Relocation of dredged material in estuaries under the aspect of the Water Framework Directive—A comparison of benthic quality indicators at dumping areas in the Elbe estuary

In the context of the requirements of the European Water Framework Directive (WFD) numerous benthic indices have been proposed recently to assess the ecological quality of marine and transitional waters. In several studies these metrics were applied to coastal and estuarine environments under diverse anthropogenic pressures. Although currently the dumping of dredged material is one of the most prominent human impacts that modify estuaries, the performance of benthic indices to detect effects of dredged sediment relocation has not yet been tested explicitly. Hence we examined a selection of common metrics (species richness, Shannon diversity, AMBI, M-AMBI, W-value, BO2A) at 11 dumping and 11 nearby reference areas in the highly modified Elbe estuary (Germany), where permanent dredging is necessary to maintain the depth of the navigation channel. In order to cover the entire estuary, the study area spanned over the whole salinity gradient from limnic to euhaline. Additionally, we investigated changes in benthic communities due to dredged material placement. All indices, except the W-value, were suitable to differentiate between dumping and reference areas and showed significantly better index values exclusively at reference areas. The applicability of AMBI and M-AMBI was restricted in the limnic stretch due to the more frequent occurrence of freshwater species there. The W-value and BO2A were non-satisfactory in the case of azoic sediment, and in most cases these two indices indicated much better ecological status classifications than the other indices tested. Furthermore, the BO2A had restricted applicability with increasing salinity. At eight of eleven sites the benthic communities differed significantly between dumping and reference areas. Our findings show that the power of conventional benthic indices to detect physical disturbances like the dumping of dredged sediment varies greatly. Having this in mind, we suggest to choose carefully the benthic indices for ecological quality assessments according to the WFD in estuaries in order to avoid misclassifications. Such errors may lead to unnecessarily expensive remediation activities or, in the opposite case, to inactivity although actions were necessary. Furthermore, in order to better meet the WFD requirements we suggest that, regarding frequency and volume, dumping should be adapted as far as possible to the natural processes of sediment movement.     

Using Fish Communities to Assess Streams in Romania: Initial Development of an Index of Biotic Integrity*

Multimetric biotic indices increasingly are used to complement physicochemical data in assessments of stream quality. We initiated development of multimetric indices, based on fish communities, to assess biotic integrity of streams in two physiographic regions of central Romania. Unlike previous efforts to develop such indices for European streams, our metrics and scoring criteria were selected largely on the basis of empirical relations in the regions of interest. We categorised 54 fish species with respect to ten natural-history attributes, then used this information to compute 32 candidate metrics of five types (taxonomic, tolerance, abundance, reproductive, and feeding) for each of 35 sites. We assessed the utility of candidate metrics for detecting anthropogenic impact based on three criteria: (a) range of values taken, (b) relation to a site-quality index (SQI), which incorporated information on hydrologic alteration, channel alteration, land-use intensity, and water chemistry, and (c) metric redundancy. We chose seven metrics from each region to include in preliminary multimetric indices (PMIs). Both PMIs included taxonomic, tolerance, and feeding metrics, but only two metrics were common to both PMIs. Although we could not validate our PMIs, their strong association with the SQI in each region suggests that such indices would be valuable tools for assessing stream quality and could provide more comprehensive assessments than the traditional approaches based solely on water chemistry.     

Taxonomic distinctness along nutrient gradients: More diverse,less diverse or not different from random?

Taxonomic distinctness indices are a family of anthropogenic stress indicators that have been used widely in marine ecosystems; however, their utility in freshwater ecosystems is still unclear. We used two taxonomic distinctness indices and species richness to assess relationships between nutrient gradients and three freshwater taxonomic groups, including diatoms, macrophytes and invertebrates. We found that the indices based on the three organismal groups showed generally rather clear relationships with the nutrient levels, indicating that these indices may bring useful additional information for the purposes of bioassessment. However, the two indices describing taxonomic distinctness showed opposite patterns in relation to nutrient levels. The indices for the three groups of organisms were generally poorly correlated with each other, showing that different organismal groups react differently to anthropogenic stress. Accordingly, taxonomic distinctness indices likely tell us about various aspects of nutrient enrichment of freshwater ecosystems. Our findings also emphasized that the value of these indices may be largely dependent on the organismal group used.     

