A methodological approach to the use of terrestrial invertebrates for the assessment of alluvial wetlands

We review progress toward developing a data-analysis system using invertebrate species lists in wetland evaluation procedures. Species lists for Mollusca, Carabidae (Coleoptera), Empidoidea and Syrphidae (Diptera), derived from samples collected at six stations along a transect established at a site on the floodplain of the River Loire (France) provide the raw data. An initial analysis using a traditional ordination method (Correspondence Analysis) is carried out. A data base was established for the 118 mollusc, carabid and syrphid species recorded, and each species was then treated not as a simple integer, but as an amalgam of digitised attributes deemed responsive to wetland conditions, in a correspondence analysis on instrumental variables. Despite the generalized nature of the attributes as defined for this example, the approach demonstrates a marked increase in interpretability of the output of analysis, in respect of the relation between the species and the floodplain environment. It also highlights the value of use of data pertaining to more than one taxonomic group and of selecting these taxonomic groups on the basis of complementarity of their bioindicator potential.Corresponding Editor: J.T.A. Verhoeven     

Metallothioneins in terrestrial invertebrates: structural aspects, biological significance and implications for their use as biomarkers.

During the last few years the subject of metallothioneins (MTs) in terrestrial invertebrates has gained increasing attention. One reason for this may be that terrestrial invertebrates provide new insights into the biological diversity of MTs, with the potential of discovering alternative models of structural and functional relationships. Four groups of terrestrial invertebrates have been studied in detail, namely nematodes, insects, snails and earthworms, with the present article focusing on MTs from the latter two groups. Snails are interesting because they possess distinct MT isoforms involved in different metal-specific tasks. In the Roman snail (Helix pomatia), for example, one isoform is predominantly expressed in the midgut gland, accounting for the accumulation, binding and detoxification of cadmium. The second isoform, which is present in the snail's mantle, is substantially different regarding its primary structure. Furthermore, it binds nearly exclusively copper, and thus is probably involved in the homeostatic regulation of essential trace elements. Earthworm MTs merit our attention because of another peculiarity: they seem to be much more unstable than snail MTs, particularly under conventional conditions of preparation. The cDNA of the brandling worm (Eisenia foetida), for instance, codes for a putative MT, which is about twice the size of the actual protein. The isolated MT peptide binds four Cd2+ ions and represents a one-domain MT entity that is stable and functional in vitro. This strongly suggests that earthworm MTs are either posttranslationally modified, or subjected to enzymatic cleavage during preparation. Both snail and earthworm MTs are inducible by metal exposure, especially by cadmium, thus supporting the idea of using them as potential biomarkers for environmental metal pollution. Whilst snail MTs have already been tested in this respect with some success, the use of earthworm MTs as biomarkers still remains to be evaluated, especially in the light of the unknown significance of their posttranslational instability.     

Overlapping genes as rare genomic markers: the phylogeny of gamma-Proteobacteria as a case study

Phylogenies can be constructed in many ways, including using shared complex characters known as rare genomic changes (RGCs), such as insertions and deletions (indels), retroposon integrations and intron positions. Here, we demonstrate that distance-based phylogenies, which were determined by shared overlapping genes from 13 completely sequenced gamma-Proteobacteria genomes, are consistent with phylogenies based on 16S rRNAs and other robust markers. These findings suggest that overlapping genes could provide interesting additional insights into the phylogenomics of completely sequenced microbial genomes.     

Using mitochondrial and nuclear sequence data for disentangling population structure in complex pest species: a case study with Dermanyssus gallinae

