Patterns of Assemblage Structure Indicate a Broader Conservation Potential of Focal Amphibians for Pond Management

Small freshwater ponds host diverse and vulnerable biotic assemblages but relatively few conspicuous, specially protected taxa. In Europe, the amphibians Triturus cristatus and Pelobates fuscus are among a few species whose populations have been successfully restored using pond restoration and management activities at the landscape scale. In this study, we explored whether the ponds constructed for those two target species have wider conservation significance, particularly for other species of conservation concern. We recorded the occurrence of amphibians and selected aquatic macro-invertebrates (dragonflies; damselflies; diving beetles; water scavenger beetles) in 66 ponds specially constructed for amphibians (up to 8 years post construction) and, for comparison, in 100 man-made ponds (created by local people for cattle or garden watering, peat excavation, etc.) and 65 natural ponds in Estonia. We analysed nestedness of the species assemblages and its dependence on the environment, and described the co-occurrence patterns between the target amphibians and other aquatic species. The assemblages in all ponds were significantly nested, but the environmental determinants of nestedness and co-occurrence of particular species differed among pond types. Constructed ponds were most species-rich irrespective of the presence of the target species; however, T. cristatus was frequent in those ponds and rare elsewhere, and it showed nested patterns in every type of pond. We thus conclude that pond construction for the protected amphibians can serve broader habitat conservation aims in the short term. However, the heterogeneity and inconsistent presence of species of conservation concern observed in other types of ponds implies that long-term perspectives on pond management require more explicit consideration of different habitat and biodiversity values. We also highlight nestedness analysis as a tool that can be used for the practical task of selecting focal species for habitat conservation.     

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.     

Once a pond in time: employing palaeoecology to inform farmland pond restoration

The restoration of highly terrestrialized farmland ponds that combines the removal of woody vegetation and pond sediment greatly enhances aquatic biodiversity. Nonetheless, questions remain regarding the historical precedent of pond restoration, and particularly if post‐restoration aquatic macrophyte communities resemble pre‐terrestrialization assemblages. We used a paleoecological approach to address these questions for a typical, recently restored farmland pond in Norfolk, eastern England. Plant and animal remains in pond sediment cores were used to infer decadal‐centennial scale changes to pond communities and to identify past pond management events. We then evaluated the resemblance of restored and historical assemblages by comparisons with contemporary post‐restoration vegetation data. Based on changes in the abundance of terrestrial leaf remains and other indicators (increases followed by declines of aquatic organisms), the study pond appears to have a long history (going back to the early‐1800s) of canopy management (at least three inferred management events), but after the mid‐1970s, steady and substantial increases in terrestrial indicators suggest cessation of management resulting in uninterrupted terrestrialization. Aquatic macrophyte communities arising after restoration showed some similarities with historical assemblages, but also contained apparently new species. This study demonstrates how paleolimnological methods can improve understanding of pond ecological histories to better inform restoration targets and practices.     

Species richness and rarity of crane flies (Diptera, Tipuloidea) in a boreal mire

Species richness and abundance are central in biodiversity inventories and in measuring the structure of communities. Neglecting the assessment of sampling efficiency may lead to spurious estimates of species richness and conservation value. Our aim was to examine species richness, sampling effectiveness, species-abundance distribution (SAD) and rarity of a boreal, mire-dwelling crane fly (Diptera, Tipuloidea) assemblage in western Finland. 12 Malaise traps dispersed in 4 subplots and standardized sweep net samples were used to collect adult flies from the mire. A total of 23 species and 1,569 specimens were identified. In general all species richness estimators were highly correlated and indicated rather good sampling effort. Sample completeness, expressed as percentage of observed richness divided by estimated richness, was higher for mire-dwellers (mean 75 %) than for all species (mean 63 %). Crane fly assemblages of subplots and combined data fitted best with log-series SAD. Species spatial distribution was positively correlated with average abundance. In other words, the most abundant species occurred in the most of Malaise traps. Seven mire-dwelling species greatly outnumbered (94 % of the collected specimens) all other members in the assemblage, and only one observed species was rare by several definitions (local abundance, extent of occurrence in Finland and area of occupancy). Although the studied assemblage was characterized by commonness, five of the species have threatened status in Europe south of Finland. Separate species richness estimation of all species (vagrants and occasional species included) and focal species (here mire-dwellers) is supported if ecological information is available on the taxonomic group being studied.     

