Area‐wide monitoring of potato tuberworm (Phthorimaea operculella) by pheromone trapping in Northern Italy: phenology,spatial distribution and relationships between catches and tuber damage

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Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations

The enzyme biotin carboxylase (BC) uses adenosine triphosphate (ATP) to carboxylate biotin and is involved in fatty acid synthesis. Structural evidence suggests that the B domain of BC undergoes a large hinge motion of ～45° when binding and releasing substrates. Escherichia coli BC can function as a natural homodimer and as a mutant monomer. Using molecular dynamics simulations, we evaluate the free energy profile along a closure angle of the B domain of E. coli BC for three cases: a monomer without bound Mg(2)ATP, a monomer with bound Mg(2)ATP, and a homodimer with bound Mg(2)ATP in one subunit. The simulation results show that a closed state is the most probable for the monomer with or without bound Mg(2)ATP. For the dimer with Mg(2)ATP in one of its subunits, communication between the two subunits was observed. Specifically, in the dimer, the opening of the subunit without Mg(2)ATP caused the other subunit to open, and hysteresis was observed upon reclosing it. The most stable state of the dimer is one in which the B domain of both subunits is closed; however, the open state for the B domain without Mg(2)ATP is only approximately 2k(B)T higher in free energy than the closed state. A simple diffusion model indicates that the mean times for opening and closing of the B domain in the monomer with and without Mg(2)ATP are much smaller than the overall reaction time, which is on the order of seconds.     

Activity budget of inshore Indo‐Pacific bottlenose dolphins (Tursiops aduncus): A critical evaluation of methods and comparison among other populations

Activity budgets are widely used to compare behavior patterns but sampling methods vary, rendering comparisons difficult. The two main methods used are instantaneous and continuous sampling. Their comparability was examined by applying them to data obtained from bottlenose dolphins in the Port River estuary, South Australia. They gave comparable results for activity budgets, but instantaneous sampling did not detect most of the behavioral events. Individual differences in behavior and/or follow duration influenced results. Variability in activity definitions and categories among studies makes comparative analysis difficult. Comparison of the Port River dolphin's activity budget with other inshore populations indicated the former spent more time feeding and resting, and less time traveling. The greater feeding time seemed to be due to small prey size rather than reduced abundance or unpredictable distribution. The reduced traveling time, possibly the result of low predation pressure and/or evenly distributed prey, gave them more time to rest. They traveled mostly at 2.5 kn or less, consistent with studies from other shallow areas. Most feeding was individual, probably on demersal species. Surface feeding incorporated physical barriers rather than cooperative behavior. Activity durations ranged from 2 s to 2.9 h, with mean durations varying from 7.8 to 22.9 min.     

Spatial patterns of plant diversity below-ground as revealed by DNA barcoding

Our understanding of the spatial organization of root diversity in plant communities and of the mechanisms of community assembly has been limited by our ability to identify plants based on root tissue, especially in diverse communities. Here, we test the effectiveness of the plastid gene rbcL, a core plant DNA barcoding marker, for investigating spatial patterns of root diversity, and relate observed patterns to above-ground community structure. We collected 3800 root fragments from four randomly positioned, 1-m-deep soil profiles (two vertical transects per plot), located in an old-field community in southern Ontario, Canada, and extracted and sequenced DNA from 1531 subsampled fragments. We identified species by comparing sequences with a DNA barcode reference library developed previously for the local flora. Nearly 85% of sampled root fragments were successfully sequenced and identified as belonging to 29 plant species or species groups. Root abundance and species richness varied in horizontal space and were negatively correlated with soil depth. The relative abundance of taxa below-ground was correlated with their frequency above-ground (r = 0.73, P = 0.0001), but several species detected in root tissue were not observed in above-ground quadrats. Multivariate analyses indicated that diversity was highly structured below-ground, and associated with depth, root morphology, soil chemistry and soil texture, whereas little structure was evident above-ground. Furthermore, analyses of species co-occurrence indicates strong species segregation overall but random co-occurrence among confamilials. Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below-ground, and also demonstrate the utility of barcoding for the identification of plant roots.     

