Fish diversity in European lakes: geographical factors dominate over anthropogenic pressures

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Inter and intraspecific variation in fish body size constrains microhabitat use in a subtropical drainage

Microhabitat characteristics are expected to influence the distribution of stream fish species at fine spatial scales (e.g., within riffle segments). Body size is probably the most important trait that constrains microhabitat occupation by fish, but the effect of intraspecific variation has been understudied. We investigated how physical microhabitat characteristics affect species and body size distribution of fish within a stream riffle segment in a coastal subtropical drainage of Brazil. Fishes were sampled by electrofishing 56 riffle plots along a 730-m long stream segment. Species composition was significantly related to four microhabitat characteristics: substrate size, flow velocity, distance to margin and depth. In addition, mean body size increased with increasing substrate size and depth of microhabitat sampling plots. However, when including species identity in linear mixed-effects models (LMM), we observed a different relationship between body size and microhabitat characteristics, but most of the variation was explained by species identity. Thus, we fitted LMMs separately for each species and found species-specific relations between intraspecific variation in body size and microhabitat characteristics. The low variation explained in the models suggests that other fine scale factors, such as biotic interactions and dispersal from adjacent habitat patches, should be incorporated in modeling microhabitat use by stream fish. Our findings suggest that body size is important by itself, but intraspecific variation in body size also constrains microhabitat use differently for each species, which may depend on other species-specific traits, such as morphology, behavior and life history.     

Mechanistic considerations in small fish carcinogenicity testing

Historically, small fish species have proven useful both as environmental sentinels and as versatile test animals in toxicity and carcinogenicity bioassays. They can be bred in large numbers, have low maintenance and bioassay costs, and have a low background incidence of tumors. However, more mechanistic information is needed to help validate the information garnered from these models and to keep pace with other more fully developed animal models. This paper focuses on mechanistic considerations when using small fish models for carcinogenicity testing. Several small aquarium fish species have proven useful. The Japanese medaka is perhaps the best characterized small fish model for carcinogenicity testing; however, the zebrafish is emerging as an important model because it is well characterized genetically. Both route and methodology of exposure may affect the outcome of the study. Most studies have been conducted by introducing the test compound into the ambient water, but dietary exposures and embryo microinjection have also been used. Other considerations in study design include use of an initiating carcinogen, such as diethlynitrosamine, and differences in xenobiotic metabolism, such as the fact that fish CYP2B is refractory to phenobarbital induction. The small size of these models has perhaps limited some types of mechanistic studies, such as formation and repair of DNA adducts in response to carcinogen exposure. However, improved analytical methods are allowing greater resolution and should be applied to small fish species. Slide-based methods such as immunohistochemistry are an important adjunct to routine histopathology and should be included in study design. However, there is a need for development of more species-specific antibodies for fish research. There is also a need for more fish-specific data on cytokines, serum biochemistry, and oncogenes to strengthen the use of these important test models.     

Are orientation mechanisms among migratory birds speciesospecific?

The mechanisms by which migratory birds find their way from breeding grounds to winter quarters and back have been the subject of intensive research during the past four decades. Birds are equipped with genetic information about the migratory direction, and they can use the earth's magnetic field, star patterns and the sun and/or skylight polarization patterns as compass references. Studies on a number of North American and European species have suggested possible species-specific differences in the relative role of the compass mechanisms. This may be largely the result of divergent experimental designs, which make results difficult to compare. Comparative studies with identical methods are needed to see how much species-specific variation exists in basic orientation mechanisms.     

