Are diatom-based biotic indices developed in eutrophic,organically enriched waters reliable monitoring metrics in clean waters?

The application of diatom indices developed for organically enriched and eutrophic waters in oligotrophic and relatively pristine streams in the Eastern Highlands of Zimbabwe was investigated based on data collected in May–August 2007. Better suitability of diatom indices in investigating the quality of eutrophic, organically enriched waters compared to oligotrophic waters is demonstrated. More robust data sets on taxonomy and autecology of a great number of diatom species are required to make the indices more powerful tools in monitoring water quality and ecological integrity of streams in the region.     

Are landscape-based wetland condition indices reflected by invertebrate and diatom communities?

Assessments of wetland condition are generally based on measures of variables related to plants or large animals (birds, fish), and catchment or landscape features. This approach ignores the considerable biodiversity and functional values of small aquatic organisms. The aim of this study was to assess the correspondence between landscape-based indices of wetland condition and the community composition of both aquatic invertebrates and diatoms across a broad range of wetlands in the West Coast region of New Zealand. Aquatic invertebrates and diatoms were sampled from 29 lowland wetlands subject to varying degrees of catchment modification. Wetland condition was assessed independently using two methods: a field-based method to give the Wetland Condition Index, and a GIS-based method that gave an Index of Ecological Integrity. Strong relationships existed between community composition and pH, so we partitioned the community data into groups according to wetland pH. We found only weak relationships between wetland condition scores and invertebrate and diatom communities within each pH group. In most cases, data describing the nutrient status of the water had the strongest influence on invertebrate and diatom communities. Lack of strong associations between measured wetland condition indices and either diatom or invertebrate community composition suggests that neither index was dominated by variables directly influencing the aquatic component of wetland biota. The challenges now are to identify the critical variables, and to develop complementary wetland scoring systems that better reflect the status of small aquatic organisms.     

Are protected areas maintaining bird diversity?

Evaluating the effectiveness of protected areas for sustaining biodiversity is crucial to achieving conservation outcomes. While studies of effectiveness have improved our understanding of protected‐area design and management, few investigations (< 5%) have quantified the ecological performance of reserves for conserving species. Here, we present an empirical evaluation of protected‐area effectiveness using long‐term measures of a vulnerable assemblage of species. We compare forest and woodland bird diversity in the Australian Capital Territory over 11 yr on protected and unprotected areas located in temperate eucalypt woodland and matched by key habitat attributes. We examine separately the response of birds to protected areas established prior to 1995 and after 1995 when fundamental changes were made to regional conservation policy. Bird diversity was measured in richness, occurrence of vulnerable species, individual species trajectories and functional trait groups. We found that protected areas were effective in maintaining woody vegetation cover in the study region, but were less effective in the protection of the target bird species assemblage. Protected areas were less species rich than unprotected areas, with significant declines in richness across sites protected prior to 1995. Small, specialised and vulnerable species showed stronger associations with unprotected areas than protected areas. Our findings indicate that recently established reserves (post‐1995) are performing similarly to unprotected woodland areas in terms of maintaining woodland bird diversity, and that both of these areas are more effective in the conservation of woodland bird populations than reserves established prior to 1995. We demonstrate that the conservation value of protected areas is strongly influenced by the physical characteristics, as well as the landscape context, of a given reserve and can diminish with changes in surrounding land use over time. Both protected areas and off‐reserve conservation schemes have important roles to play in securing species populations.     

Are viruses driving microbial diversification and diversity?

Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change.     

Are classification and phytopathological diversity compatible in Xanthomonas?

The genus Xanthomonas is characterized by its phytopathogenic diversity and the host specificity of its members. In the past, the classification of the members of this genus has been based primarily on the criterion of host specificity. This has led to a classification system which focused only on naming phytopathogenic variants on different hosts. Extensive taxonomic examination of Xanthomonas has shown that the phytopathogenic specialization of the bacteria is not correlated with the actual relationships within the genus. Based upon total genomic DNA homology, the genus has been reclassified into 20 species. At present, non-pathogenic xanthomonads are frequently isolated from plant material. As these strains often cannot be classified to existing species, it becomes clear that the diversity of the genus is much greater than expected from the phytopathogenic subpopulation, which has been the primary subject in the past. The example of Xanthomonas also illustrates that attempts to divide bacterial populations into discrete taxa conflict with the actual continuous nature of biodiversity. Received 16 April 1996/ Accepted in revised form 27 September 1996     

Are alien fish a reliable indicator of river health?

