Evolution of tissue-specific expression of ancestral genes across vertebrates and insects.

Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 bilaterian species and performed analyses using a symmetric phylogeny that allowed the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes (for example, novel cell types). Such pervasive evolution of tissue specificity was linked to gene duplication coupled with expression specialization of one of the copies, revealing an unappreciated prolonged effect of whole-genome duplications on recent vertebrate evolution.

The efficiency of varying methods and degrees of time compensation for the solar azimuth.

Daytime migrants are known to orientate using the position of the sun, compensating for its changing position throughout the day with a 'time-compensated sun compass'. This compass has been demonstrated in many migratory species, with various degrees of accuracy for the actual movement of the sun. Here, we present a model for differing levels of compensation for the solar ephemeris that shows that a high degree of efficiency, in terms of distance travelled, can be achieved without full time compensation. In our model, compensating for the sun's position had a diminishing return with an accuracy of 80% leading to only a 2% reduction in distance travelled. We compare various modes of time compensation-full, partial, time averaged and step-revealing their directional efficiency in terms of distance travelled under an autumn migration scenario. We find that the benefit of time compensation varies with latitude, with time averaging performing very well, especially at all high latitudes, but step compensation performing better at very low latitudes. Importantly, even rudimentary adjustment can dramatically increase the efficiency of migration, which suggests an easy pathway for the independent evolution of time compensation.

The genome sequence of the Lesser Hornet Hoverfly, Volucella inanis (Linnaeus, 1758).

We present a genome assembly from an individual female Volucella inanis (the Lesser Hornet Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 961 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, including the assembled X sex chromosome. The mitochondrial genome has also been assembled and is 16.0 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,616 protein coding genes.

The genome sequence of the Vagrant Hoverfly, Eupeodes corollae (Fabricius, 1794).

We present a genome assembly from an individual female Eupeodes corollae (the Vagrant Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 648.2 megabases in span. Most of the assembly is scaffolded into four chromosomal pseudomolecules, including with the X sex chromosome. The mitochondrial genome has also been assembled and is 18.3 kilobases in length.

Bat activity correlated with migratory insect bioflows in the Pyrenees.

High altitude mountain passes in the Pyrenees are known to be important migratory hotspots for autumn migrating insects originating from large swathes of northern Europe. In the Pyrenees, prior research has focused on diurnal migratory insects. In this study, we investigate the nocturnal component of the migratory assemblage and ask if this transient food source is also used by bat species. Three seasons of insect trapping revealed 66 species of four different orders, 90% of which were Noctuid moths, including the destructive pest Helicoverpa armigera, otherwise known as the cotton bollworm. Acoustic bat detectors revealed that high activity of Nyctalus spp. and Tadarida teniotis bats were closely synchronized with the arrival of the migratory moths, suggesting this food source is important for both resident and migratory bats to build or maintain energy reserves. Bats of the Nyctalus spp. are likely migrating through the study site using fly-and-forage strategies or stopping over in the area, while resident T. teniotis may be exploiting the abundant food source to build fat stores for hibernation. This study shows that nocturnal migratory insects are abundant in the Pyrenees during autumn and interact during migration, not only with their co-migrant bats but also with resident bat species.

Migratory hoverflies orientate north during spring migration.

Migratory hoverflies are long-range migrants that, in the Northern Hemisphere, move seasonally to higher latitudes in the spring and lower latitudes in the autumn. The preferred migratory direction of hoverflies in the autumn has been the subject of radar and flight simulator studies, while spring migration has proved to be more difficult to characterize owing to a lack of ground observations. Consequently, the preferred migratory direction during spring has only been inferred from entomological radar studies and patterns of local abundance, and currently lacks ground confirmation. Here, during a springtime arrival of migratory insects onto the Isles of Scilly and mainland Cornwall, UK, we provide ground proof that spring hoverfly migrants have an innate northward preference. Captured migratory hoverflies displayed northward vanishing bearings when released under sunny conditions under both favourable wind and zero-wind conditions. In addition, and unlike autumn migrants, spring individuals were also able to orientate when the sun was obscured. Analysis of winds suggests an origin for insects arriving on the Isles of Scilly as being in western France. These findings of spring migration routes and preferred migration directions are likely to extend to the diverse set of insects found within the western European migratory assemblage.

Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration.

Insects are capable of extraordinary feats of long-distance movement that have profound impacts on the function of terrestrial ecosystems. The ability to undertake these movements arose multiple times through the evolution of a suite of traits that make up the migratory syndrome, however the underlying genetic pathways involved remain poorly understood. Migratory hoverflies (Diptera: Syrphidae) are an emerging model group for studies of migration. They undertake seasonal movements in huge numbers across large parts of the globe and are important pollinators, biological control agents and decomposers. Here, we assembled a high-quality draft genome of the marmalade hoverfly (Episyrphus balteatus). We leveraged this genomic resource to undertake a genome-wide transcriptomic comparison of actively migrating Episyrphus, captured from a high mountain pass as they flew south to overwinter, with the transcriptomes of summer forms which were non-migratory. We identified 1543 genes with very strong evidence for differential expression. Interrogation of this gene set reveals a remarkable range of roles in metabolism, muscle structure and function, hormonal regulation, immunity, stress resistance, flight and feeding behaviour, longevity, reproductive diapause and sensory perception. These features of the migrant phenotype have arisen by the integration and modification of pathways such as insulin signalling for diapause and longevity, JAK/SAT for immunity, and those leading to octopamine production and fuelling to boost flight capabilities. Our results provide a powerful genomic resource for future research, and paint a comprehensive picture of global expression changes in an actively migrating insect, identifying key genomic components involved in this important life-history strategy.

Hoverflies use a time-compensated sun compass to orientate during autumn migration.

The sun is the most reliable celestial cue for orientation available to daytime migrants. It is widely assumed that diurnal migratory insects use a 'time-compensated sun compass' to adjust for the changing position of the sun throughout the day, as demonstrated in some butterfly species. The mechanisms used by other groups of diurnal insect migrants remain to be elucidated. Migratory species of hoverflies (Diptera: Syrphidae) are one of the most abundant and beneficial groups of diurnal migrants, providing multiple ecosystem services and undergoing directed seasonal movements throughout much of the temperate zone. To identify the hoverfly navigational strategy, a flight simulator was used to measure orientation responses of the hoverflies Scaeva pyrastri and Scaeva selenitica to celestial cues during their autumn migration. Hoverflies oriented southwards when they could see the sun and shifted this orientation westward following a 6 h advance of their circadian clocks. Our results demonstrate the use of a time-compensated sun compass as the primary navigational mechanism, consistent with field observations that hoverfly migration occurs predominately under clear and sunny conditions.

Adaptive strategies of high-flying migratory hoverflies in response to wind currents.

Large migrating insects, flying at high altitude, often exhibit complex behaviour. They frequently elect to fly on winds with directions quite different from the prevailing direction, and they show a degree of common orientation, both of which facilitate transport in seasonally beneficial directions. Much less is known about the migration behaviour of smaller (10-70 mg) insects. To address this issue, we used radar to examine the high-altitude flight of hoverflies (Diptera: Syrphidae), a group of day-active, medium-sized insects commonly migrating over the UK. We found that autumn migrants, which must move south, did indeed show migration timings and orientation responses that would take them in this direction, despite the unfavourability of the prevailing winds. Evidently, these hoverfly migrants must have a compass (probably a time-compensated solar mechanism), and a means of sensing the wind direction (which may be determined with sufficient accuracy at ground level, before take-off). By contrast, hoverflies arriving in the UK in spring showed weaker orientation tendencies, and did not correct for wind drift away from their seasonally adaptive direction (northwards). However, the spring migrants necessarily come from the south (on warm southerly winds), so we surmise that complex orientation behaviour may not be so crucial for the spring movements.

Pollination by hoverflies in the Anthropocene.