Anthropogenic disturbance homogenizes seagrass fish communities

Anthropogenic activities have led to the biotic homogenization of many ecological communities, yet in coastal systems this phenomenon remains understudied. In particular, activities that locally affect marine habitat‐forming foundation species may perturb habitat and promote species with generalist, opportunistic traits, in turn affecting spatial patterns of biodiversity. Here, we quantified fish diversity in seagrass communities across 89 sites spanning 6° latitude along the Pacific coast of Canada, to test the hypothesis that anthropogenic disturbances homogenize (i.e., lower beta‐diversity) assemblages within coastal ecosystems. We test for patterns of biotic homogenization at sites within different anthropogenic disturbance categories (low, medium, and high) at two spatial scales (within and across regions) using both abundance‐ and incidence‐based beta‐diversity metrics. Our models provide clear evidence that fish communities in high anthropogenic disturbance seagrass areas are homogenized relative to those in low disturbance areas. These results were consistent across within‐region comparisons using abundance‐ and incidence‐based measures of beta‐diversity, and in across‐region comparisons using incidence‐based measures. Physical and biotic characteristics of seagrass meadows also influenced fish beta‐diversity. Biotic habitat characteristics including seagrass biomass and shoot density were more differentiated among high disturbance sites, potentially indicative of a perturbed environment. Indicator species and trait analyses revealed fishes associated with low disturbance sites had characteristics including stenotopy, lower swimming ability, and egg guarding behavior. Our study is the first to show biotic homogenization of fishes across seagrass meadows within areas of relatively high human impact. These results support the importance of targeting conservation efforts in low anthropogenic disturbance areas across land‐ and seascapes, as well as managing anthropogenic impacts in high activity areas.     

Edge effects influence the composition and density of reef residents on subtidal restored oyster reefs

Within estuarine and coastal ecosystems globally, extensive habitat degradation and loss threaten critical ecosystem functions and necessitate widescale restoration efforts. There is abundant evidence that ecological processes and species interactions can vary with habitat characteristics, which has important implications for the design and implementation of restoration efforts aimed at enhancing specific ecosystem functions and services. We conducted an experiment examining how habitat characteristics (presence; edge vs. interior) influence the communities of resident fish and mobile invertebrates on restored oyster (Crassostrea virginica) reefs. Similar to previous studies, we found that restored reefs altered community composition and augmented total abundance and biomass relative to unstructured sand habitat. Community composition and biomass also differed between the edge and interior of individual reefs as a result of species-specific patterns over small spatial scales. These patterns were only weakly linked to oyster density, suggesting that other factors that vary between edge and interior (e.g. predator access or species interactions) are likely more important for community structure on oyster reefs. Fine-scale information on resident species' use of oyster reefs will help facilitate restoration by allowing decision makers to optimize the amount of edge versus interior habitat. To improve the prediction of faunal use and benefits from habitat restoration, we recommend investigations into the mechanisms shaping edge and interior preferences on oyster reefs.     

Elasticity Analysis of Green Sturgeon Life History

I provide an analysis of a simplified life history model for green sturgeon, Acipenser medirostris, based on published and recent estimates of reproduction and growth rates and survival rates from life history theory. The deterministic life cycle models serve as a tool for qualitative analysis of the impacts of perturbations on green sturgeon, including harvest regulations based on minimum and maximum size limits (“slot limits”). Elasticity analysis of models with two alternative age–length relationships give similar results, with a high sensitivity of population growth rate to changes in the survival rate of subadult and adult fish. A dramatic increase in the survival of young of the year sturgeon or annual egg production is required to compensate for relatively low levels of fishing mortality. Peak reproductive values occur from ages 25 to 40. An increase or decrease in the maximum and minimum size limits can have a profound effect on the elasticity of population growth to changes in the annual survival rate of age classes specified by the slot, due to changes in the number of age classes of subadults and adults that are available for harvest. This analysis provides managers with a simple tool to assess the relative impacts of alternative harvest regulations. In general, green sturgeon follow life history patterns similar to other sturgeon, but species-specific demographic information is needed to produce more complex assessment and viability analysis models.     

Occupancy Models for Monitoring Marine Fish: A Bayesian Hierarchical Approach to Model Imperfect Detection with a Novel Gear Combination

Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors influencing fish population distribution and dynamics.     