Variation of aquatic insect assemblages among seasons and microhabitats in Hungarian second-order streams

The assemblages of aquatic insects are important members of water ecosystems. Based on former studies among the most important factors structuring the assemblages are numerous abiotic ones, such as the sort and the particle size of the substratum. Most of the sampling protocols, e.g. AQEM, determine microhabitats based on those. Nevertheless, we have no information yet about whether or not these different, precisely determined microhabitats have different assemblages. In this study we compared the aquatic insect assemblages of different microhabitat types in three seasons using ADONIS and linear discriminant analyses. We proved that seasonal changes of abiotic factors had a major role in structuring the assemblages. In spring and summer the assemblages differed significantly, however, in autumn no significant differences were found. We supposed that the variation among the assemblages was due to the abundance patterns of frequent species instead of the presence of rare or sparse species. The indicator species analyses also corroborated this suppososition while symmetrical indicator species were not found.     

The significance of littoral and shoreline habitat integrity to the conservation of lacustrine damselflies (Odonata)

Human development of pond and lake shorelines may significantly impact native lacustrine biota including a variety of aquatic macroinvertebrate groups. In an effort to better understand the habitat associations and sensitivities of lacustrine damselflies (Odonata: Zygoptera), we sampled adults in littoral macrophyte habitat during two flight periods at 35 randomly selected pond and lake sites in southern Maine during 2000 and 2001. Data were also collected to help characterize water body, shoreline disturbance, and aquatic vegetation at each study site. Nonmetric multidimensional scaling was used for ordination of damselfly assemblages, and coordinates from the most stable solution were related to site variables using forward stepwise multiple regression. Our results suggest that the diversity and composition of damselfly assemblages is related to the abundance and richness of littoral zone macrophytes, extent of riparian disturbance, benthic substrate granularity, and lake productivity; all variables subject to anthropogenic degradation on excessively developed waterbodies. Additionally, we developed a Habitat Tolerance Index useful for distinguishing between relative habitat specialists and generalists from among a diverse assemblage of 19 lacustrine species. Finally, species-specific damselfly associations with multiple genera of floating and emergent macrophytes were assessed using both nonparametric correlation and multiplicative regression yielding significant relationships for 17 species, including two damselflies of global conservation concern (Enallagma laterale and E. pictum). We conclude that the protection of littoral and shoreline habitat integrity, with special emphasis on emergent and floating macrophytes, is critical to the conservation of lacustrine biodiversity.     

Are cladoceran diversity and community structure linked to spatial heterogeneity in urban landscapes and pond environments?

Biodiversity patterns in cladoceran communities were investigated in urban waterbodies in relation with residential land use, pond management, and waterbody environments. We evaluated species richness in the pelagic and littoral zones of eighteen waterbodies of a large Canadian city. Gamma diversity (26 species) observed at a small scale in the urban survey was important comparatively to large-scale surveys of lakes. Beta diversity ranged from 1 to 8 species among waterbodies. We tested if littoral species greatly contributed to regional diversity in urban waterbodies. Littoral species (Chydoridae, Ilyocryptidae, Macrothricidae, Polyphemidae) accounted for 58% of the total species pool. We distinguished five cladoceran assemblages associated to different waterbodies (temporary ponds, permanent lakes, and wetlands). Cladoceran communities were more diverse and variable in permanent lakes than in temporary ponds. Changes in cladoceran species assemblages among waterbodies were driven by variations in waterbody size and phosphorus enrichment, macrophyte and algal biomass, urban density, pond management practices, and the presence of potential predators as fish and macroinvertebrates. Our study indicates that both artificial ponds and lakes and natural wetlands are valuable habitats for the conservation of cladoceran biodiversity and rare endemic species in urban regions. Further research on pond management strategies promoting urban aquatic biodiversity should be undertaken.     

