GCalignR: An R package for aligning gas-chromatography data for ecological and evolutionary studies

Expression of Elongase- and Desaturase-Encoding Genes Shapes the Cuticular Hydrocarbon Profiles of Honey Bees

Most terrestrial insects have a layer of cuticular hydrocarbons (CHCs) protecting them from desiccation and mediating chemical communication. The composition of these hydrocarbons is highly plastic and changes during their lifetime and with environmental conditions. How these changes in CHC composition are achieved is largely unknown. CHC profiles of Apis mellifera honey bees vary among castes, task groups and subspecies adapted to different climates. This makes A. mellifera an excellent model for studying the molecular mechanism underlying CHC biosynthesis. We correlated the expression of specific elongase- and desaturase-encoding genes with the CHC composition in bees performing different social tasks in two highly divergent A. mellifera subspecies. Elongases are enzymes that lengthen the hydrocarbon chain, while desaturases introduce double bonds in it. We evaluated the hypothesis that the expression of the genes encoding these enzymes determines CHC profiles of the worker bees. Our results revealed that the specificity of desaturases and elongases shapes the CHC profiles of worker bees performing different social tasks. Expression of the desaturase-encoding gene LOC100576797 and the elongase-encoding gene LOC550828 seemed to be strongly associated with the abundance of compounds that were characteristic of the CHC profile of nurse bees. In contrast, the compounds that characterised the CHC profiles of the forager bees seemed to be associated with the desaturase-encoding gene LOC551527 and the elongase-encoding gene LOC409638. Our data shed light on the genetic basis for task-specific CHC composition differences in social hymenopterans and paved the ground for unravelling the genetic underpinning of CHC biosynthesis.

Lack of significant effect of gut microbiota on weight gain in newly emerged worker honeybee

The western honeybee, Apis mellifera, harbours a simple and distinct microbiota that has been linked to various positive outcomes for the host. Among these cited benefits is improved weight gain for bees that have been inoculated with their native microbes. This result has been challenged by recent studies which investigated the impact of the gut microbiota on behavioural maturation and associated physiological changes and revealed no effect of the gut microbiota on weight gain. Therefore, we re-examined the role of the microbiota in weight gain by comparing microbiota-deprived bees with those inoculated with gut homogenate or defined communities composed of isolates representing the major bacterial taxa inhabiting the bee gut. We observed no differences in weight gain of adult bees or of their gut tissues across these groups. Further analysis based on nurse/forager cuticular hydrocarbon status and bacterial composition also revealed no significant changes. These results suggest the need for more nuanced investigations aimed at exploring factors such as the conditions in the hive of origin, including larval nutrition.

Invited review: Research on ruminal biohydrogenation-Achievements, gaps in knowledge, and future approaches from the perspective of dairy science

Scientific knowledge about ruminal biohydrogenation (BH) has improved greatly since this metabolic process was empirically confirmed in 1951. For years, BH had mostly been perceived as a process to be avoided to increase the postruminal flow of UFA from the diet. Two milestones changed this perception and stimulated great interest in BH intermediates themselves: In 1987, the in vitro anticarcinogenic properties of CLA were described, and in 2000, the inhibition of milk fat synthesis by trans-10,cis-12 CLA was confirmed. Since then, numerous BH metabolites have been described in small and large ruminants, and the major deviation from the common BH pathway (i.e., the trans-10 shift) has been reasonably well established. However, there are some less well-characterized alterations, and the comprehensive description of new BH intermediates (e.g., using isotopic tracers) has not been coupled with research on their biological effects. In this regard, the low quality of some published fatty acid profiles may also be limiting the advance of knowledge in BH. Furthermore, although BH seems to no longer be considered a metabolic niche inhabited by a few bacterial species with a highly specific metabolic capability, researchers have failed to elucidate which specific microbial groups are involved in the process and the basis for alterations in BH pathways (i.e., changes in microbial populations or their activity). Unraveling both issues may be beneficial for the description of new microbial enzymes involved in ruminal lipid metabolism that have industrial interest. From the perspective of dairy science, other knowledge gaps that require additional research in the coming years are evaluation of the relationship between BH and feed efficiency and enteric methane emissions, as well as improving our understanding of how alterations in BH are involved in milk fat depression. Addressing these issues will have relevant practical implications in dairy science.