Pollinator declines, changes in land use and climate-induced shifts in phenology have the potential to seriously affect ecosystem function and food security by disrupting pollination services provided by insects. Much of the current research focuses on bees, or groups other insects together as 'non-bee pollinators', obscuring the relative contribution of this diverse group of organisms. Prominent among the 'non-bee pollinators' are the hoverflies, known to visit at least 72% of global food crops, which we estimate to be worth around US$300 billion per year, together with over 70% of animal pollinated wildflowers. In addition, hoverflies provide ecosystem functions not seen in bees, such as crop protection from pests, recycling of organic matter and long-distance pollen transfer. Migratory species, in particular, can be hugely abundant and unlike many insect pollinators, do not yet appear to be in serious decline. In this review, we contrast the roles of hoverflies and bees as pollinators, discuss the need for research and monitoring of different pollinator responses to anthropogenic change and examine emerging research into large populations of migratory hoverflies, the threats they face and how they might be used to improve sustainable agriculture.

Mass Seasonal Migrations of Hoverflies Provide Extensive Pollination and Crop Protection Services.

Despite the fact that migratory insects dominate aerial bioflows in terms of diversity, abundance, and biomass [1-6], the migration patterns of most species, and the effects of their annual fluxes between high- and low-latitude regions, are poorly known. One important group of long-range migrants that remain understudied is a suite of highly beneficial species of hoverfly in the tribe Syrphini, which we collectively term "migrant hoverflies." Adults are key pollinators [7-10] and larvae are significant biocontrol agents of aphid crop pests [11], and thus, it is important to quantify the scale of their migrations and the crucial ecosystem services they provide with respect to energy, nutrient, and biomass transport; regulation of crop pests; and pollen transfer. Such assessments cannot be made by sporadic observations of mass arrivals at ground level, because hoverflies largely migrate unnoticed high above ground. We used insect-monitoring radars [12] to show that up to 4 billion hoverflies (80 tons of biomass) travel high above southern Britain each year in seasonally adaptive directions. The long-range migrations redistribute tons of essential nutrients (nitrogen [N] and phosphorus [P]) and transport billions of pollen grains between Britain and Europe, and locally produced populations consume 6 trillion aphids and make billions of flower visits. Migrant hoverfly abundance fluctuated greatly between years, but there was no evidence of a population trend during the 10-year study period. Considering that many beneficial insects are seriously declining [7, 10, 13-19], our results demonstrate that migrant hoverflies are key to maintaining essential ecosystem services.

Quantification of migrant hoverfly movements (Diptera: Syrphidae) on the West Coast of North America.

The seasonal migration of huge numbers of hoverflies is frequently reported in Europe from mountain passes or spurs of land. The movement of such large numbers of beneficial insects is thought to provide significant ecosystem services in terms of pollination and pest control. Observations from the East Coast of the USA during the 1920s indicate the presence of migratory life histories among some hoverfly species there, but 90 years have now passed since the last reported observation of hoverfly migration in the USA. Here, we analyse video footage taken during a huge northward migration of hoverflies on 20 April 2017 on the West Coast of California. The quantification of migrant numbers from this footage allows us to estimate the passage of over 100 000 hoverflies in half an hour over a 200 m section of headland in Montaña de Oro State Park (San Luis Obispo County). Field collections and analysis of citizen science data indicate different species from the previously reported Eristalis tenax migrations on the East Coast of the USA and provide evidence for migration among North American hoverflies. We wish to raise awareness of this phenomenon and suggest approaches to advance the study of hoverfly migration in North America and elsewhere.

tarsal-less is expressed as a gap gene but has no gap gene phenotype in the moth midge Clogmia albipunctata.