Effects of sample standardization on mean species detectabilities and estimates of relative differences in species richness among assemblages

Ecological surveys provide the basic information needed to estimate differences in species richness among assemblages. Comparable estimates of the differences in richness between assemblages require equal mean species detectabilities across assemblages. However, mean species detectabilities are often unknown, typically low, and potentially different from one assemblage to another. As a result, inferences regarding differences in species richness among assemblages can be biased. We evaluated how well three methods used to produce comparable estimates of species richness achieved equal mean species detectabilities across diverse assemblages: rarefaction, statistical estimators, and standardization of sampling effort on mean taxonomic similarity among replicate samples (MRS). We used simulated assemblages to mimic a wide range of species-occurrence distributions and species richness to compare the performance of these three methods. Inferences regarding differences in species richness based on rarefaction were highly biased when richness estimates were compared among assemblages with distinctly different species-occurrence distributions. Statistical estimators only marginally reduced this bias. Standardization on MRS yielded the most comparable estimates of differences in species richness. These findings have important implications for our understanding of species-richness patterns, inferences drawn from biological monitoring data, and planning for biodiversity conservation.     

Diurnal habitat segregation by tadpoles in two temporary ponds in an Atlantic Rainforest remnant, Northeastern Brazil

Tadpoles are found in diverse aquatic habitats, where they share resources in various dimensions. Tadpole assemblages were studied in two temporary ponds in Atlantic Rainforest. Our aim was to analyze the temporal and spatial distribution patterns and their correlation with abiotic factors. Tadpoles were sampled weekly using nets, from March to December 2008. Samples were collected during the day and at night, and taken near the shore and in the centre of the ponds. Samples in inshore and pond centres were taken from both areas with and without aquatic vegetation. The assemblage consisted of 15 species in pond A and 12 species in pond B. The majority of species was accidental, and used the pond continuously. The assemblage was predominantly diurnal, which may be related to greater activity rate. In pond A the tadpoles primarily used the centre of ponds, whereas in pond B tadpoles primarily used shore areas. However, some populations showed preferences for particular environments. In pond A, environmental heterogeneity in the centre had the greatest influence on tadpole abundance. Our data suggest that temporal distribution facilitated the coexistence of different species of tadpoles in the pond but this conclusion is tentative and requires verification. Hence, more data needs to be collected so that we can propose effective area management plans.     

Lazy ecologist's guide to water beetle diversity: Which sampling methods are the best?

Biodiversity surveys of aquatic macroinvertebrates in standing water rely on various methods, but a thorough comparison of the techniques is lacking. This hampers analyses across surveys and impedes development of efficient sampling schemes. We compare the selectivity and efficiency of four methods commonly used to collect aquatic insects – activity traps (ATs), box trap (BT), handnetting (HN) and light trap (LT) – using a large dataset on water beetles in a site with ～100 species. We propose to use time investment as a natural basis to compare efficiency, since it applies to any method. The results inherently differ from results based on samples or individuals because methods are neither equally demanding nor equally rewarding. Most differences between methods arise from their size selectivity: ATs select for larger species, while HN and BT seem least selective. Attraction to light is taxon-specific and LT yields more depauperate samples than ATs, BT and HN, limiting the use of LT in community studies. To boost the development of cost-effective protocols, we also identify the best designs for rapid bioassesment by simulating short surveys from the data. Combinations of ATs and BT give most species; the results are robust to partitioning of effort between both methods. However, these rapid surveys miss on average more than 40% of all species in our study. Our results therefore emphasize that long-term studies using multiple methods are vital for measuring diversity in species-rich freshwater habitats.     

Determinant landscape‐scale factors on pond odonate assemblages

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Evaluation of Common Methods for Sampling Invertebrate Pollinator Assemblages: Net Sampling Out-Perform Pan Traps

Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km² area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service.     