Uncovering the Counterfeit: A study of whiskey authenticity through volatile organic compound fingerprinting, aroma and color sensory analysis

This study presents a method employing gas chromatography coupled with mass spectrometry and headspace solid-phase microextraction (HS-SPME-GC-MS), supplemented with chemometrics (Soft independent modelling of class analogies - SIMCA), to analyze volatile organic compound (VOCs) profiles in suspect whiskey samples. Furthermore, a sensory analysis of aroma and color was conducted with a panel of 52 non-trained volunteers to evaluate their ability to discriminate and preference for counterfeit whiskeys. The HS-SPME-GC-MS method successfully distinguished 41 seized samples from authentic beverages. Interestingly, sensory analysis revealed that panelists could differentiate between counterfeit and authentic samples with a reference standard but did not consistently show a preference for aroma. In some cases, there was even a preference for the color of counterfeit whiskeys. The findings suggest that sensorial tests alone may not effectively distinguish counterfeit from authentic whiskeys, especially for non-expert consumers, highlighting the need for analytical instrumentation methods in fraud detection.

No sex difference in preen oil chemical composition during incubation in Kentish plovers

Preen oil, the secretion from the uropygial gland of birds, may have a specific function in incubation. Consistent with this, during incubation, the chemical composition of preen oil is more likely to differ between sexes in species where only one sex incubates than in species where both sexes incubate. In this study, we tested the generality of this apparent difference, by investigating sex differences in the preen oil composition of a shorebird species, the Kentish plover (Anarhynchus, formerly Charadrius, alexandrinus). As both sexes incubate in this species, we predicted the absence of sex differences in preen oil composition during incubation. In the field, we sampled preen oil from nine females and 11 males during incubation, which we analysed with gas chromatography-mass spectrometry (GC-MS). Consistent with predictions, we found no sex difference in preen oil composition, neither in beta diversity (Bray-Curtis dissimilarities) nor in alpha diversity (Shannon index and number of substances). Based on these results, we cannot conclude whether preen oil has a function during incubation in Kentish plovers. Still, we discuss hypothetical roles, such as olfactory crypsis, protection against ectoparasites or olfactory intraspecific communication, which remain to be tested.

No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals

Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background. We addressed this issue in Antarctic fur seals by analysing skin swabs together with full-length MHC DQB II exon 2 sequences and data from 41 genome-wide distributed microsatellites. We did not find any effects of MHC relatedness on chemical similarity and there was also no relationship between MHC heterozygosity and chemical diversity. However, multilocus heterozygosity showed a significant positive association with chemical diversity, even after controlling for MHC heterozygosity. Our results appear to rule out a dominant role of the MHC in the chemical encoding of genetic information in a wild vertebrate population and highlight the need for genome-wide approaches to elucidate the mechanism(s) and specific genes underlying genotype-odour associations.

Adverse effects of the fungal biopesticide Beauveria bassiana on a predatory social wasp

Biopesticides are considered eco-friendly alternatives to synthetic agrochemicals. However, their impact on non-target organisms is still poorly understood. Social wasps, in particular, are a largely neglected group when it comes to risk assessment of plant protection products, despite the relevant ecological and economic services provided by these insects. In the present study, we evaluated the impact of a common biopesticide, the entomopathogenic fungus Beauveria bassiana, on the paper wasp Polistes dominula. We adopted a holistic approach in ecotoxicology by focusing not only on the detrimental effects on isolated individuals, but also on the whole colony. Both adult wasps belonging to different castes and immature larvae were topically exposed to a field-realistic concentration of fungal spores from the commercial strain of B. bassiana ATCC 74040 to assess the impact of the biopesticide on their survival, behavior and physiology. Our results showed that the fungus causes a number of adverse effects on P. dominula, that include increased mortality, altered locomotion and feeding rate, selective ejection of exposed larvae from nests, reduced oviposition rate and ovary development in foundresses, and colony failure. Our findings provide new insights on the often-neglected sublethal effects of pollutants that can jeopardize not only individual beneficial insects, but also the delicate social balance of their colonies and their valuable ecosystem services, highlighting that the natural origin of plant-protection products does not always guarantee environmental safety.

