DNA methylation machinery is involved in development and reproduction in the viviparous pea aphid (Acyrthosiphon pisum).

Epigenetic mechanisms, such as DNA methylation, have been proposed to mediate plastic responses in insects. The pea aphid (Acyrthosiphon pisum), like the majority of extant aphids, displays cyclical parthenogenesis - the ability of mothers to switch the reproductive mode of their offspring from reproducing parthenogenetically to sexually in response to environmental cues. The pea aphid genome encodes two paralogs of the de novo DNA methyltransferase gene, dnmt3a and dnmt3x. Here we show, using phylogenetic analysis, that this gene duplication event occurred at least 150 million years ago, likely after the divergence of the lineage leading to the Aphidomorpha (phylloxerans, adelgids and true aphids) from that leading to the scale insects (Coccomorpha) and that the two paralogs are maintained in the genomes of all aphids examined. We also show that the mRNA of both dnmt3 paralogs is maternally expressed in the viviparous aphid ovary. During development both paralogs are expressed in the germ cells of embryos beginning at stage 5 and persisting throughout development. Treatment with 5-azactyidine, a chemical that generally inhibits the DNA methylation machinery, leads to defects of oocytes and early-stage embryos and causes a proportion of later stage embryos to be born dead or die soon after birth. These phenotypes suggest a role for DNA methyltransferases in reproduction, consistent with that seen in other insects. Taking the vast evolutionary history of the dnmt3 paralogs, and the localisation of their mRNAs in the ovary, we suggest there is a role for dnmt3a and/or dnmt3x in early development, and a role for DNA methylation machinery in reproduction and development of the viviparous pea aphid.

Sensory perception of rivals has trait-dependent effects on plasticity in Drosophila melanogaster.

The social environment has myriad effects on individuals, altering reproduction, immune function, cognition, and aging. Phenotypic plasticity enables animals to respond to heterogeneous environments such as the social environment but requires that they assess those environments accurately. It has been suggested that combinations of sensory cues allow animals to respond rapidly and accurately to changeable environments, but it is unclear whether the same sensory inputs are required in all traits that respond to a particular environmental cue. Drosophila melanogaster males, in the presence of rival males, exhibit a consistent behavioral response by extending mating duration. However, exposure to a rival also results in a reduction in their lifespan, a phenomenon interpreted as a trade-off associated with sperm competition strategies. D. melanogaster perceive their rivals by using multiple sensory cues; interfering with at least two olfactory, auditory, or tactile cues eliminates the extension of mating duration. Here, we assessed whether these same cues were implicated in the lifespan reduction. Removal of combinations of auditory and olfactory cues removed the extended mating duration response to a rival, as previously found. However, we found that these manipulations did not alter the reduction in lifespan of males exposed to rivals or induce any changes in activity patterns, grooming, or male-male aggression. Therefore, our analysis suggests that lifespan reduction is not a cost associated with the behavioral responses to sperm competition. Moreover, this highlights the trait-specific nature of the mechanisms underlying plasticity in response to the same environmental conditions.

One genome, multiple phenotypes: decoding the evolution and mechanisms of environmentally induced developmental plasticity in insects.

Plasticity in developmental processes gives rise to remarkable environmentally induced phenotypes. Some of the most striking and well-studied examples of developmental plasticity are seen in insects. For example, beetle horn size responds to nutritional state, butterfly eyespots are enlarged in response to temperature and humidity, and environmental cues also give rise to the queen and worker castes of eusocial insects. These phenotypes arise from essentially identical genomes in response to an environmental cue during development. Developmental plasticity is taxonomically widespread, affects individual fitness, and may act as a rapid-response mechanism allowing individuals to adapt to changing environments. Despite the importance and prevalence of developmental plasticity, there remains scant mechanistic understanding of how it works or evolves. In this review, we use key examples to discuss what is known about developmental plasticity in insects and identify fundamental gaps in the current knowledge. We highlight the importance of working towards a fully integrated understanding of developmental plasticity in a diverse range of species. Furthermore, we advocate for the use of comparative studies in an evo-devo framework to address how developmental plasticity works and how it evolves.