The use of ants and other soil and litter arthropods as bio-indicators of the impacts of rainforest clearing and subsequent land use

The present study investigated the impacts of rainforest clearance, and associated subsequent land␣use for pasture, on assemblages of soil and litter arthropods in eastern subtropical Australia. We assessed the utility of soil and litter arthropods as potential bio-indicators of cleared and forested habitats. Arthropods were sampled from 24 sites (12 sites each in rainforest and pasture) using two methods (extraction from litter, pitfall traps). Responses of taxa were analysed at various levels of taxonomic resolution, including ‘coarse’ arthropods (all arthropods sorted to Order/Class), ant genera and ant species. Multivariate analyses of arthropod composition indicated that an increase in the level of taxonomic resolution did not provide a commensurate increase in the sensitivity of assemblage response. Indicator values (IndVals), computed for each taxon, showed that a number of arthropod taxa may have potential as bio-indicators of habitat change. However the use of many of these, especially many ant species found in our study, may be unreliable because even after extensive numbers of sites were sampled, most species showed patchy distributions. To overcome this problem, we generated ‘composite indices’, by combining information from sets of indicator taxa. The utility of these composite indices is discussed.     

Identifying functional species pool of planktonic protozoa for discriminating water quality status in marine ecosystems

It is cost-effective protocol to identify a functional species pool for marine bioassessment by removing redundant species from a raw dataset. The feasibility of functional species pool for discriminating water quality status was studied based on a dataset of 120 samples of ciliated protozoa. From the full 60-species dataset of the whole ciliate communities, a 35-species subset was identified as a functional species pool, the species number, abundance and biodiversity indices of which were significantly correlated with those of the full species dataset. The spatial pattern of the subset was significantly related to the changes in nutrients soluble reactive phosphates (SRP), nitrate/nitrite nitrogen (NO₃-N/NO₂-N) and ammonium nitrogen (NH₄-N). Four indices of the taxonomic diversity (Δ), taxonomic distinctness (Δ*), average in taxonomic distinctness (Δ⁺) and the variation in taxonomic distinctness (Λ⁺) based on this small species pool were significantly correlated with the changes of nutrients NO₃-N and/or (NH₄-N). The paired indices Δ⁺ and Λ⁺ showed a clear decreasing trend of departure from the expected taxonomic pattern. These findings suggest that the 35-species functional species subset may be used as a feasible functional surrogate of ciliated protozoan assemblages for community-based bioassessment in marine ecosystems.     

Bringing indices of species vulnerability to climate change into geographic space: an assessment across the Coronado national forest

Indices that rate the vulnerability of species to climate change in a given area are increasingly used to inform conservation and climate change adaptation strategies. These species vulnerability indices (SVI) are not commonly associated with landscape features that may affect local-scale vulnerability. To do so would increase their utility by allowing managers to examine how the distributions of vulnerable species coincide with environmental features such as topography and land use, and to detect landscape-scale patterns of vulnerability across species. In this study we evaluated 15 animal species that had been scored with the USDA-Forest Service Rocky Mountain Research Station’s system for assessing vulnerability of species to climate change. We applied the vulnerability scores to each species’ respective habitat models in order to visualize the spatial patterns of cross-species vulnerability across the biologically diverse Coronado national forest, and to identify the considerations of spatially referencing such indices. Across the study extent, cross-species vulnerability was higher in higher-elevation woodlands and lower in desert scrub. The results of spatially referencing SVI scores may vary according to the species examined, the area of interest, the selection of habitat models, and the method by which cross-species vulnerability indices are created. We show that it is simple and constructive to bring species vulnerability indices into geographic space: landscape-scale patterns of vulnerability can be detected, and relevant ecological and socioeconomic contexts can be taken into account, allowing for more robust conservation and management strategies.     

An assessment of scientific approaches towards species relocations in Australia

Species relocation programmes are increasingly performed with the intention of establishing a self‐sustaining population of threatened or declining native species. However, the use of experimental quantitative approaches in species relocation programmes is still relatively uncommon, despite a number of international studies recommending clear guidelines and standards. This paper evaluates species relocation programmes conducted within Australia to assess how programmes performed in relation to such standards. The search techniques identified 54 species relocation programmes, the majority of which were reintroductions (52%) and supplementations (30%). Only 25 (46%) of the species relocation programmes claimed success, with a lack of effective predator control recognized as contributing to the failure of 14 programmes. There was considerable variation in the quality of species relocation programmes in relation to key features such as whether the programme integrated experimental approaches with testable hypotheses, whether there were explicit statements of criteria for success, whether suitable habitat was identified for the release site and whether long‐term monitoring was conducted. We propose guidelines to improve scientific rigour and success rates of species relocation programmes.     