Species- and sex-specific chemical composition from an internal gland-like tissue of an African frog family

Intraspecific chemical communication in frogs is understudied and the few published cases are limited to externally visible and male-specific breeding glands. Frogs of the family Odontobatrachidae, a West African endemic complex of five morphologically cryptic species, have large, fatty gland-like strands along their lower mandible. We investigated the general anatomy of this gland-like strand and analysed its chemical composition. We found the strand to be present in males and females of all species. The strand varies in markedness, with well-developed strands usually found in reproductively active individuals. The strands are situated under particularly thin skin sections, the vocal sac in male frogs and a respective area in females. Gas-chromatography/mass spectrometry and multivariate analysis revealed that the strands contain sex- and species-specific chemical profiles, which are consistent across geographically distant populations. The profiles varied between reproductive and non-reproductive individuals. These results indicate that the mandibular strands in the Odontobatrachidae comprise a so far overlooked structure (potentially a gland) that most likely plays a role in the mating and/or breeding behaviour of the five Odontobatrachus species. Our results highlight the relevance of multimodal signalling in anurans, and indicate that chemical communication in frogs may not be restricted to sexually dimorphic, apparent skin glands.

Dimethylpolysulfides production as the major mechanism behind wheat fungal pathogen biocontrol, by Arthrobacter and Microbacterium actinomycetes

IMPORTANCE

As the management of wheat fungal diseases becomes increasingly challenging, the use of bacterial agents with biocontrol potential against the two major wheat phytopathogens, Fusarium graminearum and Zymoseptoria tritici, may prove to be an interesting alternative to conventional pest management. Here, we have shown that dimethylpolysulfide volatiles are ubiquitously and predominantly produced by wheat-associated Microbacterium and Arthrobacter actinomycetes, displaying antifungal activity against both pathogens. By limiting pathogen growth and DON virulence factor production, the use of such DMPS-producing strains as soil biocontrol inoculants could limit the supply of pathogen inocula in soil and plant residues, providing an attractive alternative to dimethyldisulfide fumigant, which has many non-targeted toxicities. Notably, this study demonstrates the importance of bacterial volatile organic compound uptake by inhibited F. graminearum, providing new insights for the study of volatiles-mediated toxicity mechanisms within bacteria-fungus signaling crosstalk.

A supergene in seaweed flies modulates male traits and female perception

Supergenes, tightly linked sets of alleles, offer some of the most spectacular examples of polymorphism persisting under long-term balancing selection. However, we still do not understand their evolution and persistence, especially in the face of accumulation of deleterious elements. Here, we show that an overdominant supergene in seaweed flies, Coelopa frigida, modulates male traits, potentially facilitating disassortative mating and promoting intraspecific polymorphism. Across two continents, the Cf-Inv(1) supergene strongly affected the composition of male cuticular hydrocarbons (CHCs) but only weakly affected CHC composition in females. Using gas chromatography-electroantennographic detection, we show that females can sense male CHCs and that there may be differential perception between genotypes. Combining our phenotypic results with RNA-seq data, we show that candidate genes for CHC biosynthesis primarily show differential expression for Cf-Inv(1) in males but not females. Conversely, candidate genes for odorant detection were differentially expressed in both sexes but showed high levels of divergence between supergene haplotypes. We suggest that the reduced recombination between supergene haplotypes may have led to rapid divergence in mate preferences as well as increasing linkage between male traits, and overdominant loci. Together this probably helped to maintain the polymorphism despite deleterious effects in homozygotes.

Genetic variation for rectal gland volatiles among recently collected isofemale lines and a domesticated strain of Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)

Divergence between populations in mating behaviour can function as a potent premating isolating mechanism and promote speciation. However, very few cases of inherited intraspecific variation in sexual signalling have been reported in tephritid fruit flies, despite them being a highly speciose family. We tested for such variation in one tephritid, the Queensland fruit fly, Bactrocera tryoni (Qfly). Qfly mating behaviour depends on volatiles secreted from male rectal glands but no role for the volatiles from female rectal glands has yet been reported. We previously detected over 100 volatile compounds in male rectal glands and identified over 30 of them. Similar numbers were recorded in females. However, many compounds showed presence/absence differences between the sexes and many others showed quantitative differences between them. Here we report inherited variation among 24 Qfly lines (23 isofemale lines established from recent field collections and one domesticated line) in the abundance of three esters, two alcohols, two amides, an aldehyde and 18 unidentified volatiles in male rectal glands. We did not find any compounds in female rectal glands that varied significantly among the lines, although this may at least partly reflect lower female sample numbers. Most of the 26 male compounds that differed between lines were more abundant in the domesticated line than any of the recently established isofemale lines, which concurs with other evidence for changes in mating behaviour during domestication of this species. There were also large differences in several of the 26 compounds among the isofemale lines, and some of these differences were associated with the regions from which the lines were collected. While some of the variation in different compounds was correlated across lines, much of it was not, implicating involvement of multiple genes. Our findings parallel reports of geographic variation in other Qfly traits and point to inherited differences in reproductive physiology that could provide a basis for evolution of premating isolation between ecotypes.