Honeybee queen mandibular pheromone induces a starvation response in Drosophila melanogaster.

Eusocial insect societies are defined by the reproductive division of labour, a social structure that is generally enforced by the reproductive dominant(s) or 'queen(s)'. Reproductive dominance is maintained through behavioural dominance or production of queen pheromones, or a mixture of both. Queen mandibular pheromone (QMP) is a queen pheromone produced by queen honeybees (Apis mellifera) which represses reproduction in worker honeybees. How QMP acts to repress worker reproduction, the mechanisms by which this repression is induced, and how it has evolved this activity, remain poorly understood. Surprisingly, QMP is capable of repressing reproduction in non-target arthropods. Here we show that in Drosophila melanogaster QMP treatment mimics the starvation response, disrupting reproduction. QMP exposure induces an increase in food consumption and activation of checkpoints in the ovary that reduce fecundity and depresses insulin signalling. The magnitude of these effects is indistinguishable between QMP-treated and starved individuals. As QMP triggers a starvation response in an insect diverged from honeybees, we propose that QMP originally evolved by co-opting nutrition signalling pathways to regulate reproduction.

Environmentally responsive reproduction: neuroendocrine signalling and the evolution of eusociality.

Eusociality is a rare but successful life-history strategy that is defined by the reproductive division of labour. In eusocial species, most females forgo their own reproduction to support that of a dominant female or queen. In many eusocial insects, worker reproduction is inhibited via dominance hierarchies or by pheromones produced by the queen and her brood. Here, we consider whether these cues may act as generic 'environmental signals', similar to temperature or nutrition stress, which induce a state of reproductive dormancy in some solitary insects. We review the recent findings regarding the mechanisms of reproductive dormancy in insects and highlight key gaps in our understanding of how environmental cues inhibit reproduction.

Noggin proteins are multifunctional extracellular regulators of cell signaling.

Noggin is an extracellular cysteine knot protein that plays a crucial role in vertebrate dorsoventral patterning. Noggin binds and inhibits the activity of bone morphogenetic proteins via a conserved N-terminal clip domain. Noncanonical orthologs of Noggin that lack a clip domain ("Noggin-like" proteins) are encoded in many arthropod genomes and are thought to have evolved into receptor tyrosine kinase ligands that promote Torso/receptor tyrosine kinase signaling rather than inhibiting bone morphogenic protein signaling. Here, we examined the molecular function of noggin/noggin-like genes (ApNL1 and ApNL2) from the arthropod pea aphid using the dorso-ventral patterning of Xenopus and the terminal patterning system of Drosophila to identify whether these proteins function as bone morphogenic protein or receptor tyrosine kinase signaling regulators. Our findings reveal that ApNL1 from the pea aphid can regulate both bone morphogenic protein and receptor tyrosine kinase signaling pathways, and unexpectedly, that the clip domain is not essential for its antagonism of bone morphogenic protein signaling. Our findings indicate that ancestral noggin/noggin-like genes were multifunctional regulators of signaling that have specialized to regulate multiple cell signaling pathways during the evolution of animals.

Phenotypic Plasticity: What Has DNA Methylation Got to Do with It?

How does one genome give rise to multiple, often markedly different, phenotypes in response to an environmental cue? This phenomenon, known as phenotypic plasticity, is common amongst plants and animals, but arguably the most striking examples are seen in insects. Well-known insect examples include seasonal morphs of butterfly wing patterns, sexual and asexual reproduction in aphids, and queen and worker castes of eusocial insects. Ultimately, we need to understand how phenotypic plasticity works at a mechanistic level; how do environmental signals alter gene expression, and how are changes in gene expression translated into novel morphology, physiology and behaviour? Understanding how plasticity works is of major interest in evolutionary-developmental biology and may have implications for understanding how insects respond to global change. It has been proposed that epigenetic mechanisms, specifically DNA methylation, are the key link between environmental cues and changes in gene expression. Here, we review the available evidence on the function of DNA methylation of insects, the possible role(s) for DNA methylation in phenotypic plasticity and also highlight key outstanding questions in this field as well as new experimental approaches to address these questions.