1. The ability of many introduced fish species to thrive in degraded aquatic habitats and their potential to impact on aquatic ecosystem structure and function suggest that introduced fish may represent both a symptom and a cause of decline in river health and the integrity of native aquatic communities. 2. The varying sensitivities of many commonly introduced fish species to degraded stream conditions, the mechanism and reason for their introduction and the differential susceptibility of local stream habitats to invasion because of the environmental and biological characteristics of the receiving water body, are all confounding factors that may obscure the interpretation of patterns of introduced fish species distribution and abundance and therefore their reliability as indicators of river health. 3. In the present study, we address the question of whether alien fish (i.e. those species introduced from other countries) are a reliable indicator of the health of streams and rivers in south‐eastern Queensland, Australia. We examine the relationships of alien fish species distributions and indices of abundance and biomass with the natural environmental features, the biotic characteristics of the local native fish assemblages and indicators of anthropogenic disturbance at a large number of sites subject to varying sources and intensities of human impact. 4. Alien fish species were found to be widespread and often abundant in south‐eastern Queensland rivers and streams, and the five species collected were considered to be relatively tolerant to river degradation, making them good candidate indicators of river health. Variation in alien species indices was unrelated to the size of the study sites, the sampling effort expended or natural environmental gradients. The biological resistance of the native fish fauna was not concluded to be an important factor mediating invasion success by alien species. Variation in alien fish indices was, however, strongly related to indicators of disturbance intensity describing local in‐stream habitat and riparian degradation, water quality and surrounding land use, particularly the amount of urban development in the catchment. 5. Potential confounding factors that may influence the likelihood of introduction and successful establishment of an alien species and the implications of these factors for river bioassessment are discussed. We conclude that the potentially strong impact that many alien fish species can have on the biological integrity of natural aquatic ecosystems, together with their potential to be used as an initial basis to find out other forms of human disturbance impacts, suggest that some alien species (particularly species from the family Poeciliidae) can represent a reliable ‘first cut’ indicator of river health.     

Are we selecting appropriate metrics to assess human impacts on biodiversity?

Biased and subjective choices of metrics to be used in ecological studies could lead researchers to reach misleading conclusions regarding patterns of biodiversity response to human disturbances. Nevertheless, little attention has been given to the choices of variables in the majority of studies published to date. Here, we used the literature concerning land use change effects on dung beetles to assess the extent to which variables commonly employed in ecological studies correspond to those deemed to be most important by researchers of the same studies. Specifically, we examined both biodiversity (response) and environmental (explanatory) metrics from a comprehensive literature review and compared their use with their relative importance, according to a survey of the authors of the studies. Our results highlight marked disparities between researchers opinion expressed in our survey and their choice of variables in published papers. We suggest that these disparities are due to the high costs of sampling and processing some variables, logistical constraints and different perceptions of importance amongst researchers. We highlight the importance of these issues for our understanding of the biodiversity consequences of land use change, and highlight some recommendations for alleviating this issue.     

Are mapped markers more useful for assessing genetic diversity?

Genetic diversity within populations of organisms and species is commonly measured using molecular-marker data. It has been claimed that more reliable diversity measurements can be obtained using selected genetically mapped markers to ensure that all regions of the genome are represented in the data sets employed. However, this has not been tested. In the present study, using rice (Oryza sativa L.) as a model species, we have shown that the use of unmapped AFLP markers reveals a pattern of diversity that is very similar to that obtained using a range of other marker types and which reflects the known crossability groups within this species. In contrast, we show that use of mapped-marker data can, in some cases, result in highly misleading patterns of diversity; the results obtained are critically related to the choice ofparents used in the cross from which the mapping population was produced. For diversity analyses, we propose that it is appropriate to use unmapped markers provided that the marker-type has been shown to have a wide distribution over the genome. Received: 13 November 1998 / Accepted: 17 June 1999     

Developing a monitoring program of genetic diversity: what do stakeholders say?

