Systematics and evolution of predatory flower flies (Diptera Syrphidae) based on exon-capture sequencing

Flower flies (Diptera: Syrphidae) are one of the most species-rich dipteran families and provide important ecosystem services such as pollination, biological control of pests, recycling of organic matter and redistributions of essential nutrients. Flower fly adults generally feed on pollen and nectar, but their larval feeding habits are strikingly diverse. In the present study, high-throughput sequencing was used to capture and enrich phylogenetically and evolutionary informative exonic regions. With the help of the baitfisher software, we developed a new bait kit (SYRPHIDAE1.0) to target 1945 CDS regions belonging to 1312 orthologous genes. This new bait kit was successfully used to exon capture the targeted loci in 121 flower fly species across the different subfamilies of Syrphidae. We analysed different amino acid and nucleotide data sets (1302 loci and 154 loci) with maximum likelihood and multispecies coalescent models. Our analyses yielded highly supported similar topologies, although the degree of the SRH (global stationarity, reversibility and homogeneity) conditions varied greatly between amino acid and nucleotide data sets. The sisterhood of subfamilies Pipizinae and Syrphinae is supported in all our analyses, confirming a common origin of taxa feeding on soft-bodied arthropods. Based on our results, we define Syrphini stat.rev. to include the genera Toxomerus and Paragus. Our divergence estimate analyses with beast inferred the origin of the Syrphidae in the Lower Cretaceous (125.5-98.5 Ma) and the diversification of predatory flower flies around the K-Pg boundary (70.61-54.4 Ma), coinciding with the rise and diversification of their prey.Peer reviewe

Finding flies in the mushroom soup : Host specificity of fungus-associated communities revisited with a novel molecular method

Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples-regardless of biomass or other properties-being successfully PCR-amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities.Peer reviewe

Global population genetic structure and demographic trajectories of the black soldier fly, Hermetia illucens

Background The black soldier fly (Hermetia illucens) is the most promising insect candidate for nutrient-recycling through bioconversion of organic waste into biomass, thereby improving sustainability of protein supplies for animal feed and facilitating transition to a circular economy. Contrary to conventional livestock, genetic resources of farmed insects remain poorly characterised. We present the first comprehensive population genetic characterisation of H. illucens. Based on 15 novel microsatellite markers, we genotyped and analysed 2862 individuals from 150 wild and captive populations originating from 57 countries on seven subcontinents. Results We identified 16 well-distinguished genetic clusters indicating substantial global population structure. The data revealed genetic hotspots in central South America and successive northwards range expansions within the indigenous ranges of the Americas. Colonisations and naturalisations of largely unique genetic profiles occurred on all non-native continents, either preceded by demographically independent founder events from various single sources or involving admixture scenarios. A decisive primarily admixed Polynesian bridgehead population serially colonised the entire Australasian region and its secondarily admixed descendants successively mediated invasions into Africa and Europe. Conversely, captive populations from several continents traced back to a single North American origin and exhibit considerably reduced genetic diversity, although some farmed strains carry distinct genetic signatures. We highlight genetic footprints characteristic of progressing domestication due to increasing socio-economic importance of H. illucens, and ongoing introgression between domesticated strains globally traded for large-scale farming and wild populations in some regions. Conclusions We document the dynamic population genetic history of a cosmopolitan dipteran of South American origin shaped by striking geographic patterns. These reflect both ancient dispersal routes, and stochastic and heterogeneous anthropogenic introductions during the last century leading to pronounced diversification of worldwide structure of H. illucens. Upon the recent advent of its agronomic commercialisation, however, current human-mediated translocations of the black soldier fly largely involve genetically highly uniform domesticated strains, which meanwhile threaten the genetic integrity of differentiated unique local resources through introgression. Our in-depth reconstruction of the contemporary and historical demographic trajectories of H. illucens emphasises benchmarking potential for applied future research on this emerging model of the prospering insect-livestock sector.Additional co-authors: Santos Rojo, Chrysantus M. Tanga, Rudolf Meier, Clint Rhode, Christine J. Picard, Chris D. Jiggins, Florian Leiber, Jeffery K. Tomberlin, Martin Hasselmann, Wolf U. Blanckenhorn, Martin Kapun & Christoph Sandroc

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.Peer reviewe

A molecular-based identification resource for the arthropods of Finland

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.</p

Datamatrices for Volucellini study

DNA sequence matrices: 1) mitochondrial COI gene and nuclear 28S rDNA for phylogenetic study, and 2) morphological characters of immatures and imagoes.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

A comparative analysis of the evolution of imperfect mimicry.