Among global changes induced by human activities, association of breakdown of geographical barriers and impoverishered biodiversity of agroecosystems may have a strong evolutionary impact on pest species. As a consequence of trade networks' expansion, secondary contacts between incipient species, if hybrid incompatibility is not yet reached, may result in hybrid swarms, even more when empty niches are available as usual in crop fields and farms. By providing important sources of genetic novelty for organisms to adapt in changing environments, hybridization may be strongly involved in the emergence of invasive populations. Because national and international trade networks offered multiple hybridization opportunities during the previous and current centuries, population structure of many pest species is expected to be the most intricate and its inference often blurred when using fast-evolving markers. Here we show that mito-nuclear sequence datasets may be the most helpful in disentangling successive layers of admixture in the composition of pest populations. As a model we used D. gallinae s. l., a mesostigmatid mite complex of two species primarily parasitizing birds, namely D. gallinae L1 and D. gallinae s. str. The latter is a pest species, considered invading layer farms in Brazil. The structure of the pest as represented by isolates from both wild and domestic birds, from European (with a focus on France), Australian and Brazilian farms, revealed past hybridization events and very recent contact between deeply divergent lineages. The role of wild birds in the dissemination of mites appears to be null in European and Australian farms, but not in Brazilian ones. In French farms, some recent secondary contact is obviously consecutive to trade flows. Scenarios of populations' history were established, showing five different combinations of more or less dramatic bottlenecks and founder events, nearly interspecific hybridizations and recent population mixing within D. gallinae s. str.     

A multinomial model for estimating the size of a whale population from incomplete census data

This paper adapts the removal method of population size estimation to the problem of estimating the size of the western Arctic stock of bowhead whales. The whales are counted during their spring migration as they pass two census camps located near Point Barrow, Alaska. Whales seen at the first camp are "removed" from the population of concern to the second camp, where only whales missed by the first camp are counted. If both camps were in operation throughout the migration and if the probability of missing a whale were constant, the removal method would provide a population size estimate based on a trinomial model in which the size of the population would be the number of trials, whales counted by each camp would provide the observed cell totals, and whales missed by both camps would represent an unobserved cell total. Since the probability of missing a whale depends on visibility, we model the population size as the sum of the number of trials of several independent trinomial distributions, each of which represents a particular visibility condition occurring during the census. To account for the fact that watch cannot be maintained at both camps throughout the migration, we derive a confidence interval estimate of the number of trials under a more general model allowing for incomplete observation of totals within particular cells as well as for completely unobserved cells.     

Management of drug resistance in the population: influenza as a case study

The rise of drug resistance remains a major impediment to the treatment of some diseases caused by fast-evolving pathogens that undergo genetic mutations. Models describing the within-host infectious dynamics suggest that the resistance is unlikely to emerge if the pathogen-specific immune responses are maintained above a certain threshold during therapy. However, emergence of resistance in the population involves both within-host and between-host infection mechanisms. Here, we employ a mathematical model to identify an effective treatment strategy for the management of drug resistance in the population. We show that, in the absence of pre-existing immunity, the population-wide spread of drug-resistant pathogen strains can be averted if a sizable portion of susceptible hosts is depleted before drugs are used on a large scale. The findings, based on simulations for influenza infection as a case study, suggest that the initial prevalence of the drug-sensitive strain under low pressure of drugs, followed by a timely implementation of intensive treatment, can minimize the total number of infections while preventing outbreaks of drug-resistant infections.     

Dispersal of freshwater invertebrates by large terrestrial mammals: a case study with wild boar (Sus scrofa) in Mediterranean wetlands

1. Many invertebrates inhabiting insular aquatic habitats rely on external agents or vectors to disperse. Besides water connections and wind, waterfowl and amphibians are known to mediate passive dispersal of freshwater invertebrates. However, the possibility of dispersal by terrestrial mammals has been largely overlooked. 2. We investigated the potential of both external and internal zoochorous dispersal of aquatic invertebrates by the wild boar (Sus scrofa) in Mediterranean wetlands in the Camargue (France). As wild boar frequently visit wetlands for feeding and wallowing purposes, we hypothesized that they may be important passive dispersal vectors of aquatic invertebrates at a local scale. Dried mud was collected from selected ‘rubbing trees’ used by boars to dispose of parasites. Additionally, faecal pellets were collected from different locations in the wetland area. 3. Seventeen freshwater invertebrate taxa including rotifers, cladocerans, copepods and ostracods hatched from sediment obtained from ‘rubbing trees’, while invertebrates hatching from dried faeces (10 taxa) were mainly rotifers. Dispersing invertebrates were collected up to 318 m from a nearest potential dispersal source. Both abundance and richness of invertebrates significantly decreased with dispersal distance. 4. Our results demonstrate that large mammals such as wild boar can act as dispersal vectors of aquatic invertebrates at a local scale in the wetland area of the Camargue and suggest that external transport may be quantitatively more important than internal transport. As wallowing (mud bathing) is common in many terrestrial mammals, this mode of dispersal may be quite widespread.     