Conservation Genetics - Genetic diversity is a fundamental component of biological diversity, and its conservation is considered key to ensure the long-term survival of natural populations and...     

Are fingernail lead levels a reliable biomarker of lead internal dose?

BackgroundPotentially toxic elements, such as lead, can bioaccumulate and alter human physiology. Human biomonitoring is an essential tool to evaluate chemical exposures in different biological matrices (blood, urine, saliva, nails, and hair). Of these biological matrices, nails are favorable for their ease of sampling, transport and storage. The aim of this study was to investigate possible correlations between blood lead levels (BLL) and washed and non-washed fingernail lead levels (FLL) in 55 adults living in a lead-contaminated area.MethodVenous blood and fingernail (thumbs and forefingers) samples were collected. Nails from the left hand were washed with Triton X-100 (0.5 % m/v) and HNO₃ solution, while nails from the right hand were not submitted to the pre-analytical procedures. Samples were analyzed by graphite furnace atomic absorption spectrometry, and pairwise correlations were used to correlate lead concentrations between BLL and FLL; nails from fingers of the same hand and between washed and unwashed fingernails. Principal component analysis was performed and scatter diagrams were plotted to investigate correlations.ResultsA non-significant positive correlation was found between BLL and washed forefinger nails lead (r = 0.219, p = 0.112) and between BLL and thumbnail lead levels (r = 0.182, p = 0.191). Comparison of fingernails from the same hand (thumb and forefinger), showed that lead concentrations of non-washed nails varied widely, even on analyses of transversal fragments from the same nail. Lead levels in non-washed forefinger nails were not correlated with non-washed thumbnails (r = 0.169, p = 0.219). Conversely, washed thumb and forefinger nails were found to be correlated (r = 0.39, p = 0.003). Washed and non-washed nails were also found to be correlated (p < 0.0001).ConclusionIn conclusion, the results showed that non-washed nails are not a reliable biomarker for lead exposure. Although washing nails before analysis may reduce external contamination, the correlation of lead concentrations between fingers is poor for fingernail lead levels to serve as an internal dose biomarker to lead exposure. In addition, levels in washed nails were not significantly correlated with blood lead levels. Fingernail lead levels seem to serve as an indicator of lead exposure sources in contact with the individual, but not as a reliable biomarker of internal dose.     

Are we ready for therapeutic drug monitoring of biologic therapeutics?

In the previous issue of Arthritis Research & Therapy, Ducourau and colleagues report that they retrospectively detected anti-infliximab antibodies in 21% of patients with rheumatic diseases. Patients with anti-infliximab antibodies had lower serum drug concentrations. These findings contribute to the existing evidence of immunogenicity of biologicals and its clinical relevance. We argue for therapeutic drug monitoring to optimize treatment response.     

Are local patterns of anthropoid primate diversity related to patterns of diversity at a larger scale?

Aims (1) To determine the relationship between local and regional anthropoid primate species richness. (2) To establish the spatial and temporal scale at which the ultimate processes influencing patterns of primate species coexistence operate. Location Continental landmasses of Africa, South America and Asia (India to China, and all islands as far south as New Guinea). Methods The local–regional species richness relationship for anthropoid primates is estimated by regressing local richness against regional richness (independent variable). Local richness is estimated in small, replicate local assemblages sampled in regions that vary in total species richness. A strong linear relationship is taken as evidence that local assemblages are unsaturated and local richness results from proportional sampling of the regional pool. An asymptotic curvilinear relationship is interpreted to reflect saturated communities, where strong biotic interactions limit local richness and local processes structure the species assemblage. As a further test of the assumption of local assemblage saturation, we looked for density compensation in high‐density local primate assemblages. Results The local–regional species richness relationship was linear for Africa and South America, and the slope of the relationship did not differ between the two continents. For Asia, curvilinearity best described the relationship between local and regional richness. Asian primate assemblages appear to be saturated and this is confirmed by density compensation among Asian primates. However, density compensation was also observed among African primates. The apparent assemblage saturation in Asia is not a species–area phenomenon related to the small size of the isolated islands and their forest blocks, since similar low local species richness occurs in large forests on mainland and/or peninsular Asia. Main conclusions In Africa and South America local primate assemblage composition appears to reflect the influence of biogeographic processes operating on regional spatial scales and historical time scales. In Asia the composition of primate assemblages are by‐and‐large subject to ecological constraint operating over a relatively small spatial and temporal scale. The possible local influence of the El Niño Southern Oscillations on the evolution and selection of life‐history characteristics among Asian primates, and in determining local patterns of primate species coexistence, warrants closer inspection.     