Immune Stimulation via Wounding Alters Chemical Profiles of Adult Tribolium castaneum

Group-living individuals experience immense risk of disease transmission and parasite infection. In social and in some non-social insects, disease control with immunomodulation arises not only via individual immune defenses, but also via infochemicals such as contact cues and (defensive) volatiles to mount a group-level immunity. However, little is known about whether activation of the immune system elicits changes in chemical phenotypes, which may mediate these responses. We here asked whether individual immune experience resulting from wounding or injection of heat-killed Bacillus thuringiensis (priming) leads to changes in the chemical profiles of female and male adult red flour beetles, Tribolium castaneum, which are non-social but gregarious. We analyzed insect extracts using GC-FID to study the chemical composition of (1) cuticular hydrocarbons (CHCs) as candidates for the transfer of immunity-related information between individuals via contact, and (2) stink gland secretions, with analysis of benzoquinones as main active compounds regulating 'external immunity'. Despite a pronounced sexual dimorphism in CHC profiles, wounding stimulation led to similar profile changes in males and females with increases in the proportion of methyl-branched alkanes compared to naïve beetles. While changes in the overall secretion profiles were less pronounced, absolute amounts of benzoquinones were transiently elevated in wounded compared to naïve females. Responses to priming were insignificant in CHCs and secretions. We suggest that changes in different infochemicals after wounding may mediate immune status signaling in the context of both internal and external immune responses in groups of this non-social insect, thus showing parallels to social immunity.

A pachyderm perfume: odour encodes identity and group membership in African elephants

Group-living animals that live in complex social systems require effective modes of communication to maintain social cohesion, and several acoustic, olfactory and visual signaling systems have been described. Individuals need to discriminate between in- and out-group odour to both avoid inbreeding and to identify recipients for reciprocal behaviour. The presence of a unique group odour, identified in several social mammals, is a proposed mechanism whereby conspecifics can distinguish group from non-group members. African elephants (Loxodonta africana) live in stable, socially complex, multi-female, fission-fusion groups, characterized by female philopatry, male dispersal and linear dominance hierarchies. Elephant social behaviour suggests that individuals use odour to monitor the sex, reproductive status, location, health, identity and social status of conspecifics. To date, it is not clear what fixed or variable information is contained in African elephant secretions, and whether odour encodes kinship or group membership information. Here we use SPME GC-MS generated semiochemical profiles for temporal, buccal and genital secretions for 113 wild African elephants and test their relationship with measures of genetic relatedness. Our results reveal the existence of individual identity odour profiles in African elephants as well as a signature for age encoded in temporal gland and buccal secretions. Olfactory signatures for genetic relatedness were found in labial secretions of adult sisters. While group odour was not correlated with group genetic relatedness, our analysis identified "group membership" as a significant factor explaining chemical differences between social groups. Saturated and short-chain fatty acids (SCFAs), derived from key volatile compounds from bacterial fermentation, were identified in temporal, buccal and genital secretions suggesting that group odour in African elephants may be the result of bacterial elements of the gut microbiome. The frequent affiliative behavior of African elephants is posited as a likely mechanism for bacterial transmission. Our findings favour flexible group-specific bacterial odours, which have already been proposed for other social mammals and present a useful form of olfactory communication that promotes bond group cohesion among non-relatives in fission-fusion mammals.

Diversity and sex differences in rectal gland volatiles of Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)

Rectal gland volatiles are key mediators of sexual interactions in tephritid fruit flies. We used solid-phase microextraction (SPME) plus gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detection (GC-FID) to substantially expand rectal gland chemical characterisation of the Queensland fruit fly (Bactrocera tryoni (Diptera: Tephritidae); Qfly). The SPME GC-MS analysis identified 24 of the 30 compounds previously recorded from Qfly rectal glands, plus another 21 compounds that had not previously been reported. A few amides and fatty acid esters dominated the chromatograms of males and females respectively, but we also found other esters, alcohols and aldehydes and a ketone. The GC-FID analyses also revealed over 150 others, as yet unidentified, volatiles, generally in lesser amounts. The GC-FID analyses also showed 49 and 12 compounds were male- and female-specific, respectively, both in single sex (virgin) and mixed sex (mostly mated) groups. Another ten compounds were male-specific among virgins but undetected in mixed sex groups, and 29 were undetected in virgins but male-specific in mixed sex groups. The corresponding figures for females were four and zero, respectively. Most short retention time peaks (including a ketone and an ester) were male-specific, whereas most female-biased peaks (including five fatty acid esters) had long retention times. Our results indicate previously unsuspected diversity of rectal gland volatiles that might have pheromone functions in males, but far fewer in females.