Can taxonomic distinctness assess anthropogenic impacts in inland waters? A case study from a Mediterranean river basin

1. It is increasingly recognised that adequate measures of biodiversity should include information on the ‘relatedness’ of species within ecological assemblages, or the phylogenetic levels at which diversity is expressed. Taxonomic distinctness measures provide a series of indices to achieve this, which are independent of sample size. Taxonomic distinctness has been employed widely in marine systems, where it has been suggested that this index can provide a reliable measure of anthropogenic impact. 2. We tested the behaviour of three related taxonomic distinctiveness indices (Average Taxonomic Distinctness, Δ⁺; Variation in Taxonomic Distinctness, Λ⁺; and Total Taxonomic Distinctness, sΔ⁺) in relation to putative levels of anthropogenic impact in inland waters and their potential utility in environmental monitoring, using an extensive data set for aquatic beetles from the south‐east of the Iberian Peninsula. 3. Taxonomic distinctness measures were not able to identify human disturbance effects and there were no clear relationships between these new biodiversity measures and the disturbance level recorded at individual localities. Furthermore, the taxonomic distinctness measures used were apparently less sensitive to the effects of anthropogenic impact than other diversity metrics, such as species richness and rarity. 4. We conclude that taxonomic distinctness indices may not always perform as well as other metrics in the assessment of environmental quality. In addition, taxonomic distinctness measure should be interpreted with caution, as their performance and ability to detect anthropogenic disturbance may depend on the phylogenetic structure of sampled taxa within a region, and their evolutionary and ecological history.     

Influence of taxonomic resolution on mutualistic network properties

1. Ecologists are increasingly interested in plant–pollinator networks that synthesize in a single object the species and the interactions linking them within their ecological context. Numerous indices have been developed to describe the structural properties and resilience of these networks, but currently, these indices are calculated for a network resolved to the species level, thus preventing the full exploitation of numerous datasets with a lower taxonomic resolution. Here, we used datasets from the literature to study whether taxonomic resolution has an impact on the properties of plant–pollinator networks.
2. For a set of 41 plant–pollinator networks from the literature, we calculated nine network index values at three different taxonomic resolutions: species, genus, and family. We used nine common indices assessing the structural properties or resilience of networks: nestedness (estimated using the nestedness index based on overlap and decreasing fill [NODF], weighted NODF, discrepancy [BR], and spectral radius [SR]), connectance, modularity, robustness to species loss, motifs frequencies, and normalized degree.
3. We observed that modifying the taxonomic resolution of these networks significantly changes the absolute values of the indices that describe their properties, except for the spectral radius and robustness. After the standardization of indices measuring nestedness with the Z‐score, three indices—NODF, BR, and SR for binary matrices—are not significantly different at different taxonomic resolutions. Finally, the relative values of all indices are strongly conserved at different taxonomic resolutions.
4. We conclude that it is possible to meaningfully estimate the properties of plant–pollinator interaction networks with a taxonomic resolution lower than the species level. We would advise using either the SR or robustness on untransformed data, or the NODF, discrepancy, or SR (for weighted networks only) on Z‐scores. Additionally, connectance and modularity can be compared between low taxonomic resolution networks using the rank instead of the absolute values.

     

The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland,Australia

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered ‘species’ of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.     

Assessing diversity in plant communities: The importance of within-species variation

While the measurement of plant species diversity continues to play a central role in ecology and conservation, few formal attempts have been made at defining the concept of diversity, and, specifically, at evaluating the utility of taxonomic species as units for diversity indices. Ecological diversity is defined here as a measure of the degree of biotic and/or abiotic dissimilitude within a community that is perceivable and utilizable by organisms. Although indices based merely on ‘species’ may be useful for cataloging taxonomic diversity in communities, plant taxa are generally unreliable units for quantifying the ecological diversity perceived and utilized by most organisms in communities. Recent research highlights the shortcomings of the unit of species for characterizing ecological diversity, and we advocate the further exploration of alternative diversity classes with which to describe plant communities.     

