斑马纹贻贝的空间分布规律及其环境影响因素.研究结果表明:在3个评价指标中,4个生态位模型预测精度均达到优良水平,其中Maxent在物种现实生境模拟、主要生态环境因子筛选、环境因子对物种生境影响的定量描述方面都表现出了优越的性能;距水源距离、海拔高度、降水频率、太阳辐射是影响物种空间分布的主要环境因子.论文提出的研究方法对中国外来入侵物种生境预测具有较强的借鉴意义,研究结果对中国海洋外来入侵物种沙筛贝的预测与防治,具有一定的指导作用.     

Eelgrass,Zostera marina,as essential fish habitat for young‐of‐the‐year winter flounder,Pseudopleuronectes americanus (Walbaum, 1792) in Maine estuaries

Distribution and density by habitat for age‐0, young‐of‐the‐year (YOY) winter flounder, Pseudopleuronectes americanus (Walbaum, 1792), were compared for two Maine estuaries to help define essential fish habitat for this life history stage. Two estuaries (Weskeag River and Penobscot Bay) along Mid‐coast Maine were sampled monthly with daytime 1.0 m² fixed‐frame throw traps around neap low tide, May–December over two consecutive years (2003–2004). Both eelgrass and adjacent sand/mud (20–60 cm deep) were randomly sampled with equal effort (4–12 samples per month) at two sites in both the Weskeag River and Penobscot Bay. Significantly higher densities of YOY winter flounder (2–9 cm TL) occurred in eelgrass relative to sand/mud. Density increased significantly in both habitats in 2004, and was higher in Penobscot Bay relative to the Weskeag River. YOY densities compared by eelgrass coverage within throw traps were found to be significantly higher in eelgrass that exceeded 30% coverage when compared with adjacent sand/mud areas and eelgrass coverage of 10–20%. YOY occurred in all months sampled (May–December); no density differences existed by month. These results indicate that very shallow (<0.6 m) eelgrass habitat is of key importance to YOY winter flounder in Maine estuaries and should be viewed as essential fish habitat (EFH) for this species and life stage.     

Young‐of‐the‐year (YOY) assemblage sampling as a tool for assessing the ecological quality of running waters

The aim of this study was to test young‐of‐the‐year (YOY) assemblage applicability for the ecological quality assessment on the basis of samples from 55 sites scattered across the entire Czech Republic. European Fish Index (EFI) values estimated with YOY and adults were positively correlated, indicating that YOY and adult sampling is comparable. YOY bias the EFI toward significantly lower values, however, adults also lead to underestimated EFI values on some occasions. Relative differences between EFI YOY and EFI adults show almost normal distributions and indicate that there is no detectable systematic bias caused by environmental conditions or intensity of sampling. As shown in the Elbe River example, the reason for lower EFI YOY values could be found in a longer period of detection of evident changes in adult fish assemblages, reflecting longevity of adult fishes or regular stocking. YOY sampling was suggested as a useful method for assessing river ecological quality, with the ability to provide a sensitive response to the habitat structure regardless of the effect of stocking or river size.     

Cost of predation avoidance in young-of-year lake trout (Salvelinus namaycush): growth differential in sub-optimal habitats

Selection of habitat to avoid predation may affect the diet of young-of-year (YOY) lake trout (Salvelinus namaycush). YOY lake trout may use inshore habitat to avoid predation; this habitat may be sub-optimal for growth. To test this, YOY lake trout were penned in nearshore and offshore pelagic areas of two arctic lakes. Toolik Lake had a lake trout population, the other lake, S6, did not. YOY lake trout in Toolik Lake lost weight, but those offshore lost less weight. The YOY lake trout in Lake S6 gained weight and those offshore gained more weight. The primary diet item of the YOY lake trout in both lakes during this experiment was the zooplankter Diaptomis probilofensis; it was also one of the most abundant species. However, its density inshore in Lake S6 was similar to inshore and offshore densities in Toolik Lake. The increased availability of alternative zooplankton prey in Lake S6 may account for the growth differential of YOY lake trout in Lake S6 relative to Toolik Lake. Bioenergetic modeling of YOY lake trout suggests that growth similar to that in the offshore of Lake S6 would be necessary for successful recruitment. If the reduced zooplankton availability in Toolik Lake leads to the reduced growth of YOY in the inshore and offshore pelagic areas, then these fish will be more susceptable to winter predation/starvation. For YOY lake trout to survive in Toolik Lake they most likely shift to feeding on benthic prey before the end of their first summer. Dept. of Chemical Engineering     