Chemical Modification of Biomarkers through Accelerated Degradation: Implications for Ancient Plant Identification in Archaeo-Organic Residues

Biochemical and biomolecular archaeology is increasingly used to elucidate the consumption, use, origin, and trade of plants in the past. However, it can be challenging to use biomarkers to identify the taxonomic origin of archaeological plants due to limited knowledge of molecular survival and degradation for many key plant compounds in archaeological contexts. To gain a fundamental understanding of the chemical alterations associated with chemical degradation processes in ancient samples, we conducted accelerated degradation experiments with essential oil derived from cedar (Cedrus atlantica) exposed to materials commonly found in the archaeological record. Using GC-MS and multivariate analysis, we detected a total of 102 compounds across 19 treatments that were classified into three groups. The first group comprised compounds that were abundant in fresh cedar oil but would be unlikely to remain in ancient residues due to rapid degradation. The second group consisted of compounds that remained relatively stable or increased over time, which could be potential biomarkers for identifying cedar in archaeological residues. Compounds in the third group were absent in fresh cedar oil but were formed during specific experiments that could be indicative for certain storage conditions. These results show that caution is warranted for applying biomolecular profiles of fresh plants to ancient samples and that carefully designed accelerated degradation experiments can, at least in part, overcome this limitation.

Evidence of female preference for odor of distant over local males in a bat with female dispersal

Geographic variation of sexually selected male traits is common in animals. Female choice also varies geographically and several studies found female preference for local males, which is assumed to lead to local adaptation and, therefore, increases fitness. As females are the nondispersing sex in most mammalian taxa, this preference for local males might be explained by the learning of male characteristics. Studies on the preference of females in female-dispersing species are lacking so far. To find out whether such females would also show preferences for local males, we conducted a study on greater sac-winged bats (Saccopteryx bilineata), a species where females disperse and males stay in their natal colony. Male greater sac-winged bats possess a wing pouch that is filled with odoriferous secretion and fanned toward females during courtship display. In a combination of chemical analysis and behavioral preference tests, we analyzed whether the composition of wing sac secretion varies between two geographically distinct populations (300 km), and whether females show a preference for local or distant male scent. Using gas chromatography, we found significant differences in the composition of the wing sac odors between the two geographically distinct populations. In addition, the behavioral preference experiments revealed that females of both populations preferred the scent of geographically distant males over local males. The wing sac odor might thus be used to guarantee optimal outbreeding when dispersing to a new colony. This is—to our knowledge—the first study on odor preference of females of a species with female-biased dispersal.

Transcriptional regulation of wound suberin deposition in potato cultivars with differential wound healing capacity

Wounding during mechanical harvesting and post-harvest handling results in tuber desiccation and provides an entry point for pathogens resulting in substantial post​-harvest crop losses. Poor wound healing is a major culprit of these losses. Wound tissue in potato (Solanum tuberosum) tubers, and all higher plants, is composed of a large proportion of suberin that is deposited in a specialized tissue called the wound periderm. However, the genetic regulatory pathway controlling wound-induced suberization remains unknown. Here, we implicate two potato transcription factors, StMYB102 (PGSC0003DMG400011250) and StMYB74 (PGSC0003DMG400022399), as regulators of wound suberin biosynthesis and deposition. Using targeted metabolomics and transcript profiling from the wound healing tissues of two commercial potato cultivars, as well as heterologous expression, we provide evidence for the molecular-genetic basis of the differential wound suberization capacities of different potato cultivars. Our results suggest that (i) the export of suberin from the cytosol to the apoplast and ligno-suberin deposition may be limiting factors for wound suberization, (ii) StMYB74 and StMYB102 are important regulators of the wound suberization process in tubers, and (iii) polymorphisms in StMYB102 may influence cultivar-specific wound suberization capacity. These results represent an important step in understanding the regulated biosynthesis and deposition of wound suberin and provide a practical foundation for targeted breeding approaches aimed at improving potato tuber storage life.

