Species specificity and intraspecific variation in the chemical profiles of Heliconius butterflies across a large geographic range

In many animals, mate choice is important for the maintenance of reproductive isolation between species. Traits important for mate choice and behavioral isolation are predicted to be under strong stabilizing selection within species; however, such traits can also exhibit variation at the population level driven by neutral and adaptive evolutionary processes. Here, we describe patterns of divergence among androconial and genital chemical profiles at inter‐ and intraspecific levels in mimetic Heliconius butterflies. Most variation in chemical bouquets was found between species, but there were also quantitative differences at the population level. We found a strong correlation between interspecific chemical and genetic divergence, but this correlation varied in intraspecific comparisons. We identified “indicator” compounds characteristic of particular species that included compounds already known to elicit a behavioral response, suggesting an approach for identification of candidate compounds for future behavioral studies in novel systems. Overall, the strong signal of species identity suggests a role for these compounds in species recognition, but with additional potentially neutral variation at the population level.     

Three critical factors affecting automated image species recognition performance for camera traps

Ecological camera traps are increasingly used by wildlife biologists to unobtrusively monitor an ecosystems animal population. However, manual inspection of the images produced is expensive, laborious, and time‐consuming. The success of deep learning systems using camera trap images has been previously explored in preliminary stages. These studies, however, are lacking in their practicality. They are primarily focused on extremely large datasets, often millions of images, and there is little to no focus on performance when tasked with species identification in new locations not seen during training. Our goal was to test the capabilities of deep learning systems trained on camera trap images using modestly sized training data, compare performance when considering unseen background locations, and quantify the gradient of lower bound performance to provide a guideline of data requirements in correspondence to performance expectations. We use a dataset provided by Parks Canada containing 47,279 images collected from 36 unique geographic locations across multiple environments. Images represent 55 animal species and human activity with high‐class imbalance. We trained, tested, and compared the capabilities of six deep learning computer vision networks using transfer learning and image augmentation: DenseNet201, Inception‐ResNet‐V3, InceptionV3, NASNetMobile, MobileNetV2, and Xception. We compare overall performance on “trained” locations where DenseNet201 performed best with 95.6% top‐1 accuracy showing promise for deep learning methods for smaller scale research efforts. Using trained locations, classifications with <500 images had low and highly variable recall of 0.750 ± 0.329, while classifications with over 1,000 images had a high and stable recall of 0.971 ± 0.0137. Models tasked with classifying species from untrained locations were less accurate, with DenseNet201 performing best with 68.7% top‐1 accuracy. Finally, we provide an open repository where ecologists can insert their image data to train and test custom species detection models for their desired ecological domain.     

Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land

Plants provide resources and shape the habitat of soil organisms thereby affecting the composition and functioning of soil communities. Effects of plants on soil communities are largely taxon‐dependent, but how different functional groups of herbaceous plants affect trophic niches of individual animal species in soil needs further investigation. Here, we studied the use of basal resources and trophic levels of dominating soil meso‐ and macrofauna using stable isotope ratios of carbon and nitrogen in arable fallow systems 3 and 14–16 years after abandonment. Animals were sampled from the rhizosphere of three plant species of different functional groups: a legume (Medicaco sativa), a nonlegume herb (Taraxacum officinale), and a grass (Bromus sterilis). We found virtually no consistent effects of plant identity on stable isotope composition of soil animals and on thirteen isotopic metrics that reflect general food‐web structure. However, in old fallows, the carbon isotope composition of some predatory macrofauna taxa had shifted closer to that of co‐occurring plants, which was particularly evident for Lasius, an aphid‐associated ant genus. Trophic levels and trophic‐chain lengths in food webs were similar across plant species and fallow ages. Overall, the results suggest that variations in local plant diversity of grassland communities may little affect the basal resources and the trophic level of prey consumed by individual species of meso‐ and macrofauna belowground. By contrast, successional changes in grassland communities are associated with shifts in the trophic niches of certain species, reflecting establishment of trophic interactions with time, which shapes the functioning and stability of soil food webs.     

The development and characterization of an E. coli O25B bioconjugate vaccine

Extraintestinal pathogenic Escherichia coli (ExPEC) cause a wide range of clinical diseases such as bacteremia and urinary tract infections. The increase of multidrug resistant ExPEC strains is becoming a major concern for the treatment of these infections and E. coli has been identified as a critical priority pathogen by the WHO. Therefore, the development of vaccines has become increasingly important, with the surface lipopolysaccharide constituting a promising vaccine target. This study presents genetic and structural analysis of clinical urine isolates from Switzerland belonging to the serotype O25. Approximately 75% of these isolates were shown to correspond to the substructure O25B only recently described in an emerging clone of E. coli sequence type 131. To address the high occurrence of O25B in clinical isolates, an O25B glycoconjugate vaccine was prepared using an E. coli glycosylation system. The O antigen cluster was integrated into the genome of E. coli W3110, thereby generating an E. coli strain able to synthesize the O25B polysaccharide on a carrier lipid. The polysaccharide was enzymatically conjugated to specific asparagine side chains of the carrier protein exotoxin A (EPA) of Pseudomonas aeruginosa by the PglB oligosaccharyltransferase from Campylobacter jejuni. Detailed characterization of the O25B-EPA conjugate by use of physicochemical methods including NMR and GC-MS confirmed the O25B polysaccharide structure in the conjugate, opening up the possibility to develop a multivalent E. coli conjugate vaccine containing O25B-EPA.

     

Chromoplast differentiation in bell pepper (Capsicum annuum) fruits

We report here a detailed analysis of the proteome adjustments that accompany chromoplast differentiation from chloroplasts during bell pepper (Capsicum annuum) fruit ripening. While the two photosystems are disassembled and their constituents degraded, the cytochrome b₆f complex, the ATPase complex, and Calvin cycle enzymes are maintained at high levels up to fully mature chromoplasts. This is also true for ferredoxin (Fd) and Fd-dependent NADP reductase, suggesting that ferredoxin retains a central role in the chromoplasts’ redox metabolism. There is a significant increase in the amount of enzymes of the typical metabolism of heterotrophic plastids, such as the oxidative pentose phosphate pathway (OPPP) and amino acid and fatty acid biosynthesis. Enzymes of chlorophyll catabolism and carotenoid biosynthesis increase in abundance, supporting the pigment reorganization that goes together with chromoplast differentiation. The majority of plastid encoded proteins decline but constituents of the plastid ribosome and AccD increase in abundance. Furthermore, the amount of plastid terminal oxidase (PTOX) remains unchanged despite a significant increase in phytoene desaturase (PDS) levels, suggesting that the electrons from phytoene desaturation are consumed by another oxidase. This may be a particularity of non-climacteric fruits such as bell pepper that lack a respiratory burst at the onset of fruit ripening.