Although exceptional examples of adaptation are frequently celebrated, some outcomes of natural selection seem far from perfect. For example, many hoverflies (Diptera: Syrphidae) are harmless (Batesian) mimics of stinging Hymenoptera. However, although some hoverfly species are considered excellent mimics, other species bear only a superficial resemblance to their models and it is unclear why this is so. To evaluate hypotheses that have been put forward to explain interspecific variation in the mimetic fidelity of Palearctic Syrphidae we use a comparative approach. We show that the most plausible explanation is that predators impose less selection for mimetic fidelity on smaller hoverfly species because they are less profitable prey items. In particular, our findings, in combination with previous results, allow us to reject several key hypotheses for imperfect mimicry: first, human ratings of mimetic fidelity are positively correlated with both morphometric measures and avian rankings, indicating that variation in mimetic fidelity is not simply an illusion based on human perception; second, no species of syrphid maps out in multidimensional space as being intermediate in appearance between several different hymenopteran model species, as the multimodel hypothesis requires; and third, we find no evidence for a negative relationship between mimetic fidelity and abundance, which calls into question the kin-selection hypothesis. By contrast, a strong positive relationship between mimetic fidelity and body size supports the relaxed-selection hypothesis, suggesting that reduced predation pressure on less profitable prey species limits the selection for mimetic perfection

Investigando relaciones planta - polinizador en el Egeo: los enfoques del proyecto POL-AEGIS (Los polinizadores del archipiélago Egeo: diversidad y amenazas)

Worldwide, there is a well-documented crisis for bees and other pollinators which represent a fundamental biotic capital for wild life conservation, ecosystem function, and crop production. Among all pollinators of the world, bees (Hymenoptera: Apoidea) constitute the major group in species number and importance, followed by hover flies (Diptera: Syrphidae). The Aegean constitutes one of the world’s hotspots for wild bee and other pollinator diversity including flies (mainly hover flies and bee flies), beetles, and butterflies. Despite this advantage, our present knowledge on Greek pollinators is poor, due to a lack of focused and systematic research, absence of relevant taxonomic keys, and a general lack of taxonomic experts in the country. As a result, assessments of pollinator loss cannot be carried out and the causes for the potential pollinator loss in the country remain unknown. Consequently, the desperately needed National Red Data list for pollinators cannot be compiled. This new research (2012–2015) aims to contribute to the knowledge of the pollinator diversity in Greece, the threats pollinators face, as well as the impacts these threats may have on pollination services. The research is conducted in the Aegean archipelago on >20 islands and several mainland sites in Greece and Turkey. Prime goals are: i. the assessment of bee and hover fly diversity (species, genetic); ii. their pollination services; and iii. the effects of climate change, grazing, intensive bee-keeping, fires, electromagnetic radiation on bee diversity and ecology, as well as on plant–pollinator networks. At the same time, this research contributes to the taxonomic capital in Greece and the Eastern Mediterranean, focusing on the creation of the first identification keys for pollinators, the training of new scientists, as well as the enrichment and further development of the Melissotheque of the Aegean, a permanent reference collection of insect pollinators established at the University of the Aegean.En todo el mundo hay una crisis bien documentada para las abejas y otros polinizadores los cuales representan un capital biótico fundamental para la conservación de la vida silvestre, la función de los ecosistemas, y la producción de cultivos. Entre todos los polinizadores del mundo, las abejas (Hymenoptera: Apoidea) constituyen el grupo principal en cuanto al número de especies y su importancia, seguido por los sírfidos (Diptera: Syrphidae). El Egeo constituye uno de los puntos importantes de diversidad de abejas silvestres y otros polinizadores del mundo, incluyendo moscas (principalmente sírfidos y bombílidos), escarabajos y mariposas. A pesar de esta ventaja, los conocimientos actuales sobre los polinizadores griegos son reducidos, debido a la falta de una investigación focalizada y sistemática, la ausencia de claves taxonómicas pertinentes, y una falta general de expertos en taxonomía en el país. Como resultado, no se pueden llevar a cabo evaluaciones de la pérdida de polinizadores y las causas de la pérdida potencial de polinizadores en el país siguen siendo desconocidas. En consecuencia, la imperiosamente necesitaba Lista Roja de datos para polinizadores no se puede compilar. Esta nueva investigación (2012-2015) tiene como objetivo contribuir al conocimiento de la diversidad de polinizadores en Grecia, enfrentarse a las amenazas para los polinizadores, así como investigar el impacto que estas amenazas pueden tener sobre los servicios de polinización. La investigación se llevará a cabo en el archipiélago del mar Egeo en más de 20 islas y en varios sitios del continente en Grecia y Turquía. Los principales objetivos son: i. la evaluación de la diversidad de abejas y sírfidos (especies, genética); ii. sus servicios de polinización, y iii. los efectos del cambio climático, el pastoreo, la apicultura intensiva, los incendios y las radiaciones electromagnéticas sobre la diversidad de abejas y la ecología, así como en las redes planta-polinizador. Al mismo tiempo, esta investigación contribuirá a la taxonomía en Grecia y el Mediterráneo Oriental, centrándose en primer lugar en la creación de las claves de identificación para polinizadores, la formación de nuevos científicos, así como el enriquecimiento y el desarrollo de la Melisoteca del Egeo, una colección de referencia permanente de los insectos polinizadores establecidos en la Universidad del Egeo.This research is co-financed by the European Union (European Social Fund—ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF) - Research Funding Program: Thales -Investing in knowledge society through the European Social Fund