Why replication is important in landscape genetics: American black bear in the Rocky Mountains

We investigated how landscape features influence gene flow of black bears by testing the relative support for 36 alternative landscape resistance hypotheses, including isolation by distance (IBD) in each of 12 study areas in the north central U.S. Rocky Mountains. The study areas all contained the same basic elements, but differed in extent of forest fragmentation, altitude, variation in elevation and road coverage. In all but one of the study areas, isolation by landscape resistance was more supported than IBD suggesting gene flow is likely influenced by elevation, forest cover, and roads. However, the landscape features influencing gene flow varied among study areas. Using subsets of loci usually gave models with the very similar landscape features influencing gene flow as with all loci, suggesting the landscape features influencing gene flow were correctly identified. To test if the cause of the variability of supported landscape features in study areas resulted from landscape differences among study areas, we conducted a limiting factor analysis. We found that features were supported in landscape models only when the features were highly variable. This is perhaps not surprising but suggests an important cautionary note - that if landscape features are not found to influence gene flow, researchers should not automatically conclude that the features are unimportant to the species' movement and gene flow. Failure to investigate multiple study areas that have a range of variability in landscape features could cause misleading inferences about which landscape features generally limit gene flow. This could lead to potentially erroneous identification of corridors and barriers if models are transferred between areas with different landscape characteristics.     

Fusarium species complex and mycotoxins in grain maize from maize hybrid trials and from grower's fields

Aims: To quantify and to compare the occurrence of Fusarium species in maize kernels and stalk pieces, to analyse mycotoxins in kernels and maize crop residues, to evaluate two approaches to obtain kernel samples and to compare two methods for mycotoxin analyses. Methods and Results: The occurrence of Fusarium species in maize kernels and stalk pieces from a three‐year maize hybrid trial and 12 kernel samples from grower’s fields was assessed. Nine to 16 different Fusarium species were detected in maize kernels and stalks. In kernels, F. graminearum, F. verticillioides and F. proliferatum were the most prevalent species whereas in stalks, they were F. equiseti, F. proliferatum and F. verticillioides. In 2006, 68% of the kernel samples exceeded the recommended limit for pig feed for deoxynivalenol (DON) and 42% for zearalenone (ZON), respectively. Similarly, 75% of the samples from grower’s fields exceeded the limits for DON and 50% for ZON. In maize crop residues, toxin concentrations ranged from 2·6 to 15·3 mg kg^?1 for DON and from 0·7 to 7·4 mg kg^?1 for ZON. Both approaches to obtain maize kernel samples were valid, and a strong correlation between mycotoxin analysis using ELISA and LC‐MS/MS was found. Conclusions: The contamination of maize kernels, stalk pieces and remaining crop residues with various mycotoxins could pose a risk not only to animal health but also to the environment. With the hand‐picked sample, the entire Fusarium complex can be estimated, whereas combine harvested samples are more representative for the mycotoxin contents in harvested goods. Significance and Impact of the Study: This is the first multi‐year study investigating mycotoxin contamination in maize kernels as well as in crop residues. The results indicate a high need to identify cropping factors influencing the infection of maize by Fusarium species to establish recommendations for growers.     

Finessing atlas data for species distribution models

Aim The spatial resolution of species atlases and therefore resulting model predictions are often too coarse for local applications. Collecting distribution data at a finer resolution for large numbers of species requires a comprehensive sampling effort, making it impractical and expensive. This study outlines the incorporation of existing knowledge into a conventional approach to predict the distribution of Bonelli’s eagle (Aquila fasciata) at a resolution 100 times finer than available atlas data. Location Malaga province, Andalusia, southern Spain. Methods A Bayesian expert system was proposed to utilize the knowledge from distribution models to yield the probability of a species being recorded at a finer resolution (1 × 1 km) than the original atlas data (10 × 10 km). The recorded probability was then used as a weight vector to generate a sampling scheme from the species atlas to enhance the accuracy of the modelling procedure. The maximum entropy for species distribution modelling (MaxEnt) was used as the species distribution model. A comparison was made between the results of the MaxEnt using the enhanced and, the random sampling scheme, based on four groups of environmental variables: topographic, climatic, biological and anthropogenic. Results The models with the sampling scheme enhanced by an expert system had a higher discriminative capacity than the baseline models. The downscaled (i.e. finer scale) species distribution maps using a hybrid MaxEnt/expert system approach were more specific to the nest locations and were more contrasted than those of the baseline model. Main conclusions The proposed method is a feasible substitute for comprehensive field work. The approach developed in this study is applicable for predicting the distribution of Bonelli’s eagle at a local scale from a national‐level occurrence data set; however, the usefulness of this approach may be limited to well‐known species.     