No effect of round goby <Emphasis Type="Italic">Neogobius melanostomus</Emphasis> colonisation on young-of-the-year fish density or microhabitat use

The round goby Neogobius melanostomus has recently invaded several major freshwater systems in Europe and North America. Despite numerous studies predicting an impact on native fish assemblages, few have attempted to demonstrate it. In this case study, we monitored the effect of N. melanostomus colonisation on abundance and habitat utilisation of both young-of-the-year (YOY) native fish and YOY western tubenose goby Proterorhinus semilunaris in a typical, medium-sized European river. Colonisation by N. melanostomus had no apparent effect on either native fish abundance and species richness or P. semilunaris abundance. Moreover, after colonisation, both native fish and P. semilunaris occupied similar niches (i.e. microhabitats) to those occupied before colonisation. While niche use of YOY N. melanostomus and P. semilunaris overlapped significantly, YOY native fish utilised different habitats from the gobiids. We suggest that N. melanostomus did not compete for resources with YOY fish in our study area due to lack of niche overlap and/or surplus resources. As N. melanostomus rapidly dominated the fish assemblage at our site, we further suggest that utilisation of an empty niche, rather than competitive superiority, was the main factor facilitating its success.     

The Impact of Climate Change on the Potential Distribution of Agricultural Pests: The Case of the Coffee White Stem Borer (Monochamus leuconotus P.) in Zimbabwe

The production of agricultural commodities faces increased risk of pests, diseases and other stresses due to climate change and variability. This study assesses the potential distribution of agricultural pests under projected climatic scenarios using evidence from the African coffee white stem borer (CWB), Monochamus leuconotus (Pascoe) (Coleoptera: Cerambycidae), an important pest of coffee in Zimbabwe. A species distribution modeling approach utilising Boosted Regression Trees (BRT) and Generalized Linear Models (GLM) was applied on current and projected climate data obtained from the WorldClim database and occurrence data (presence and absence) collected through on-farm biological surveys in Chipinge, Chimanimani, Mutare and Mutasa districts in Zimbabwe. Results from both the BRT and GLM indicate that precipitation-related variables are more important in determining species range for the CWB than temperature related variables. The CWB has extensive potential habitats in all coffee areas with Mutasa district having the largest model average area suitable for CWB under current and projected climatic conditions. Habitat ranges for CWB will increase under future climate scenarios for Chipinge, Chimanimani and Mutare districts while it will decrease in Mutasa district. The highest percentage change in area suitable for the CWB was for Chimanimani district with a model average of 49.1% (3 906 ha) increase in CWB range by 2080. The BRT and GLM predictions gave similar predicted ranges for Chipinge, Chimanimani and Mutasa districts compared to the high variation in current and projected habitat area for CWB in Mutare district. The study concludes that suitable area for CWB will increase significantly in Zimbabwe due to climate change and there is need to develop adaptation mechanisms.     

Prediction of marine species distribution from presence–absence acoustic data: comparing the fitting efficiency and the predictive capacity of conventional and novel distribution models

The accurate representation of species distribution derived from sampled data is essential for management purposes and to underpin population modelling. Additionally, the prediction of species distribution for an expanded area, beyond the sampling area can reduce sampling costs. Here, several well-established and recently developed habitat modelling techniques are investigated in order to identify the most suitable approach to use with presence–absence acoustic data. The fitting efficiency of the modelling techniques are initially tested on the training dataset while their predictive capacity is evaluated using a verification set. For the comparison among models, Receiver Operating Characteristics (ROC), Kappa statistics, correlation and confusion matrices are used. Boosted Regression Trees (BRT) and Associative Neural Networks (ASNN), which are both within the machine learning category, outperformed the other modelling approaches tested.     