Estimation of river ecosystem biodiversity based on the Chao estimator

The research was focused on identification of plant diversity assessment approach which would be suitable for flowing waters. Moreover, the study attempted to estimate the extent of the survey (sampling effort) needed for detection of full plant diversity in river ecosystems. The analysed data were collected in a botanical survey carried out on the lowland sandy bottom Wel river, which is a very common river type in Europe. The Chao method of estimation of total species richness of macrophytes and Hill numbers were used to estimate the diversity based on very common plants (inverse Simpson index) as well as frequent species (Shannon index) and also including rare species (species richness). The analysis showed that using standard macrophyte survey approach for rivers, it is relatively easy to record abundant plants, but it is not possible to detect all species, because many aquatic macrophytes occur with low frequency and abundance requiring enormous sampling effort to detect all of them. It exceeds capabilities of most scientific projects. To improve the accuracy of diversity estimation, the rarefaction and extrapolation method was recommended. This method can reduce the bias in diversity estimates based on limited observational data, and thus limit inaccurate conclusions and subsequent wrong decisions in the conservation frameworks related to freshwater protection.     

Trade-off between number and length of remote videos for rapid assessments of reef fish assemblages

Remote underwater videos are widely employed to assess the structure and composition of reef fish assemblages but the sampling effort employed on each survey differs considerably, indicating that both the number of assessments and video length could be optimized. We searched for this optimal sampling effort in remote video samples to conduct rapid assessments of community composition and discussed the relation between number of replicates and video length, and how it impacts the method's efficiency to characterize species assemblages. Remote video recordings from tropical reefs in northeastern Brazil were used to investigate how fish species richness and composition builds across time and number of assays. Videos as short as 5 min successfully recorded species richness, requiring about five repetitions to record most species that compose 80% of the total biomass. Recording species composition required even less time in these reefs, setting a minimum of 3 min with the same five videos. By comparing the detected richness per analysed time unit, we found several shorter videos recorded for more species than a few longer videos, indicating that increasing the sampling coverage in the reef area might be better than just extending the video length for rapid assessments.     

Farm ponds make a contribution to the biodiversity of aquatic insects in a French agricultural landscape

Manmade ecosystems provide a variety of resources that have strong economic values. We assessed the importance of 37 farm ponds for the biodiversity of Odonata in an agricultural landscape lacking natural wetlands in southwestern France. Farm ponds captured 40% of the regional species pool, including both common and rare species. The species assemblages were not correlated with pond use (e.g., cattle watering, duck farming, etc.) or to landscape variable. Species richness was correlated with pond area, suggesting that community diversity was primarily driven by autoecological processes. Farm ponds thus made a positive contribution to the maintenance of aquatic biodiversity. This added value for biodiversity should be considered when calculating the costs and benefits of constructing water bodies for human activities.     

Patchiness of local species richness and its implication for large-scale diversity patterns: an example from the middle Miocene of the Paratethys

The best hope for understanding global diversity patterns is to compare local assemblages, which are mostly preserved in taphonomically-complex shell beds. The present study investigates the variability in faunal composition and diversity at the scale of a single outcrop. A total of 152 species (3315 shells) occurred in 25 samples from 5 tempestitic shell beds. Although sampling intensity was high, total species richness was not captured by far at the hierarchical levels present (outcrop, shell beds, samples) because the majority of species is rare. In contrast, sampling intensity was sufficient to cover the most abundant species, as indicated by stable evenness values. Four taxa dominate the assemblage, but their rank order differs strongly between individual shell beds and individual samples; significant differences between some shell beds are evident for faunal composition, and one shell bed differs from all others with respect to species accumulation curves. Within shell beds, rarefaction curves are generally characterized by strongly overlapping confidence intervals, but outliers occur in three of five shell beds. Patchiness is additionally indicated by a wide scatter of diversity indices in some shell beds and by a wide scatter of samples of one shell bed in an ordination on faunal composition. Most of the outcrop-scale variability in faunal composition and diversity can be related to differences between shell beds. This suggests that sampling a single shell bed of the outcrop is insufficient to characterize the local fauna and its diversity, even when sampling intensity (i.e. the number of samples and shells) within the shell bed was high. Similarly, a single sample from such a shell bed may not be sufficient to characterize its diversity, even when the number of counted shells was high. It is therefore confirmed that sampling strategy and sampling intensity are crucial to confidently characterize the shelly assemblages at such a small spatial scale and that dispersed sampling effort with many small replicate samples will characterize a local assemblage and its diversity better than a few large samples. Diversity comparisons of individual samples between localities must account for the high variability present at the smaller spatial scale, as observed in our study.     