Seeking functional homogeneity: A framework for definition and classification of fish assemblage types to support assessment tools on temperate reefs

Due to their important role in the ecosystem and high economic value, there is a need to assess the effect of anthropogenic impacts on marine fish assemblages. However, this can only be achieved if variations due to natural causes are known. Moreover, while most assessment tools rely on functional traits, bottom-up habitat classification frameworks tend to use species composition. The present study proposes an innovative framework to define fish assemblage types through metric pairwise constrained k-means (MPCK-means) clustering of sites based on functional guild categories and univariate metrics, an approach that takes into account within-site variability due to the sampling method and natural causes. This was followed by a label-based ensemble clustering approach, which finds patterns that minimise information loss when integrating clustering results from individual metrics. In order to test the method, fish assemblages on 14 nearshore rocky reefs along the Portuguese coast were sampled. The final typology configuration achieved through ensemble clustering consisted of three assemblage types and maintained an average normalised mutual information of 0.605 with the individual clustering results. Nested PERMANOVA found differences among types and the most variable metrics in the face of natural variation were identified. Ultimately, a k-nearest neighbours classifier is proposed to label new sites, based only on environmental variables that are unlikely to be directly affected by the presence of anthropogenic impacts. Optimal performance for the classification model was achieved with inverse distance-weighted voting of the 4 nearest neighbours with an average classification accuracy of 96.08%.     

Guidelines for health and welfare monitoring of fish used in research

The aim of this paper is to provide background material necessary for the development of international guidelines for the health and welfare monitoring of fish used in research. It provides an overview of present guidelines and discusses why more detailed and species-specific guidelines are needed. A major issue within fish research is to document the situation today and point out areas where improvements are needed.     

Incorporating species losses and gains into a fish-based index for stream bioassessment increases the detection of anthropogenic disturbances

The taxonomic completeness index (ratio of observed to expected species; O/E) is widely used in stream bioassessment programs to infer ecological impairment. However, its sensitivity to detecting anthropogenic disturbances may be reduced by (1) the modelling procedure used to determine the expected species at a site (2) the inability of the index to account for assemblage shifts through species gains as well as losses; and (3) the frequent use of a threshold that only allows assessment of the absence of prevalent species. We used a version of the BC biotic index (an adaptation of Bray-Curtis distance) that incorporated alien and translocated species into the observed component, and generated expected native species probabilities using single species ensemble models (‘BC_A’). Sensitivity analysis, bivariate correlations and multiple linear regression analyses were used to test whether BC_A better detected anthropogenic disturbances than the standard BC (i.e. without alien and translocated species) and O/E₅₀ derived from the same models. We also tested three additional fish biotic indices currently used in the Ecosystem Health Monitoring Program in Southeast Queensland, Australia. Of the indices tested, BC_A explained the greatest amount of variance in anthropogenic disturbance variables, followed by BC and the proportional sample abundance of alien species. The BC_A index was 18% more sensitive to detecting non-reference conditions, 20% more responsive to an anthropogenic disturbance gradient, and had twice the number of significant bivariate correlations with disturbance variables than the O/E₅₀ index derived from the same underlying predictive model. We suggest that the improved performance of BC_A relative to O/E₅₀ lies in its ability to detect the addition of alien, translocated, and some native species whose traits allow them to persist or thrive in degraded conditions, and the inclusion of low prevalence taxa that may be sensitive to mild levels of disturbance. Given that generation of the BC_A index requires no further information than already provided by traditional multivariate predictive models, we recommend its inclusion into bioassessment programs that use multivariate fish based indices.     

Spatial patterns of Yucatan reef fish communities: Testing models using a multi-scale survey design

Using a hierarchical multi-scale survey design, we examined the spatial patterns of reef fish communities and tested ecological models concerning the relative importance of reef geomorphology and anthropogenic pressure possibly driving community structure. Canonical redundancy analysis was used as a form of multivariate analysis of variance (MANOVA) to asses differences in reef fish community composition at two spatial scales: broad (10⁵ m) and intermediate (10⁴ m). Surveys were conducted on the east coast of the Yucatan Peninsula (Mexican Caribbean fringing reef), including regions and reefs which differed in geomophologic structure and human use. Seven hundred and fourteen line transects were distributed among 13 reef localities belonging to different regions established a priori. Transects covered four types of reef habitat: lagoon, front, slope, and terrace. Tests of significance were based on permutation procedures. Significant differences among regions were found for the lagoon, slope, and terrace fish communities, consistent with the geomorphologic model, but it is only in the reef lagoon that they were consistent with the anthropogenic model, which may indicate an effect of coastal human activities. Significant differences among reefs within regions were observed, which could be associated with local environmental gradients. Canonical nested MANOVA was an appropriate method for testing ecological hypotheses about the functioning of complex biological systems. The use of a surveying strategy that explicitly incorporated the spatial structure represents an important contribution of this paper to coral reef fish ecology.     