Genomic Signatures of Recent Adaptation in a Wild Bumblebee.

Environmental changes threaten insect pollinators, creating risks for agriculture and ecosystem stability. Despite their importance, we know little about how wild insects respond to environmental pressures. To understand the genomic bases of adaptation in an ecologically important pollinator, we analyzed genomes of Bombus terrestris bumblebees collected across Great Britain. We reveal extensive genetic diversity within this population, and strong signatures of recent adaptation throughout the genome affecting key processes including neurobiology and wing development. We also discover unusual features of the genome, including a region containing 53 genes that lacks genetic diversity in many bee species, and a horizontal gene transfer from a Wolbachia bacteria. Overall, the genetic diversity we observe and how it is distributed throughout the genome and the population should support the resilience of this important pollinator species to ongoing and future selective pressures. Applying our approach to more species should help understand how they can differ in their adaptive potential, and to develop conservation strategies for those most at risk.

The development of an unsupervised hierarchical clustering analysis of dual-polarization weather surveillance radar observations to assess nocturnal insect abundance and diversity.

Contemporary analyses of insect population trends are based, for the most part, on a large body of heterogeneous and short-term datasets of diurnal species that are representative of limited spatial domains. This makes monitoring changes in insect biomass and biodiversity difficult. What is needed is a method for monitoring that provides a consistent, high-resolution picture of insect populations through time over large areas during day and night. Here, we explore the use of X-band weather surveillance radar (WSR) for the study of local insect populations using a high-quality, multi-week time series of nocturnal moth light trapping data. Specifically, we test the hypotheses that (i) unsupervised data-driven classification algorithms can differentiate meteorological and biological phenomena, (ii) the diversity of the classes of bioscatterers are quantitatively related to the diversity of insects as measured on the ground and (iii) insect abundance measured at ground level can be predicted quantitatively based on dual-polarization Doppler WSR variables. Adapting the quasi-vertical profile analysis method and data clustering techniques developed for the analysis of hydrometeors, we demonstrate that our bioscatterer classification algorithm successfully differentiates bioscatterers from hydrometeors over a large spatial scale and at high temporal resolutions. Furthermore, our results also show a clear relationship between biological and meteorological scatterers and a link between the abundance and diversity of radar-based bioscatterer clusters and that of nocturnal aerial insects. Thus, we demonstrate the potential utility of this approach for landscape scale monitoring of biodiversity.

Development of a multiplex microsatellite marker set for the study of the solitary red mason bee, Osmia bicornis (Megachilidae).

BACKGROUND: Solitary bees, such as the red mason bee (Osmia bicornis), provide important ecosystem services including pollination. In the face of global declines of pollinator abundance, such haplodiploid Hymenopterans have a compounded extinction risk due to the potential for limited genetic diversity. In order to assess the genetic diversity of Osmia bicornis populations, we developed microsatellite markers and characterised them in two populations. METHODS AND RESULTS: Microsatellite sequences were mined from the recently published Osmia bicornis genome, which was assembled from DNA extracted from a single male bee originating from the United Kingdom. Sequences were identified that contained dinucleotide, trinucleotide, and tetranucleotide repeat regions. Seventeen polymorphic microsatellite markers were designed and tested, sixteen of which were developed into four multiplex PCR sets to facilitate cheap, fast and efficient genotyping and were characterised in unrelated females from Germany (n = 19) and England (n = 14). CONCLUSIONS: The microsatellite markers are highly informative, with a combined exclusion probability of 0.997 (first parent), which will enable studies of genetic structure and diversity to inform conservation efforts in this bee.