Changes in the taxonomic diversity of the reef fish community of San José Island, Gulf of California, Mexico

Although San José Island is considered one of the most important islands in the lower Gulf of California due to its commercial fishing activities, few studies have evaluated their fish taxonomic diversity. The aim of this study was to determine the variation in the taxonomic diversity of the conspicuous fish community in eight locations around San José Island from March 2001 to February 2002. We assessed the changes in the diversity of rocky reef fish based on the taxonomic distances between species, using Fisher’s alpha diversity index, average taxonomic distinctiveness (AvTD Δ+), and taxonomic distinctiveness (Δ*). Visual censuses were conducted in 48 transects consisting of 100?×?5?m quadrants (500?m² sampling area) at an average depth of 5?m, from 09:00 to 16:00. A total of 26,608 fishes belonging to 112 species and 76 genera were found. The index of relative abundance was used to determine the most important species, which were in order of abundance: Abudefduf troschelii, Thalassoma lucasanum, Stegastes rectifraenum, Mulloidichthys dentatus, Chromis atrilobata, Lutjanus argentiventris, and Scarus ghobban. According to Fisher’s alpha diversity index, the highest diversity of species was found in July and the lowest in February. The indices of Δ+ and Δ* indicated significant temporal and spatial differences.     

The Composition and Density of Epiphyton on Some Macrophyte Species in the Partly Meromictic Lake Verevi

In this paper, some important problems related to taxonomic resolution in water quality assessment by means of macroinvertebrates are discussed. Most quality indices based on macroinvertebrates only require identification up to genus or family level. Although this can be seen as a practical trade-off between taxonomic precision and time constraints and financial resources, it can result in biased assessment scores for certain stream types. An additional difficulty of identification levels other than species is caused by possible changes in taxonomy over time. A given genus may indeed have been split up into two or more genera or a species could be assigned to a different genus. These changes may alter biotic index values calculated over time, due to a change in number of taxa or replacement of one taxon by another one having a different tolerance class. An additional problem is caused by the invasion of exotic species. The genus Corbicula for instance is currently invading Belgian watercourses in increasing numbers. Since no Belgian Biotic Index (BBI) tolerance class is defined for Corbicula, this may cause inconsistencies in index calculations as well. In order to eliminate these, a semi-fixed taxa list, including a tolerance class for each taxon, for BBI calculation is proposed.     

Trait-based metrics as bioindicators: Responses of stream fish assemblages to a gradient of environmental degradation

The development of biomonitoring tools is increasingly appealing in light of the increasing degradation of aquatic ecosystems. In this context, we investigated the responses of stream fish communities to the gradient of environmental degradation in different basins using a variety of indices based on functional diversity, functional composition, and taxonomic diversity. We used datasets from three Brazilian ecoregions. In order to describe the gradient of environmental degradation we scored streams based on local and landscape variables. The functional structure of the assemblages was described in relation to seven functional traits related to habitat use, swimming capacity, and maneuverability. We described assemblages in each ecoregion separately in relation to 20 potential indicators, grouped in four families: indices of functional diversity based on presence/absence (FD_p/a); indices of functional diversity weighted by abundance (FD_abund); indices of functional composition (mT); and, indices based on taxonomic diversity (TDiv). The relationship between the indicators and the gradient of environmental degradation were evaluated using linear regression. We found a significant interaction effect (ANOVA, p = 0.006) between group of indices and ecoregions for the performance of indicators, suggesting a context-dependent response. The indices, on an individual basis, had variable performance and consistency among ecoregions. Four mT indicators demonstrated the highest average performance and consistency. Taxonomic diversity indicators consistently had the lowest average performance, while FD_p/a and FD_abund indicators had low average performance and variable inter-regional consistency. The differential inter-regional performance of indicators was due to the differences in the lengths of the gradients of environmental degradation. Our results indicate that functional traits have greater predictive power compared to taxonomic indicators for fish responses to a gradient of environmental degradation. Although indicators of functional composition are the most promising, we emphasize that caution is needed when generalizing functional diversity indicators across ecoregions because most of them are context-dependent.     

Assessment of Isolated Wetland Condition in Florida Using Epiphytic Diatoms at Genus, Species, and Subspecies Taxonomic Resolution