Gap genes are involved in segment determination during early development of the vinegar fly Drosophila melanogaster and other dipteran insects (flies, midges and mosquitoes). They are expressed in overlapping domains along the antero-posterior (A-P) axis of the blastoderm embryo. While gap domains cover the entire length of the A-P axis in Drosophila, there is a region in the blastoderm of the moth midge Clogmia albipunctata, which lacks canonical gap gene expression. Is a non-canonical gap gene functioning in this area? Here, we characterize tarsal-less (tal) in C. albipunctata. The homologue of tal in the flour beetle Tribolium castaneum (called milles-pattes, mlpt) is a bona fide gap gene. We find that Ca-tal is expressed in the region previously reported as lacking gap gene expression. Using RNA interference, we study the interaction of Ca-tal with gap genes. We show that Ca-tal is regulated by gap genes, but only has a very subtle effect on tailless (Ca-tll), while not affecting other gap genes at all. Moreover, cuticle phenotypes of Ca-tal depleted embryos do not show any gap phenotype. We conclude that Ca-tal is expressed and regulated like a gap gene, but does not function as a gap gene in C. albipunctata.

A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila.

Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, such as the vinegar fly Drosophila melanogaster, determine all segments simultaneously through a hierarchical cascade of gene regulation. Gap genes constitute the first layer of the Drosophila segmentation gene hierarchy, downstream of maternal gradients such as that of Caudal (Cad). We use data-driven mathematical modelling and phase space analysis to show that shifting gap domains in the posterior half of the Drosophila embryo are an emergent property of a robust damped oscillator mechanism, suggesting that the regulatory dynamics underlying long- and short-germband segmentation are much more similar than previously thought. In Tribolium, Cad has been proposed to modulate the frequency of the segmentation oscillator. Surprisingly, our simulations and experiments show that the shift rate of posterior gap domains is independent of maternal Cad levels in Drosophila. Our results suggest a novel evolutionary scenario for the short- to long-germband transition and help explain why this transition occurred convergently multiple times during the radiation of the holometabolan insects.

Non-canonical dorsoventral patterning in the moth midge Clogmia albipunctata.

BACKGROUND: Bone morphogenetic proteins (BMPs) are of central importance for dorsal-ventral (DV) axis specification. They are core components of a signalling cascade that includes the BMP ligand decapentaplegic (DPP) and its antagonist short gastrulation (SOG) in Drosophila melanogaster. These components are very ancient, with orthologs involved in DV patterning in both protostomes and deuterostomes. Despite such strong conservation, recent comparative work in insects has revealed interesting differences in the way the patterning function of the DV system is achieved in different species. RESULTS: In this paper, we characterise the expression patterns of the principal components of the BMP DV patterning system, as well as its signalling outputs and downstream targets, in the non-cyclorrhaphan moth midge Clogmia albipunctata (Diptera: Psychodidae). We previously reported ventral expression patterns of dpp in the pole regions of C. albipunctata blastoderm embryos. Strikingly, we also find ventral sog and posteriorly restricted tkv expression, as well as expanded polar activity of pMad. We use our results from gene knock-down by embryonic RNA interference to propose a mechanism of polar morphogen shuttling in C. albipunctata. We compare these results to available data from other species and discuss scenarios for the evolution of DV signalling in the holometabolan insects. CONCLUSIONS: A comparison of gene expression patterns across hemipteran and holometabolan insects reveals that expression of upstream signalling factors in the DV system is very variable, while signalling output is highly conserved. This has two major implications: first, as long as ligand shuttling and other upstream regulatory mechanisms lead to an appropriately localised activation of BMP signalling at the dorsal midline, it is of less importance exactly where the upstream components of the DV system are expressed. This, in turn, explains why the early-acting components of the DV patterning system in insects exhibit extensive amounts of developmental systems drift constrained by highly conserved downstream signalling output.

Gap Gene Regulatory Dynamics Evolve along a Genotype Network.

Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as "system drift." System drift is illustrated by the gap gene network-involved in segmental patterning-in dipteran insects. In the classic model organism Drosophila melanogaster and the nonmodel scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data in M. abdita and compare them with an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of "genotype networks" and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability).

Rearing the scuttle fly Megaselia scalaris (Diptera: Phoridae) on industrial compounds: implications on size and lifespan.