Factors relating to regional and local success of exotic plant species in their new range

Aim To estimate invasiveness of exotic plant species, many studies have used the frequency of occurrence within a defined region. This measure is informative on how widespread exotics are, however, it does not inform on their local dominance, which is crucial for conservation of biodiversity and ecosystem functioning. The aim of the present study is to determine if regional frequency of occurrence of exotic plant species indeed is indicative of their local dominance. We also determined which plant traits and other factors predict regional and local frequencies best. Location The Netherlands. Methods We used information on exotic plant species established in The Netherlands and compared traits relating to their frequency of occurrence regionally (the entire country) and their frequency of dominance locally (in 1–100 m² quadrats). We created minimal adequate models with factors explaining regional frequency and frequency of local dominance of 111 exotic plant species in The Netherlands. Results The model that used plant traits to explain regional frequency of exotic plant species differed from the models that best explained their frequency of local dominance. Regionally, the factors that correlated with frequency were: life form, height, polyploidy, length of flowering season, residence time, human use and origin. The factors that correlated to frequency of local dominance were lateral vegetative spread and residence time. Main conclusions We conclude that plant traits relating to the regional frequency of exotic plant species differ from those that relate to their frequency of local dominance. The implication of our results is that predictive studies on plant invasiveness based on regional frequencies may not be indicative of the local impacts. Since the prediction of local impacts is crucial for conservation and risk assessment, our study emphasized the need for better information on the local abundance of exotic invaders.     

Impact of spatial disjunction within biophysical classes on plant species composition: implications for conservation planning

The use of surrogates for biodiversity is a practical tool to improve the cost effectiveness of regional conservation planning. However, there is still much uncertainty about the biological representativeness of surrogates. Using a biophysical classification system known as the Mitchell Landscapes, we compare plant species composition in contiguous versus disjunct units of nine Landscape types and hence the ability of this surrogate to capture patterns of plant species composition. We found that plant species homogeneity was higher within a contiguous Landscape than between non‐contiguous units of the same Landscape. Overall, the dissimilarity between non‐contiguous units and their contiguous counterparts was significant (P = 0.004). Biophysical classes with very high dissimilarities between non‐contiguous units of the same region may be of limited utility.     

Unnecessary roughness? Testing the hypothesis that predators destined for molecular gut‐content analysis must be hand‐collected to avoid cross‐contamination

Molecular gut‐content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Mass‐collection methods, such as sweep‐netting, vacuum sampling and foliage beating, could lead to regurgitation or rupturing of predators along with uneaten prey, thereby contaminating specimens and compromising resultant gut‐content data. Proponents of this ‘cross‐contamination hypothesis’ advocate hand‐collection as the best way to avoid cross‐contamination. However, hand‐collection is inefficient when large samples are needed, as with most ecological research. We tested the cross‐contamination hypothesis by setting out onto potato plants immature Coleomegilla maculata and Podisus maculiventris that had been fed larvae of either Leptinotarsa decemlineata or Leptinotarsa juncta, or unfed individuals of these predator species along with L. decemlineata larvae. The animals were then immediately re‐collected, either by knocking them vigorously off the plants onto a beat cloth and capturing them en masse with an aspirator (‘rough’ treatment) or by hand‐searching and collection with a brush (‘best practice’). Collected predators were transferred in the field to individual vials of chilled ethanol and subsequently assayed by PCR for fragments of cytochrome oxidase I of L. decemlineata and L. juncta. Ten to 39 per cent of re‐collected fed predators tested positive by PCR for DNA of both Leptinotarsa species, and 14–38% of re‐collected unfed predators contained L. decemlineata DNA. Overall levels of cross‐contamination in the rough (31%) and best‐practice (11%) samples were statistically different and supported the cross‐contamination hypothesis. A pilot study on eliminating external DNA contamination with bleach prior to DNA extraction and amplification gave promising results.