A Machine Learning Approach to Study Demographic Alterations in Honeybee Colonies Using SDS-PAGE Fingerprinting

Honeybees, as social insects, live in highly organised colonies where tasks reflect the age of individuals. As is widely known, in this context, emergent properties arise from interactions between them. The accelerated maturation of nurses into foragers, stimulated by many negative factors, may disrupt this complex equilibrium. This complexity needs a paradigm shift: from the study of a single stressor to the study of the effects exerted by multiple stressors on colony homeostasis. The aim of this research is, therefore, to study colony population disturbances by discriminating overaged nurses from proper aged nurses and precocious foragers from proper aged foragers using SDS-PAGE patterns of haemolymph proteins and a machine-learning algorithm. The KNN (K Nearest Neighbours) model fitted on the forager dataset showed remarkably good performances (accuracy 0.93, sensitivity 0.88, specificity 1.00) in discriminating precocious foragers from proper aged ones. The main strength of this innovative approach lies in the possibility of it being deployed as a preventive tool. Depopulation is an elusive syndrome in bee pathology and early detection with the method described could shed more light on the phenomenon. In addition, it enables countermeasures to revert this vicious circle.

Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum

Plants show an extraordinary diversity in chemical composition and are characterized by different functional traits. However, relationships between the foliar primary and specialized metabolism in terms of metabolite numbers and composition as well as links with the leaf economics spectrum have rarely been explored. We investigated these relationships in leaves of 20 woody species from the Mediterranean region grown as saplings in a common garden, using a comparative ecometabolomics approach that included (semi-)polar primary and specialized metabolites. Our analyses revealed significant positive correlations between both the numbers and relative composition of primary and specialized metabolites. The leaf metabolomes were highly species-specific but in addition showed some phylogenetic imprints. Moreover, metabolomes of deciduous species were distinct from those of evergreens. Significant relationships were found between the primary metabolome and nitrogen content and carbon/nitrogen ratio, important traits of the leaf economics spectrum, ranging from acquisitive (mostly deciduous) to conservative (evergreen) leaves. A comprehensive understanding of various leaf traits and their coordination in different plant species may facilitate our understanding of plant functioning in ecosystems. Chemodiversity is thereby an important component of biodiversity.

Leaf Induction Impacts Behavior and Performance of a Pollinating Herbivore

Flowering plants use volatiles to attract pollinators while deterring herbivores. Vegetative and floral traits may interact to affect insect behavior. Pollinator behavior is most likely influenced by leaf traits when larval stages interact with plants in different ways than adult stages, such as when larvae are leaf herbivores but adult moths visit flowers as pollinators. Here, we determine how leaf induction and corresponding volatile differences in induced plants influence behavior in adult moths and whether these preferences align with larval performance. We manipulated vegetative induction in four Nicotiana species. Using paired induced and control plants of the same species with standardized artificial flowers, we measured foraging and oviposition choices by their ecologically and economically important herbivore/pollinator, Manduca sexta. In parallel, we measured growth rates of M. sexta larvae fed leaves from control or induced plants to determine if this was consistent with female oviposition preference. Lastly, we used plant headspace collections and gas chromatography to quantify volatile compounds from both induced and control leaves to link changes in plant chemistry with moth behavior. In the absence of floral chemical cues, vegetative defensive status influenced adult moth foraging preference from artificial flowers in one species (N. excelsior), where females nectared from induced plants more often than control plants. Plant vegetative resistance consistently influenced oviposition choice such that moths deposited more eggs on control plants than on induced plants of all four species. This oviposition preference for control plants aligned with higher larval growth rates on control leaves compared with induced leaves. Control and induced plants of each species had similar leaf volatile profiles, but induced plants had higher emission levels. Leaves of N. excelsior produced the most volatile compounds, including some inducible compounds typically associated with floral scent. We demonstrate that vegetative plant defensive volatiles play a role in host plant selection and that insects assess information from leaves differently when choosing between nectaring and oviposition locations. These results underscore the complex interactions between plants, their pollinators, and herbivores.

Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible

Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publication bias. Additionally, replication is often considered too difficult in field settings where many factors are beyond the investigator’s control and where spatial and temporal dependencies may be strong. We investigated the feasibility of reproducing original research findings in the field of chemical ecology by performing an exact replication of a previous study of Antarctic fur seals (Arctocephalus gazella). In the original study, skin swabs from 41 mother-offspring pairs from two adjacent breeding colonies on Bird Island, South Georgia, were analyzed using gas chromatography-mass spectrometry. Seals from the two colonies differed significantly in their chemical fingerprints, suggesting that colony membership may be chemically encoded, and mothers were also chemically similar to their pups, hinting at the possible involvement of phenotype matching in mother-offspring recognition. In the current study, we generated and analyzed chemical data from a non-overlapping sample of 50 mother-offspring pairs from the same two colonies 5 years later. The original results were corroborated in both hypothesis testing and estimation contexts, with p-values remaining highly significant and effect sizes, standardized between studies by bootstrapping the chemical data over individuals, being of comparable magnitude. However, exact replication studies are only capable of showing whether a given effect can be replicated in a specific setting. We therefore investigated whether chemical signatures are colony-specific in general by expanding the geographic coverage of our study to include pups from a total of six colonies around Bird Island. We detected significant chemical differences in all but a handful of pairwise comparisons between colonies. This finding adds weight to our original conclusion that colony membership is chemically encoded, and suggests that chemical patterns of colony membership not only persist over time but can also be generalized over space. Our study systematically confirms and extends our previous findings, while also implying more broadly that spatial and temporal heterogeneity need not necessarily negate the reproduction and generalization of ecological research findings.

The Effect of Algae or Insect Supplementation as Alternative Protein Sources on the Volatile Profile of Chicken Meat

The aim of this study was to investigate the differences in the volatile profile of meat from chickens fed with alternative protein diets (such as algae or insect) through two different trials. In Trial 1, broiler chicken at one day of age were randomly allocated to three experimental groups: a basal control diet (C) and two groups in which the soybean meal was replaced at 75% (in the starter phase) and 50% (in the grower phase) with partially defatted Hermetia illucens (HI) larvae or Arthrospira platensis (SP). In Trial 2, broiler chickens were housed and reared similar to Trial 1, with the exception that the experimental diets replaced soybean meal with either 100% partially defatted HI or 100% SP. In both trials, chickens were slaughtered at day 35. Per group, 10 chickens were submitted to volatile analysis by using solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) analysis. Results in both trials showed that levels of several lipid-derived compounds were found to be lower in chickens fed an HI diet, which could be linked to a possibly lower level of polyunsaturated fatty acid content in HI-fed chicken. In addition, the dietary treatments could be discriminated based on the volatile profile, i.e., the substitution of soy with HI or SP distinctively affected the levels of flavor compounds.

The evolution of sexually dimorphic cuticular hydrocarbons in blowflies (Diptera: Calliphoridae)

Cuticular hydrocarbons (CHCs) are organic compounds found on the cuticles of all insects which can act as close-contact pheromones, while also providing a hydrophobic barrier to water loss. Given their widespread importance in sexual behaviour and survival, CHCs have likely contributed heavily to the adaptation and speciation of insects. Despite this, the patterns and mechanisms of their diversification have been studied in very few taxa. Here, we perform the first study of CHC diversification in blowflies, focussing on wild populations of the ecologically diverse genus Chrysomya. We convert CHC profiles into qualitative and quantitative traits and assess their inter- and intra-specific variation across 10 species. We also construct a global phylogeny of Chrysomya, onto which CHCs were mapped to explore the patterns of their diversification. For the first time, we demonstrate that blowflies express an exceptional diversity of CHCs, which have diversified in a nonphylogenetic and punctuated manner, are species-specific and sexually dimorphic. It is likely that both ecological and sexual selection have shaped these patterns of CHC diversification, and our study now provides a comprehensive framework for testing such hypotheses.

Non-targeted discovery-based analysis for gas chromatography with mass spectrometry: A comparison of peak table, tile, and pixel-based Fisher ratio analysis