Spatio-temporal nested patterns in macroinvertebrate assemblages across a pond network with a wide hydroperiod range

Nestedness has been widely used to measure the structure of biological communities and occurs when species-poor sites contain subsets of species-rich ones. Here, we examine nested patterns across the macroinvertebrate assemblages of 91 ponds in Doñana National Park, Spain, and explore temporal variation of nestedness and species richness in 19 temporary ponds over 2 years with differing rainfall. Macroinvertebrate assemblages were significantly nested; both pond spatial arrangement and environmental variation being important in driving nested patterns. Despite the nested structure observed, a number of taxa and ponds deviate from this pattern (termed idiosyncratic), by occurring more frequently than expected in species-poor sites, or having assemblages dominated by species largely absent from species-rich sites. Aquatic adults of winged insects, capable of dispersal, were more highly nested than non-dispersing taxa and life-history stages. Idiosyncratic taxa were found in ponds spanning a wide range of hydroperiods, although nestedness was higher in more permanent waterbodies. Monthly sampling demonstrated a gradual increase of species richness and nestedness from pond filling to April–May, when the most temporary ponds started to dry. Although the degree of nestedness of individual pond assemblages varied from month to month, the overall degree of nestedness in the two study years was practically identical despite marked differences in hydroperiod. Our results suggest that differential colonization and environmental variation are key processes driving the nested structure of Doñana ponds, that macroinvertebrate assemblages change in a predictable manner each year in response to cycles of pond wetting and drying, and that connectivity and environmental variability maintain biodiversity in pond networks.     

Implications of the spatial variability of macroinvertebrate communities for monitoring of ephemeral lakes. An example from turloughs

Turloughs, ephemeral water bodies associated with karstified limestone, are an important habitat found in the West of Ireland. They are a priority habitat under the European Habitats Directive (92/43/EEC) and are groundwater-dependent habitats under the European Water Framework Directive (2000/60/EC; WFD). Sampling to meet the objectives of either Directive requires discrimination of inherent natural variation from anthropogenically induced disturbances and accounting for both spatial and seasonal patterns of biotic distribution. This study reports within- (submerged grassland) and between-habitat (submerged and emergent grassland) variability of macroinvertebrate communities in six turloughs. Two different habitat types were sampled from two turloughs in April 2007, and further assessment of spatial pattern in commonly found submerged grassland habitat was determined from four additional turloughs in spring 2008. While cluster analysis and non-metric multidimensional scaling identified differences in macroinvertebrate community structures between habitats in one out of two turloughs, congruence of invertebrate communities was, nevertheless, greater within than among turloughs. Within-habitat variability of macroinvertebrate communities across sampling locations of submerged grassland habitat was sufficiently low so that samples collected at any location of a turlough can provide a reliable metric of the macroinvertebrate community of a turlough as a whole. A standardized submerged grassland sampling approach for routine turlough sampling is recommended as a pressure response method to fulfil the requirements of the WFD. For a comprehensive conservation assessment, however, as demanded under the EC Habitats Directive, we suggest a multi-habitat sampling approach to obtain a thorough assessment of turlough macroinvertebrate biodiversity.     

Helminth parasite richness among vertebrates

The numbers of intestinal helminth species (parasite richnesS) recorded from each of 488 vertebrate host species are compared using data compiled from the published literature. Associations between parasite richness, sampling effort, host size and host habitat (aquatic versus terrestrial) are assessed using a method designed to control for phylogenetic association. Parasite richness increases with the number of surveys on which each estimate of parasite richness is based (sampling effort). When the effects of sampling effort are controlled for, there remains a strong positive relationship between parasite richness and host body size. There is no tendency for aquatic hosts to harbour more parasite species than terrestrial hosts independently of differences in sampling effort and body size. The results are interpreted in the context of hosts representing habitats for parasite colonization, resource allocation between parasite species, and the age of the major mammalian radiations.