Microsatellite size homoplasy, SSCP, and population structure: a case study in the freshwater snail Bulinus truncatus

The extent of microsatellite size homoplasy, as well as its effect on several population genetics statistics, was investigated in natural populations using the single-strand conformation polymorphism (SSCP) method. The analysis was conducted using 240 individuals from 13 populations of the freshwater snail Bulinus truncatus at a GT(n)CT(m) compound microsatellite locus. We showed that SSCP can be used to uncover, at least partly, size homoplasy in the core sequence of this category of loci. Eight conformers (SSCP variants) were detected among the three size variants (electromorphs). Sequencing revealed that each conformer corresponded to a different combination of repeats in the GT(n) and CT(m) arrays. Part of this additional variability was detected within populations, resulting in a substantial increase in gene diversity in four populations. Additional variability also changed the values of parameters used to analyze population differentiation among populations: pairwise tests of differentiation were significant much more often with conformers than with electromorphs. On the other hand, pairwise estimates of F(st) were either smaller or larger with conformers than with electromorphs, depending on whether or not electromorphs were shared among populations. However, estimates of F(st) (or analogs) over all populations were very similar, ranging between 0.66 and 0.75. Our results were consistent with the theoretical prediction that homoplasy should not always lead to stronger population structure. Finally, conformer sequences and electromorph size distribution suggested that single-point and/or stepwise mutations occurring simultaneously in the different repeated arrays of compound microsatellites produce sequence variation without size variation and hence generate more size homoplasy than expected under a simple stepwise mutation model.     

Cyberinfrastructure for the analysis of ecological acoustic sensor data: a use case study in grid deployment

The LTER Grid Pilot Study was conducted by the National Center for Supercomputing Applications, the University of New Mexico, and Michigan State University, to design and build a prototype grid for the ecological community. The featured grid application, the Biophony Grid Portal, manages acoustic data from field sensors and allows researchers to conduct real-time digital signal processing analysis on high-performance systems via a web-based portal. Important characteristics addressed during the study include the management, access, and analysis of a large set of field collected acoustic observations from microphone sensors, single signon, and data provenance. During the development phase of this project, new features were added to standard grid middleware software and have already been successfully leveraged by other, unrelated grid projects. This paper provides an overview of the Biophony Grid Portal application and requirements, discusses considerations regarding grid architecture and design, details the technical implementation, and summarizes key experiences and lessons learned that are generally applicable to all developers and administrators in a grid environment.     

Using habitat suitability models to sample rare species in high-altitude ecosystems: a case study with Tibetan argali

Models of the distribution of rare and endangered species are important tools for their monitoring and management. Presence data used to build up distribution models can be based on simple random sampling, but this for patchy distributed species results in small number of presences and therefore low precision. Convenience sampling, either based on easily accessible units or a priori knowledge of the species habitat but with no known probability of sampling each unit, is likely to result in biased estimates. Stratified random sampling, with strata defined using habitat suitability models [estimated in the resource selection functions (RSFs) framework] is a promising approach for improving the precision of model parameters. We used this approach to sample the Tibetan argali (Ovis ammon hodgsoni) in Indian Transhimalaya in order to estimate their distribution and to test if it can lead to a significant reduction in survey effort compared to random sampling. We first used an initial sample of argali feeding sites in 2005 and 2006 based on a priori selected vantage points and survey transects. This initial sample was used to build up an initial distribution model. The spatial predictions based on estimated RSFs were then used to define three strata of the study area. The strata were randomly sampled in 2007. As expected, much more presences per hour were obtained in the high quality strata compared to the low quality strata—1.33 obs/h vs. 0.080/h. Furthermore the best models selected on the basis of the prospective sample differed from those using the first a priori sample, suggesting bias in the initial sampling effort. The method therefore has significant implications for decreasing sampling effort in terms of sampling time in the field, especially when dealing with rare species, and removing initial sampling bias.     