Fish assemblage patterns in the littoral zone of a European reservoir

1. Although reservoirs are common aquatic habitats in Europe, there is little quantitative information on the spatial organisation of fish assemblages inhabiting their littoral zones. Consequently, we characterised fish assemblage structure in the littoral zone of a reservoir (Lake Pareloup) in SW France during late spring, summer and early autumn (the growing season).
2. We measured the relative abundance of fish weekly, from mid-May to mid-October, using point abundance sampling by electrofishing. We identified temporal patterns in assemblage structure using hierarchical cluster analysis, and then characterised the spatial distribution of 17 defined ecospecies using a Kohonen self-organising map (SOM, an unsupervised Artificial Neural Network).
3. Our analyses revealed three distinct faunal structures within the littoral zone. From mid-May to mid-July, adults and young-of-the-year (0+) occupied separate habitats, with most 0+ fish in vegetated habitats and adults in open water. From mid-July to late August, some 0+ co-occurred with adults, but most 0+ fishes remained in vegetated areas. Finally, from late August to mid-October, most fish (both 0+ and adults) left the vegetation for unvegetated littoral habitats, the exception being fish species known to be dependent on macrophytes.
4. Contrary to patterns for adult fishes, the 0+ fish assemblage was dynamic. These dynamics were driven by ontogenetic species-specific habitat changes. Consequently, there was little evidence of stable assemblages or strong assemblage–habitat relationships that would be expected of an 'interactive' assemblage. It is likely that the patterns observed are a result of species-specific response to habitat availability in the lake.     

Ecological, environmental and socioeconomic aspects of the Lake Victoria's introduced Nile perch fishery in relation to the native fisheries and the species culture potential: lessons to learn

Inland fishery ecosystems in Africa are characterized by patterns of overexploitation, environmental degradation and exotic species introductions. Ecological complexity and diversity of aquatic habitats dictate that fishes in general are not evenly distributed in a water body. However, fisheries management regimes tend to ignore this basic principle, assume generalized conditions in a water body, and focus more on ‘desired’ objectives such as maximizing catch. The result is to disregard fish habitat boundaries and anthropogenic influences from the catchment that influence fish production. Overexploitation and environmental degradation disrupt sustainable socioeconomic benefits from the fisheries, create uncertainty among investors, but leave some managers calling for more information with the expectation that the fisheries will recover with time. Open access to the fisheries and full control of fishing effort remain challenges for managers. Exotic species introductions and fish farming can increase production, but such interventions require firm commitment to sound ecological principles and strict enforcement of recommended conservation and co‐management measures in capture fisheries. The general tendency to downplay fishing effort issues, other ecosystem values and functions or rely on temperate fisheries models until a new cycle of overexploitation emerges, characterizes many management patterns in inland fisheries. Aquaculture is not an option to challenges in capture fisheries management. Aquaculture should be developed to increase fish production but even this practice may have negative environmental impacts depending on practice and scale. Decades of information on Lake Victoria fisheries trends and aquaculture development did not stop the collapse of native fisheries. The successfully introduced Nile perch (Lates niloticus) has shown signs of overexploitation and aquaculture has again been considered as the option. By reviewing significant trends associated with Nile perch and its feasibility in aquaculture this paper uses Lake Victoria to illustrate ‘special interest management’ targeting selected species of fish rather than the fisheries.     