Effect of water temperature on activity of wintering age‐0 Acipenser transmontanus and A. brevirostrum: An artificial stream study

The effect of water temperature on behaviour and life history of wintering age‐0 = young‐of‐the‐year (YOY) northern sturgeons (populations using winter refuge habitat) is poorly understood. Using artificial stream tanks, we observed the effect of water temperature on 1) day‐time activity of cultured YOY Kootenai River white sturgeon, Acipenser transmontanus, during two winters (2008 and 2009–2010), and 2) observed day‐time activity of cultured YOY Connecticut River shortnose sturgeon, A. brevirostrum, in the winter, 2009–2010. Activity of YOY was measured every 2 to 7 days by visual or video observations on each fish to determine the mean number of 10 cm² square gridlines on the tank bottom crossed by all fish in each replicate tank (two replicate tanks, 10 fish in each tank). Daily water temperature was recorded by a logger in one tank every 20 min, 24 hr per day. In 2008, YOY A. transmontanus activity was positively related to decreasing mean daily temperature (R² = 0.96, p < 0.01) with 0 to 5 gridlines (range) crossed by all fish during observation periods at the coldest temperature (≤3°C). During the winter of 2009–2010, activity of both species was significantly related to decreasing temperature, and again, a mean of 0 to 5 gridlines (range) were crossed by fish at ≤3°C. We accept the hypothesis that YOY of both species are mostly inactive in the day when winter water temperature decreases to ≤3°C. Using the daytime inactivity temperature threshold of 3°C for YOY, and recent temperatures in river reaches where wild wintering YOY likely occur, we predict (a) wild wintering YOY A. transmontanus are moderately active in the day, may be energy challenged due to elevated temperatures from the warm river discharge by Libby Dam, and have poor survival in the regulated Kootenay River, and (b) wintering YOY Connecticut River A. brevirostrum are moderately active most winter months due to elevated natural river temperatures and may be energy challenged. More research is needed on YOY wintering activity and energetics relative to temperature to insure management of river temperature includes conservation of sturgeons.     

The habitat diversity and fish reproductive function of floodplain ecosystems

Synopsis Fish reproduction in floodplain ecosystems, based on relative abundance and total biomass of 0+ juveniles, was studied using the synchronic approach to typological analysis in conjunction with Point Abundance Sampling by modified electrofishing. In 3 different flood plains of the Upper Rhône River, 1015 point samples yielding 4573 juveniles (0+) from 21 species were collected from 48 ecosystems of various geomorphological origin. The results demonstrate the lotic-to-lentic succession of floodplain ecosystems to be a series of non-sequential reproductive zones, with spawning conditions being reflected by the specific composition and guild structure of the YOY fish assemblages. The habitat diversity and the fish reproductive potential of floodplain ecosystems are strongly influenced by geomorphological origin and by past and present hydrological conditions. The YOY assemblages of autogenically driven ecosystems (usually of anastomose or meander origin) tend to differ both in composition and in quantity from those found in allogenically driven ecosystems (generally of braided origin). Ecosystems of intermediate character, and fish reproduction thereof, occur as the result of either ecosystem rejuvenation or senescence: autogenically driven ecosystems by allogenic mechanisms, or allogenically driven ecosystems by anthropic and/or autogenic mechanisms, respectively. Because of co-occurrence of ecosystems at similar and at different successional status, the flood plain as an entity is seen as stable with respect to fish reproduction.     

Effects of vessel-induced waves on the YOY-fish assemblage at two different habitat types in the main stem of a large river (Danube,Austria)

The effects of navigation on young-of-the-year (YOY) fish were investigated for the Danube River based on an integrative approach. During YOY growing season, wave height, wave frequency and water currents were recorded. Synchronously, fish drift and fish abundance of YOY were monitored in two distinct inshore nursery habitats—a gravel bar and a groyne field. The characteristics of vessel-induced waves were correlated to YOY-drift. In both habitats, an increase in drift densities during ship passages was observed. At the same time, assemblage composition and drift densities differed between habitat types. At the gravel bar, drift densities of larval cyprinids—representing many keystone species of the Danube—were higher during ship passages. In the groyne field, drift was low and percids dominated the YOY-assemblage along the shore. Banks with gentle slopes in the main channel seem to be particularly affected by vessel-induced wave wash. Precisely such habitats are often established within the scope of modern river restoration projects because they provide suitable nursery habitats for riverine fish species. Beside the positive effects on biota, the establishment of these habitats in navigable reaches may create problems for YOY-fish due to displacement effects induced by ship-generated waves.     