Hydraulic requirements of stream communities: a case study on invertebrates

1. We relate invertebrate assemblages to direct measurements of near‐bed hydraulic conditions that integrate the complex three‐dimensional structure of flow close to the bottom. 2. We sampled invertebrate taxa from a Mediterranean River along a spatial gradient of increasing shear stress in two seasons (spring and autumn) with different hydrological conditions. We used a recently described ordination technique, Outlying Mean Index (OMI) analysis, to study the response of stream invertebrates to near‐bed hydraulic parameters. 3. The distribution of nearly 70% of the taxa collected was significantly related to the hydraulic parameters assessed. In both seasons, shear stress and Froude number were the most important hydraulic parameters whereas substratum particle size and bed roughness had less influence. Most of the 31 taxa collected in both seasons had a higher OMI (an index showing the deviation between the mean environmental conditions used by a taxon and the mean environmental conditions used by a theoretical taxon uniformly distributed across the studied gradient) in autumn (when flow was greater) and were found in samples with high shear stress and high Froude number. This suggests that benthic invertebrates changed their preferences according to flow conditions. 4. Taxon richness declined with increased shear stress during lower flow in spring. Finally, and agreeing with previous results, the proportion of filter feeders and collector‐gatherers was inversely related to shear stress. 5. Our results are a first step towards better habitat suitability models that could inform management decisions.     

Large gryphaeid oysters as habitats for numerous sclerobionts: a case study from the northern Red Sea

The shell of a living specimen of the Indo-Pacific gryphaeid giant oyster Hyotissa hyotis was colonized by numerous encrusting, boring, nestling and baffling taxa which show characteristic distribution patterns. On the upper valve, sponge-induced bioerosion predominates. On the lower valve intergrowth of chamid bivalves and thick encrusting associations—consisting mostly of squamariacean and corallinacean red algae, acervulinid foraminifera, and scleractinian corals—provides numerous microhabitats for nestling arcid and mytilid bivalves as well as for encrusting bryozoans and serpulids. Such differences between exposed and cryptic surfaces are typical for many marine hard substrata and result from the long-term stable position of the oyster on the seafloor. The cryptic habitats support a species assemblage of crustose algae and foraminifera that, on exposed surfaces, would occur in much deeper water.     

Using three-dimensional kinematics to identify feedback for the Snatch: a case study

This case study evaluated the importance of peak bar velocity and starting posture adopted by a novice weightlifter to the outcome of a Snatch lift. Multiple observations of both successful and unsuccessful attempts were captured using 3D motion analysis (VICON MX: 500 Hz). The following data analysis was then used to derive feedback. In total, 133 attempts of loads ranging from 75 to 100% of 1 repetition maximum (1RM) were performed by the subject (age = 25 years, stature = 171 cm, mass = 74.8 kg, Snatch 1RM = 80 kg). Variables included peak bar velocity, pelvis, hip, knee and ankle joint angles at the starting position for the right side and the difference between (left minus right) sides. No main effects for load, success, or their interactions were found for peak bar velocity. Starting position kinematics were mostly nonsignificant between the outcome of Snatch attempts. Right ankle joint angle was the only exception, where unsuccessful attempts displayed greater (p = 0.0228) dorsiflexion. A more comprehensive finding was achieved through the partition modeling; this analysis provided valuable insight and coaching feedback for the subject in relation to his lower body kinematics at the starting position. Furthermore, the accuracy of this feedback was verified using a holdback data set. Specifically, anterior pelvic tilt (>17.6°) and hip joint (<89.6°) angle were identified as the key features to increasing the likelihood of success. In conclusion, this case study outlines a method of data collection and analysis to assist coaching feedback for an individual.     

Immune response and virus population composition: HIV as a case study

Based on the current understanding of the immune response, we present what we believe to be a new model of intrahost virus dynamics. The model takes into account the relationship between virus replication rate and the level of antigen displayed by infected cells, and shows how the cell-directed immune response controls both virus load and virus replication rate. In contrast to conventional wisdom, it shows that the predominant virus variant does not necessarily have the highest replication rate. A strong immune response produces a selective advantage for latent viruses, whereas a deteriorating immune response invites in viruses of higher replication rates. The model is analysed in light of the well-studied HIV/AIDS disease progression, and shows how a wide range of major, seemingly unrelated issues in the study of HIV may be accounted for in a simple and unified manner.     