Are morphometric indices accurate indicators of stored energy in herring Clupea harengus?

The accuracy of the morphometric indices Fulton's K, somatic K and relative condition factor, K_n, as measures of individual North Sea herring Clupea harengus muscle fat content was investigated using the Distell Fish Fat meter. The accuracy of fat‐meter readings from an individual fish was validated by comparison with Soxhlet extraction analysis. The studies conducted demonstrated that Fulton's K is not consistently or strongly correlated with individual C. harengus muscle fat content, as defined by the fat‐meter estimates. The study shows that somatic K and K_n may be better indices of individual North Sea C. harengus muscle fat content than Fulton's K. These morphometric indices, however, should only be used after prior validation against a more direct measure of fat content.     

How reliable is the monitoring of permanent vegetation plots? A test with multiple observers

Questions: A multiple plot design was developed for permanent vegetation plots. How reliable are the different methods used in this design and which changes can we measure? Location: Alpine meadows (2430 m a.s.l.) in the Swiss Alps. Methods: Four inventories were obtained from 40 m² plots: four subplots (0.4 m²) with a list of species, two 10m transects with the point method (50 points on each), one subplot (4m²) with a list of species and visual cover estimates as a percentage and the complete plot (40 m²) with a list of species and visual estimates in classes. This design was tested by five to seven experienced botanists in three plots. Results: Whatever the sampling size, only 45‐63% of the species were seen by all the observers. However, the majority of the overlooked species had cover < 0.1%. Pairs of observers overlooked 10‐20% less species than single observers. The point method was the best method for cover estimate, but it took much longer than visual cover estimates, and 100 points allowed for the monitoring of only a very limited number of species. The visual estimate as a percentage was more precise than classes. Working in pairs did not improve the estimates, but one botanist repeating the survey is more reliable than a succession of different observers. Conclusion: Lists of species are insufficient for monitoring. It is necessary to add cover estimates to allow for subsequent interpretations in spite of the overlooked species. The choice of the method depends on the available resources: the point method is time consuming but gives precise data for a limited number of species, while visual estimates are quick but allow for recording only large changes in cover. Constant pairs of observers improve the reliability of the records.     

Are we ready to detect nematode diversity by next generation sequencing?

In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439–1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful implementation of NGS for environmental DNA analysis of nematodes. Here, we describe the method's limitations and discuss prospective research questions. For instance, only a few direct extraction kits are suitable for nematode DNA extraction from bulk samples without adaptation. They enable the analysis of extracellular nematode DNA. The most crucial and unresolved issue remains the limited availability of suitable primers.     

Evaluating new technology for biodiversity monitoring: Are drone surveys biased?

Drones and machine learning‐based automated detection methods are being used by ecologists to conduct wildlife surveys with increasing frequency. When traditional survey methods have been evaluated, a range of factors have been found to influence detection probabilities, including individual differences among conspecific animals, which can thus introduce biases into survey counts. There has been no such evaluation of drone‐based surveys using automated detection in a natural setting. This is important to establish since any biases in counts made using these methods will need to be accounted for, to provide accurate data and improve decision‐making for threatened species. In this study, a rare opportunity to survey a ground‐truthed, individually marked population of 48 koalas in their natural habitat allowed for direct comparison of the factors impacting detection probability in both ground observation and drone surveys with manual and automated detection. We found that sex and host tree preferences impacted detection in ground surveys and in manual analysis of drone imagery with female koalas likely to be under‐represented, and koalas higher in taller trees detected less frequently when present. Tree species composition of a forest stand also impacted on detections. In contrast, none of these factors impacted on automated detection. This suggests that the combination of drone‐captured imagery and machine learning does not suffer from the same biases that affect conventional ground surveys. This provides further evidence that drones and machine learning are promising tools for gathering reliable detection data to better inform the management of threatened populations.