Thermal habitat use and growth in young-of-the-year Arctic charr from proximal fluvial and lacustrine populations in Labrador,Canada

Predicted increases in temperature associated with climate change are expected to have consequences for fish, in particular for Arctic charr, Salvelinus alpinus, a cold-adapted fish species. Despite differences in predicted hydroecological responses to climate change in fluvial and lacustrine environments, little is known of whether fluvial and lacustrine Arctic charr populations may respond differently to increasing temperatures. In order to compare growth and thermal habitat use between habitat types, otolith-inferred average water temperatures estimated from whole otoliths and fork lengths at capture were measured for young-of-the-year (YOY) Arctic charr obtained from two proximal fluvial and lacustrine sites in Labrador, Canada. Otolith-inferred average experienced water temperatures were not significantly correlated with air temperatures at both sites, suggestive of behavioural thermoregulation by YOY. The majority of Kogluktokoluk Brook (fluvial) YOY were found using water temperatures consistent with laboratory determined preferred temperatures for juvenile Arctic charr, whereas most Tom's Pond (lacustrine) YOY were found using temperatures ranging between preferred temperatures and optimal temperatures for growth. There was no consistent difference between mean water temperatures used between YOY from the two sites. Otolith-inferred average experienced water temperatures were only correlated to fork lengths in Tom's Pond YOY. The lack of correlation in Kogluktokoluk Brook YOY is argued to reflect resource partitioning occurring as a result of territoriality known to occur among stream salmonids. The limited range of temperatures used by fluvial YOY in this study, particularly the lack of cooler temperatures, also suggests that fluvial YOY may face barriers to thermal refugia, and as a result may be particularly vulnerable to climate change.     

Direct and indirect effects of predatory young‐of‐year fishes in a dryland river food web

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High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans

MOTIVATION: With complex traits and diseases having potential genetic contributions of thousands of genetic factors, and with current genotyping arrays consisting of millions of single nucleotide polymorphisms (SNPs), powerful high-dimensional statistical techniques are needed to comprehensively model the genetic variance. Machine learning techniques have many advantages including lack of parametric assumptions, and high power and flexibility. RESULTS: We have applied three machine learning approaches: Random Forest Regression (RFR), Boosted Regression Tree (BRT) and Support Vector Regression (SVR) to the prediction of warfarin maintenance dose in a cohort of African Americans. We have developed a multi-step approach that selects SNPs, builds prediction models with different subsets of selected SNPs along with known associated genetic and environmental variables and tests the discovered models in a cross-validation framework. Preliminary results indicate that our modeling approach gives much higher accuracy than previous models for warfarin dose prediction. A model size of 200 SNPs (in addition to the known genetic and environmental variables) gives the best accuracy. The R(2) between the predicted and actual square root of warfarin dose in this model was on average 66.4% for RFR, 57.8% for SVR and 56.9% for BRT. Thus RFR had the best accuracy, but all three techniques achieved better performance than the current published R(2) of 43% in a sample of mixed ethnicity, and 27% in an African American sample. In summary, machine learning approaches for high-dimensional pharmacogenetic prediction, and for prediction of clinical continuous traits of interest, hold great promise and warrant further research.     

Seasonal and interannual effects of hypoxia on fish habitat quality in central Lake Erie

1. Hypoxia occurs seasonally in many stratified coastal marine and freshwater ecosystems when bottom dissolved oxygen (DO) concentrations are depleted below 2–3 mg O₂ L^?1. 2. We evaluated the effects of hypoxia on fish habitat quality in the central basin of Lake Erie from 1987 to 2005, using bioenergetic growth rate potential (GRP) as a proxy for habitat quality. We compared the effect of hypoxia on habitat quality of (i) rainbow smelt, Osmerus mordax mordax Mitchill (young‐of‐year, YOY, and adult), a cold‐water planktivore, (ii) emerald shiner, Notropis atherinoides Rafinesque (adult), a warm‐water planktivore, (iii) yellow perch, Perca flavescens Mitchill (YOY and adult), a cool‐water benthopelagic omnivore and (iv) round goby Neogobius melanostomus Pallas (adult) a eurythermal benthivore. Annual thermal and DO profiles were generated from 1D thermal and DO hydrodynamics models developed for Lake Erie’s central basin. 3. Hypoxia occurred annually, typically from mid‐July to mid‐October, which spatially and temporally overlaps with otherwise high benthic habitat quality. Hypoxia reduced the habitat quality across fish species and life stages, but the magnitude of the reduction varied both among and within species because of the differences in tolerance to low DO levels and warm‐water temperatures. 4. Across years, trends in habitat quality mirrored trends in phosphorus concentration and water column oxygen demand in central Lake Erie. The per cent reduction in habitat quality owing to hypoxia was greatest for adult rainbow smelt and round goby (mean: ?35%), followed by adult emerald shiner (mean: ?12%), YOY rainbow smelt (mean: ?10%) and YOY and adult yellow perch (mean: ?8.5%). 5. Our results highlight the importance of differential spatiotemporally interactive effects of DO and temperature on relative fish habitat quality and quantity. These effects have the potential to influence the performance of individual fish species as well as population dynamics, trophic interactions and fish community structure.     