Social competition stimulates cognitive performance in a sex-specific manner.

Social interactions are thought to be a critical driver in the evolution of cognitive ability. Cooperative interactions, such as pair bonding, rather than competitive interactions have been largely implicated in the evolution of increased cognition. This is despite competition traditionally being a very strong driver of trait evolution. Males of many species track changes in their social environment and alter their reproductive strategies in response to anticipated levels of competition. We predict this to be cognitively challenging. Using a Drosophila melanogaster model, we are able to distinguish between the effects of a competitive environment versus generic social contact by exposing flies to same-sex same-species competition versus different species partners, shown to present non-competitive contacts. Males increase olfactory learning/memory and visual memory after exposure to conspecific males only, a pattern echoed by increased expression of synaptic genes and an increased need for sleep. For females, largely not affected by mating competition, the opposite pattern was seen. The results indicate that specific social contacts dependent on sex, not simply generic social stimulation, may be an important evolutionary driver for cognitive ability in fruit flies.

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus.

Social wasps of the genus Vespula have spread to nearly all landmasses worldwide and have become significant pests in their introduced ranges, affecting economies and biodiversity. Comprehensive genome assemblies and annotations for these species are required to develop the next generation of control strategies and monitor existing chemical control. We sequenced and annotated the genomes of the common wasp (Vespula vulgaris), German wasp (Vespula germanica), and the western yellowjacket (Vespula pensylvanica). Our chromosome-level Vespula assemblies each contain 176-179 Mb of total sequence assembled into 25 scaffolds, with 10-200 unanchored scaffolds, and 16,566-18,948 genes. We annotated gene sets relevant to the applied management of invasive wasp populations, including genes associated with spermatogenesis and development, pesticide resistance, olfactory receptors, immunity and venom. These genomes provide evidence for active DNA methylation in Vespidae and tandem duplications of venom genes. Our genomic resources will contribute to the development of next-generation control strategies, and monitoring potential resistance to chemical control.

The diversity and distribution of D1 proteins in cyanobacteria.

The psbA gene family in cyanobacteria encodes different forms of the D1 protein that is part of the Photosystem II reaction centre. We have identified a phylogenetically distinct D1 group that is intermediate between previously identified G3-D1 and G4-D1 proteins (Cardona et al. Mol Biol Evol 32:1310-1328, 2015). This new group contained two subgroups: D1INT, which was frequently in the genomes of heterocystous cyanobacteria and D1FR that was part of the far-red light photoacclimation gene cluster of cyanobacteria. In addition, we have identified subgroups within G3, the micro-aerobically expressed D1 protein. There are amino acid changes associated with each of the subgroups that might affect the function of Photosystem II. We show a phylogenetically broad range of cyanobacteria have these D1 types, as well as the genes encoding the G2 protein and chlorophyll f synthase. We suggest identification of additional D1 isoforms and the presence of multiple D1 isoforms in phylogenetically diverse cyanobacteria supports the role of these proteins in conferring a selective advantage under specific conditions.

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera).

Phenotypic plasticity, the ability of an organism to alter its phenotype in response to an environmental cue, facilitates rapid adaptation to changing environments. Plastic changes in morphology and behavior are underpinned by widespread gene expression changes. However, it is unknown if, or how, genomes are structured to ensure these robust responses. Here, we use repression of honeybee worker ovaries as a model of plasticity. We show that the honeybee genome is structured with respect to plasticity; genes that respond to an environmental trigger are colocated in the honeybee genome in a series of gene clusters, many of which have been assembled in the last 80 My during the evolution of the Apidae. These clusters are marked by histone modifications that prefigure the gene expression changes that occur as the ovary activates, suggesting that these genomic regions are poised to respond plastically. That the linear sequence of the honeybee genome is organized to coordinate widespread gene expression changes in response to environmental influences and that the chromatin organization in these regions is prefigured to respond to these influences is perhaps unexpected and has implications for other examples of plasticity in physiology, evolution, and human disease.