Effect of recreational-fisheries management on fish biodiversity in gravel pit lakes,with contrasts to unmanaged lakes

Gravel pit lakes are novel ecosystems that can be colonized by fish through natural or anthropogenic pathways. In central Europe, many of them are managed by recreational anglers and thus experience regular fish stocking. However, also unmanaged gravel pits may be affected by stocking, either through illegal fish introductions or, occasionally, by immigration from connected water bodies. We sampled 23 small (< 20 ha) gravel pit lakes (16 managed and 7 unmanaged) in north-western Germany using littoral electrofishing and multimesh gillnets. Our objective was to compare the fish biodiversity in gravel pit lakes in the presence or absence of recreational fisheries. Given the size of the sampled lakes, we expected species poor communities and elevated fish diversity in the managed systems due to regular stocking of game fish species. Our study lakes were primarily mesotrophic and did not differ in key abiotic and biotic environmental characteristics. Lakes of both management types hosted similar fish abundances and biomasses, but were substantially different in terms of fish community structure and species richness. Fish were present in all lakes, with a minimum of three species. Higher α-diversity and lower β-diversity was discovered in managed gravel pit lakes compared to unmanaged lakes. Consequently, recreational-fisheries management fostered homogenization of fish communities, by stocking a similar set of fish species desired by anglers such as piscivorous fish and large bodied cyprinids. However, unmanaged gravel pit lakes were also affected by human-mediated colonization, presumably by illegal fish releases. Hardly any non-native species were detected, suggesting that recreational-fisheries management did not foster the spread of exotic species in our study region.     

Towards a better understanding of small scale distribution of littoral age-0 fish in a deep-valley reservoir: day or night surveys?

The effect of diel period and littoral habitats on the distribution of age-0 fish was tested in a deep-valley reservoir using boat-modified point abundance sampling by electrofishing (PASE). Day and night samplings unveiled differences in abundance of age-0 fish while recognizing most of the commonly present age-0 fish species in the littoral zone. Night survey provided better information about the abundance of age-0 fish since most species appeared in higher numbers at night. Alternatively, night sampling underestimated bleak (Alburnus alburnus) and gudgeon (Gobio gobio), which were predominantly found in the littoral zone in the daytime. The structure of the age-0 fish assemblage was determined primarily by the characteristics of the littoral habitats, i.e. slope steepness and structure, and three different patterns of habitat use were detected among the fish species. To obtain the most comprehensive assessment of a littoral age-0 fish assemblage and to register all species-specific patterns of habitat use, it is necessary that all littoral habitats in the reservoir are sampled during both day and night periods. The boat-modified PASE could be also used as a standard monitoring tool for routine age-0 fish sampling under difficult conditions of steep-sloped shorelines in large inland waterbodies.     

Geographic isolation and climate govern the functional diversity of native fish communities in European drainage basins

Aim In times of biodiversity crisis, it is extremely important to understand diversity gradients. In particular, the study of the diversity of ecological functions is a key issue for the management of ecosystem integrity. Here we identify areas of low functional diversity of the native fish fauna in European drainage basins and we determine the relative importance of three underlying mechanisms: environmental filtering, geographic isolation and climatic history. Location The European continent. Methods Based on 14 morphological traits that are closely related to fish function (habitat and dietary niches), three independent functional diversity indices [functional richness (FR), functional evenness (FE), functional divergence (FD)] were calculated for 128 European drainage basins with a total of 230 fish species. The indices were standardized for species richness using null models. The patterns of the standardized indices are described and three potentially underlying mechanisms are tested using variance partitioning and multi‐linear regression models. Results FR and FD were highest in eastern European drainage basins and in Great Britain and lowest in the Mediterranean. FE patterns were less pronounced. All observed patterns were mainly governed by geographic isolation and present environmental conditions. Within the environmental conditions, average annual temperature and precipitation were good predictors for functional diversity. The role of habitat diversity and size was negligible. Main conclusions Geographic isolation coupled with harsh environmental conditions such as extreme temperatures and low precipitation, as in Mediterranean regions, can lead to low FR and FD. This can be explained by extinction that could not be compensated by re‐colonization and high speciation. Due to their high functional redundancy, communities in these areas might better withstand further species extinctions on a small scale. Over the short term, however, their often extremely low FR suggests a less flexible functioning that can hinder their ability to withstand today's rapid environmental and anthropogenic threats.     

How humans drive speciation as well as extinction

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.