Resource limitation during early ontogeny: constraints induced by growth capacity in larval and juvenile fish

The presence of and mechanisms behind density-dependent growth and resource limitation in larval and juvenile stages of organisms with high mortality such as fish are much debated. We compare observed consumption and growth rates with maximum consumption and growth rates to study the extent of resource limitation in young-of-the-year (YOY) roach (Rutilus rutilus) and perch (Perca fluviatilis). Diet, habitat use, consumption rate and growth rate were measured under varying YOY fish densities over 2 years in four lakes. In the first year, YOY roach and perch were studied under allopatric conditions. Experimental addition of perch roe in the second year also allowed study of YOY of the two species under sympatric conditions in two of the lakes. The diet of YOY roach was dominated by cladoceran zooplankton and YOY roach habitat use was restricted to the shore region in both years. This restricted habitat use did not involve any cost in foraging gain in the first year as consumption and growth rates were very close to maximum rates. During the second year, when the two species coexisted, resources were limited in late season, more so in the littoral than in the pelagic habitat in one lake while the reverse was the case in the other lake. The diet of YOY perch was also dominated by zooplankton, and with increasing perch size the proportion of macroinvertebrate prey in the diet increased. After hatching, YOY perch first utilized the pelagic habitat restricting their habitat use to the shore after 1 to several weeks in the pelagic zone. During the larval period, perch were not resource limited whereas juvenile perch were resource limited in both years. The fact that YOY perch were more resource limited than YOY roach was related to the higher handling capacity and lower attack rate of perch relative to roach, rendering perch more prone to resource limitation. Estimates of resource limitation based on consumption rates and growth rates yielded similar results. This supports the adequacy of our approach to measure resource limitation and suggests that this method is useful for studying resource limitation in organisms with indeterminate growth. Our results support the view that density-dependent growth is rare in larval stages. We suggest that density-dependent growth was absent because larval perch and roach were feeding at maximum levels over a wide range of larvae densities. Received: 14 June 1999 / Accepted: 29 October 1999     

Seagrass bed patchiness: effects on epifaunal communities in San Diego Bay, USA

Seagrass habitat structure influences epifaunal density, diversity, community composition and survival, but covariation of structural elements at multiple scales (e.g., shoot density or biomass per unit area, patch size, and patch configuration) can confound studies attempting to correlate habitat structure with ecological patterns and processes. In this study, we standardized simulated seagrass shoot density and bed area among artificial seagrass beds in San Diego Bay, California, USA to evaluate the singular effect of seagrass bed configuration (“patchiness”) on the density and diversity of seagrass epifauna. Artificial seagrass beds all were 1 m², but were composed of a single large patch (“continuous” treatment), four smaller patches (“patchy” treatment), or 16 very small patches (“very patchy” treatment). We allowed epifauna to colonize beds for 1 month, and then sampled beds monthly over the next 3 months. Effects of seagrass bed patchiness on total epifaunal density and species-specific densities were highly variable among sampling dates, and there was no general trend for the effects of fragmentation on epifaunal densities to be positive or negative. Epifaunal diversity (measured as Simpson's index of diversity) was highest in very patchy or patchy beds on two out of the three sampling dates. Very patchy beds exhibited the highest dissimilarity in community composition in the first two sampling periods (August and September), but patchy beds exhibited the highest dissimilarity in the third sampling period (October). Our results indicate that seagrass patch configuration affects patterns of epifaunal density, diversity, and community composition in the absence of covarying bed area or structural complexity, and that patchy seagrass beds may be no less valuable as a habitat than are continuous seagrass beds. The spatial pattern employed when harvesting or planting seagrass may influence epifaunal habitat use and should be a key consideration in restoration plans.