Diatoms are useful indicators of aquatic conditions, and metrics based on published autecological indicator values have been developed utilizing their sensitivities to various ambient physical and chemical conditions. The autecological values often differ within genera, and indeed within species taxonomic levels, requiring identification to subspecies taxonomic level for accurate application. This study was conducted to determine if autecological metrics, and ultimately indices of biotic integrity, could be developed using mean autecological values at the genus, species, and subspecies taxonomic levels, and to investigate the potential benefits of increased taxonomic resolution. Sixty-nine isolated herbaceous wetlands in various land use modalities in peninsular Florida were sampled a single time for epiphytic diatoms, and soil/water physicochemical parameters. Thirty genera, 148 species, and 26 subspecies were identified. The proportional matrices at each taxonomic level were highly similar (Mantel’s r > 0.75, P < 0.0001). Autecological metrics and two sensitive or tolerant measures were developed at each taxonomic level. Wetland condition, as determined by summed metric values, was strongly correlated across taxonomic level (r ² > 0.83, P < 0.0001), and no significant difference was found when sites were placed into bins of excellent, good, fair, or poor, based on quartile scoring, for each taxonomic level. Specific conductance, soil pH, soil and water total phosphorous, and water color were significantly related to site non-metric multidimensional scaling (NMDS) ordination scores at each taxonomic level. This study concludes that indices of biotic integrity, when developed using autecological indices, provide similar qualitative conditional information across taxonomic levels for isolated herbaceous wetlands. Electronic supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genome-Wide SNPs Clarify a Complex Radiation and Support Recognition of an Additional Cat Species

Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when postspeciation gene flow is present. Leopardus is a Neotropical cat genus that has a long history of recalcitrant taxonomic problems, along with both ancient and current episodes of interspecies admixture. Here, we employ genome-wide SNP data from all presently recognized Leopardus species, including several individuals from the tigrina complex (representing Leopardus guttulus and two distinct populations of Leopardus tigrinus), to investigate the evolutionary history of this genus. Our results reveal that the tigrina complex is paraphyletic, containing at least three distinct species. While one can be assigned to L. guttulus, the other two remain uncertain regarding their taxonomic assignment. Our findings indicate that the “tigrina” morphology may be plesiomorphic within this group, which has led to a longstanding taxonomic trend of lumping these poorly known felids into a single species.     

Messelogale, eine neue Raubtiergattung aus dem Mitteleozän von Messel (Deutschland)

Another juvenile specimen of the small carnivoranMiacis?kessleri Springhorn 1982 from the lower Middle Eocene oilshales (MP 11) of Messel near Darmstadt (South Hesse, Germany) is described. The nearly complete skeleton displays characteristics in dentition, skull, and limbs showing additional anatomical details and suggesting a taxonomic revision. Especially the assumption that there exist two molars only in the lower and upper jaw, as well as the trenchant talonid of the lower carnassial contradict the allocation to the genusMiacis. The species consequently is assigned to a new genusMesselogale. The higher taxonomic status of miacids in relation to the system of Carnivora is discussed.Messelogale kessleri shows basicranial characters, which indicate a classification within the Caniformia. On the other hand the loss of M3 suggests a relationship to the Feliformia. The species has an almost completely reduced (cf. holotype) or moderately well-developed dP³-Parastyl (this specimen), but it is not as enlarged as in primitive Feliformia, nor as reduced as in some Caniformia. Moreover, a calcaneal fibular facet cannot be excluded. Both attributes are representing the primitive morphology of the species. That does not ally the species with the Feliformia, but makes it, according toFlynn &; Galiano (1982), a very primitive Caniformia.     

Impact of Oreochromis niloticus (Linnaeus, 1758) (Pisces: Cichlidae) invasion on taxonomic and functional diversity of native fish species in the upper Kabompo River,northwest of Zambia

Invasive alien species have been revealed to drastically alter the structure of native communities; however, there is scarce information on whether taxonomic and functional spaces occupied by native species are equally filled by exotic species. We investigated the diversity of native species to understand the impact of exotic Oreochromis niloticus in the upper Kabompo River, northwest of Zambia using taxonomic and functional diversity indices. To achieve this, two tests were performed (Test 1, compared natives in invaded and uninvaded sections; Test 2, compared natives in invaded section). A total of 17 species were collected for functional diversity computation, out of which fourteen (14) functional trait measurements linked to feeding, locomotion, and life history strategy were taken. Findings revealed that taxonomic and functional diversity values changed with invasion in both tests. Taxonomic diversity was 15% more in invaded than uninvaded sections in Test 1 and was not consistent across sampling points of invaded section in Test 2. Invaded areas were taxonomically less diverse, but functionally diverse in both tests. The analysis of similarity and nonmetric multidimensional scaling revealed no difference in Bray–Curtis similarity assemblages in both tests. Our findings revealed that exotic species more often occupy unfilled gaps in the communities often occupied by the native species; this is achieved by occupying functional spaces. Overall, changes in taxonomic and functional diversity of native species documented here partially confirmed impacts of O. niloticus invasion. Therefore, we recommend a multifaceted approach to assess cumulative impacts of invasion on native species.