Using surrogate data in population viability analysis: the case of the critically endangered cranberry fritillary butterfly

Population viability analyses (PVA) are central tools for the management of threatened populations. However, the parameterisation of effective PVA models is very demanding in high quality data, which are often impossible to collect on endangered populations. Here we propose the use of a generalisation strategy to bypass this limitation: management measures for an endangered metapopulation of the cranberry fritillary butterfly in the Netherlands are evaluated with RAMAS/GIS by using parameters estimated from a healthier metapopulation in Belgium. The Belgian metapopulation seems viable, with stable abundance and number of local populations, despite their erratic dynamics, whereas the Dutch metapopulation shows a continuous decline in the course of time, with many vacant habitat patches. Simulations of various scenarios indicated that (1) large scale restoration of habitat patches would be necessary to ensure long-term survival of the species in the Netherlands as not enough suitable habitats are currently remaining; and that (2) global warming is expected to put a major threat on both metapopulations by reducing the growth rate of this glacial relict species, and/or increasing environmental stochasticity (amplified climatic variations).     

The use of chemical composition as a population marker in insects: a study of the Brimstone butterfly

ABSTRACT.

• 1 The elemental composition of 249 adult Brimstone butterflies (Gonepteryx rhamni L.) was studied by wavelength dispersive X-ray fluorescence spectrometry, to determine whether site/population-specific differences could be detected. The chemical elements studied were K, Ca, Fe, Cu, Zn, Ti, P, CI and S.
• 2 Marked differences were found in the chemical composition of the two sexes, and between individuals caught on different sites and in different years and seasons.
• 3 Multivariate analyses of the data using principal component analysis and canonical variate analysis showed a clear separation of the butterflies by sex, and within each sex, by seasons. Of the elements studied, the main discriminating ones for this butterfly were K, Ca, P, Zn, CI and S.
• 4 Whilst differences in chemical composition appear to result from variations in the composition of soil and food-plants in different localities, any site/population-specific differences are soon masked by the passage of time, as adults age and feed. This makes the technique of limited value in the study of dispersal in this species.

     

Fungi as a source of marker compounds for the control of illicit use of drugs: mesterolone as a case study

Introduction

Anabolic steroids are frequently misused for performance enhancement during sports competitions. One of the major bottlenecks in the confident analysis of steroids and their metabolites is the non-availability/cost of standard reference compounds.

Objective

The study objective was to identify the common metabolites of prohibited anabolic steroids that are produced in both fungi and human and thus can be synthesized in bulk using fungal cultures. Mesterolone is used as a case study.

Methods

The study was conducted in three steps; we first studied the fungal transformation of mesterolone. In the second step, these metabolites were used as references to detect in human urine after the oral use of mesterolone using LC-ESI-QqQ-MS/MS. In the third step, 12 fungal cultures were screened to evaluate their potential to produce reference markers.

Results

This led to the detection of two metabolites, 6α-hydroxymesterolone (M1) and 7α-hydroxymesterolone (M2) that were found to be common in both, fungal cultures and human urine samples. Moreover, Rhizopus stolonifer and Beauveria bassiana can be considered as good candidates to produce M1 and M2 metabolites, respectively.

Conclusion

This approach can be employed for the synthesis of marker compounds of other prohibited anabolic steroids thus can be detected efficiently during national and international sports competitions.

     

Euclidean geometry explains why lengths allow precise body mass estimates in terrestrial invertebrates: the case of oribatid mites

Indirect measures of soil invertebrate body mass M based on equations relating the latter to body length (l) are becoming increasingly used due to the required painstaking laboratory work and the technical difficulties involved in obtaining some thousands of reliable weight estimates for animals that can be very small. The implicit assumption of such equations is that dM/dV=δ, where V is body volume and δ is a constant density value. Classical Euclidean scaling implies that V∝l³∝M. One may thus derive M from l when the latter can provide a good estimate of V and the assumption of a constant δ is respected. In invertebrates, equations relating weight to length indicate that the power model always provides the best fit. However, authors only focused on the empirical estimation of slopes linking the body mass to the length measure variables, sometimes fitting exponential and linear models that are not theoretically grounded. This paper explicates how power laws derive from fundamental Euclidean scaling and describes the expected allometric exponents under the above assumptions. Based on the classical Euclidean scaling theory, an equivalent sphere is defined as a theoretical sphere with a volume equal to that of the organism whose body mass must be estimated. The illustrated application to a data set on soil oribatid mites helps clarify all these issues. Lastly, a general procedure for more precise estimation of M from V and δ is suggested.