Mating status and the evolution of eusociality: Oogenesis is independent of mating status in the solitary bee Osmia bicornis.

The fundamental trait underlying eusociality is the reproductive division of labour. In honeybees (Apis mellifera), queens lay eggs while workers forage, defend and care for brood. The division of labour is maintained by pheromones including queen mandibular pheromone (QMP) produced by the queen. QMP constrains reproduction in adult honeybee workers, but in the absence of their queen workers can activate their ovaries and, although they cannot mate, they lay haploid male eggs. The reproductive ground plan hypothesis suggests that reproductive constraint may have evolved by co-opting mechanisms of reproductive control in solitary ancestors. In many insects mating is required to activate or accelerate oogenesis. Here, we use the solitary bee Osmia bicornis (Megachilidae) to test whether reproductive constraint evolved from ancestral control of reproduction by mating status. We present a structural study of the O. bicornis ovary, and compare key stages of oogenesis with honeybee workers. Importantly, we show that mating does not affect any aspect of the reproductive physiology of O. bicornis. We therefore conclude that mechanisms governing reproductive constraint in honeybees were unlikely to have been co-opted from mechanisms pertaining to mating status.

Ancestral hymenopteran queen pheromones do not share the broad phylogenetic repressive effects of honeybee queen mandibular pheromone.

Queen pheromones effect the reproductive division of labour, a defining feature of eusociality. Reproductive division of labour ensures that one, or a small number of, females are responsible for the majority of reproduction within a colony. Much work on the evolution and function of these pheromones has focussed on Queen Mandibular Pheromone (QMP) which is produced by the Western or European honeybee (Apis mellifera). QMP has phylogenetically broad effects, repressing reproduction in a variety of arthropods, including those distantly related to the honeybee such as the fruit fly Drosophila melanogaster. QMP is highly derived and has little chemical similarity to the majority of hymenopteran queen pheromones which are derived from cuticular hydrocarbons. This raises the question of whether the phylogenetically widespread repression of reproduction by QMP also occurs with more basal saturated hydrocarbon-based queen-pheromones. Using D. melanogaster we show that saturated hydrocarbons are incapable of repressing reproduction, unlike QMP. We also show no interaction between the four saturated hydrocarbons tested or between the saturated hydrocarbons and QMP, implying that there is no conservation in the mechanism of detection or action between these compounds. We propose that the phylogenetically broad reproductive repression seen in response to QMP is not a feature of all queen pheromones, but unique to QMP itself, which has implications for our understanding of how queen pheromones act and evolve.

Correction to: From genes to environment in shaping of an embryo: understanding embryonic-extraembryonic interactions at the BSDB autumn meeting in Oxford.

The authors of the article Ajduk & Duncan 2019 sincerely apologize for specifying the incorrect institutional affiliation for Professor Ali Brivanlou and also the incorrect spelling of Professor Brivanlou's surname in the text of the article.

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

BACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

From genes to environment in shaping of an embryo: understanding embryonic-extraembryonic interactions at the BSDB autumn meeting in Oxford.

The British Society for Developmental Biology Autumn Meeting, held in Oxford in September 2018, was the third in a series of international workshops which have been focussed on development at the extraembryonic-embryonic interface. This workshop, entitled "Embryonic-Extraembryonic Interactions: from Genetics to Environment" built on the two previous workshops held in 2011 (Leuven, Belgium) and 2015 (Göttingen, Germany). This workshop brought together researchers utilising a diverse range of organisms (including both vertebrate and invertebrate species) and a range of experimental approaches to answer core questions in developmental biology. This meeting report highlights some of the major themes emerging from the workshop including an evolutionary perspective as well as recent advances that have been made through the adoption of emerging techniques and technologies.