Megaselia scalaris (Loew, 1866) (Diptera, phoridae) is a cosmopolitan fly species used in forensic science, and has been developed as a laboratory model species. They feed on decaying corpses as well as a wide variety of organic matter, and previous studies have even found them feeding on liquid paint or shoe polish, suggesting the possibility that they could breakdown industrial compounds. To test this possibility, we fed M. scalaris on a variety of industrially obtained materials and found that it was unable to complete its life cycle, dying at the larval stage, with the majority of compounds tested. However, when fed on modeling clay, a substrate that contains starch and inedible compounds, it was able to complete its life cycle. On this diet we observed increased larval development time, decreased pupal development time and a shortened adult life span. Additionally, pupae and adult flies were smaller than control flies. Contrary to previous reports, we find no evidence that M. scalaris is able to survive on modern formulations of liquid paint.

High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita.

Gap genes are involved in segment determination during early development in dipteran insects (flies, midges, and mosquitoes). We carried out a systematic quantitative comparative analysis of the gap gene network across different dipteran species. Our work provides mechanistic insights into the evolution of this pattern-forming network. As a central component of our project, we created a high-resolution quantitative spatio-temporal data set of gap and maternal co-ordinate gene expression in the blastoderm embryo of the non-drosophilid scuttle fly, Megaselia abdita. Our data include expression patterns in both wild-type and RNAi-treated embryos. The data-covering 10 genes, 10 time points, and over 1,000 individual embryos-consist of original embryo images, quantified expression profiles, extracted positions of expression boundaries, and integrated expression patterns, plus metadata and intermediate processing steps. These data provide a valuable resource for researchers interested in the comparative study of gene regulatory networks and pattern formation, an essential step towards a more quantitative and mechanistic understanding of developmental evolution.

Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita.

Axis specification and segment determination in dipteran insects are an excellent model system for comparative analyses of gene network evolution. Antero-posterior polarity of the embryo is established through systems of maternal morphogen gradients. In Drosophila melanogaster, the anterior system acts through opposing gradients of Bicoid (Bcd) and Caudal (Cad), while the posterior system involves Nanos (Nos) and Hunchback (Hb) protein. These systems act redundantly. Both Bcd and Hb need to be eliminated to cause a complete loss of polarity resulting in mirror-duplicated abdomens, so-called bicaudal phenotypes. In contrast, knock-down of bcd alone is sufficient to induce double abdomens in non-drosophilid cyclorrhaphan dipterans such as the hoverfly Episyrphus balteatus or the scuttle fly Megaselia abdita. We investigate conserved and divergent aspects of axis specification in the cyclorrhaphan lineage through a detailed study of the establishment and regulatory effect of maternal gradients in M. abdita. Our results show that the function of the anterior maternal system is highly conserved in this species, despite the loss of maternal cad expression. In contrast, hb does not activate gap genes in this species. The absence of this activatory role provides a precise genetic explanation for the loss of polarity upon bcd knock-down in M. abdita, and suggests a general scenario in which the posterior maternal system is increasingly replaced by the anterior one during the evolution of the cyclorrhaphan dipteran lineage.

Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita.

The segmentation gene network in insects can produce equivalent phenotypic outputs despite differences in upstream regulatory inputs between species. We investigate the mechanistic basis of this phenomenon through a systems-level analysis of the gap gene network in the scuttle fly Megaselia abdita (Phoridae). It combines quantification of gene expression at high spatio-temporal resolution with systematic knock-downs by RNA interference (RNAi). Initiation and dynamics of gap gene expression differ markedly between M. abdita and Drosophila melanogaster, while the output of the system converges to equivalent patterns at the end of the blastoderm stage. Although the qualitative structure of the gap gene network is conserved, there are differences in the strength of regulatory interactions between species. We term such network rewiring 'quantitative system drift'. It provides a mechanistic explanation for the developmental hourglass model in the dipteran lineage. Quantitative system drift is likely to be a widespread mechanism for developmental evolution.