The ability to discover minute differences between samples or sample classes for gas chromatography coupled to mass spectrometry (GC-MS) can be a challenging endeavor, especially when those differences are not a priori. Fisher ratio (F-ratio) analysis is an apt technique to probe the differences between GC-MS chromatograms. F-ratio analysis is a supervised, non-targeted, discovery-based method that compares two different samples (or sample classes) to reduce the GC-MS dataset into a hit list composed of class distinguishing compounds. Three different F-ratio techniques, peak table, tile, and pixel-based were used to "discover" nine non-native analytes that were spiked into gasoline at four different nominal concentrations of 250, 85, 25, 5 parts-per-million (ppm). For the tile and pixel-based F-ratio calculations, a novel methodology is introduced to improve the sensitivity of the F-ratio calculations while reducing false positives. Furthermore, we use a combinatorial technique using null class comparisons, termed null distribution analysis, to determine a statistical F-ratio cutoff for analysis of the hit lists. The pixel-based algorithm was the most sensitive method and was able to "discover" all nine spiked analytes at a nominal concentration of 250 ppm albeit with one false positive interspersed towards the bottom of the hit list. The pixel-based software was also able to "discover" more of the spiked analytes at the lower concentrations with seven of the spiked analytes "discovered" at 85 ppm, four of the spiked analytes "discovered" at 25 ppm, and one analyte "discovered" at 5 ppm.

Genetic divergence and phenotypic plasticity contribute to variation in cuticular hydrocarbons in the seaweed fly Coelopa frigida

Cuticular hydrocarbons (CHCs) form the boundary between insects and their environments and often act as essential cues for species, mate, and kin recognition. This complex polygenic trait can be highly variable both among and within species, but the causes of this variation, especially the genetic basis, are largely unknown. In this study, we investigated phenotypic and genetic variation of CHCs in the seaweed fly, Coelopa frigida, and found that composition was affected by both genetic (sex and population) and environmental (larval diet) factors. We subsequently conducted behavioral trials that show CHCs are likely used as a sexual signal. We identified general shifts in CHC chemistry as well as individual compounds and found that the methylated compounds, mean chain length, proportion of alkenes, and normalized total CHCs differed between sexes and populations. We combined these data with whole genome resequencing data to examine the genetic underpinnings of these differences. We identified 11 genes related to CHC synthesis and found population-level outlier SNPs in 5 that are concordant with phenotypic differences. Together these results reveal that the CHC composition of C. frigida is dynamic, strongly affected by the larval environment, and likely under natural and sexual selection.

Desiccation-Driven Senescence in the Resurrection Plant Xerophyta schlechteri (Baker) N.L. Menezes: Comparison of Anatomical, Ultrastructural, and Metabolic Responses Between Senescent and Non-Senescent Tissues

Drought-induced senescence is a degenerative process that involves the degradation of cellular metabolites and photosynthetic pigments and uncontrolled dismantling of cellular membranes and organelles. Angiosperm resurrection plants display vegetative desiccation tolerance and avoid drought-induced senescence in most of their tissues. Developmentally older tissues, however, fail to recover during rehydration and ultimately senesce. Comparison of the desiccation-associated responses of older senescent tissues (ST) with non-ST (NST) will allow for understanding of mechanisms promoting senescence in the former and prevention of senescence in the latter. In the monocotyledonous resurrection plant Xerophyta schlechteri (Baker) N.L. Menezes*, leaf tips senesce following desiccation, whereas the rest of the leaf blade survives. We characterized structural and metabolic changes in ST and NST at varying water contents during desiccation and rehydration. Light and transmission electron microscopy was used to follow anatomical and subcellular responses, and metabolic differences were studied using gas chromatography-mass spectrometry and colorimetric metabolite assays. The results show that drying below 35% relative water content (0.7 gH2O/g dry mass) in ST resulted in the initiation of age-related senescence hallmarks and that these tissues continue this process after rehydration. We propose that an age-related desiccation sensitivity occurs in older tissues, in a process metabolically similar to that observed during age-related senescence in Arabidopsis thaliana.

The metaRbolomics Toolbox in Bioconductor and beyond

Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.

A Toolbox for Diverse Oxyfunctionalisation of Monoterpenes

The successful implementation of synthetic biology for chemicals biosynthesis relies on the availability of large libraries of well-characterized enzymatic building blocks. Here we present a scalable pipeline that applies the methodology of synthetic biology itself to bootstrap the creation of such a library. By designing and building a cytochrome P450 enzyme collection and testing it in a custom-made untargeted GC/MS-metabolomics-based approach, we were able to rapidly create and characterize a comprehensive enzyme library for the controlled oxyfunctionalisation of terpene scaffolds with a wide range of activities and selectivities towards several monoterpenes. This novel resource can now be used to access the extensive chemical diversity of terpenoids by pathway engineering and the assembly of biocatalytic cascades to subsequently produce libraries of oxygenated terpenoids and their derivatives for diverse applications, including drug discovery.