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.     

Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.     

Demography and population parameters of two species of eristaline flower flies (Diptera,Syrphidae, Eristalini)

The importance of eristaline flies (Diptera, Syrphidae, Eristalini) as pollinators in natural ecosystems and for agricultural crops is well known. However, in-depth studies on the life cycle of most of these species have yet to be carried out. The aim of this research was to study the life cycle of Eristalis tenax (Linnaeus, 1758) and Eristalinus aeneus (Scopoli, 1763) in order to improve the current rearing system employed at the University of Alicante. The results were analysed using the age-stage, two-sex life table method. As one of the main results, the mean duration of the life history of E. tenax and E. aeneus was 46.06 and 65.12 days (d), respectively. The most critical step for both species was found at the beginning of the larval stage (first instar), when the highest mortality was recorded. Population parameters were also analysed and compared. The intrinsic rate of increase (r), the finite rate of increase (λ), the net reproductive rate (R₀) and the mean generation time (T) were 0.09 (d⁻¹), 1.09 (d⁻¹), 42.11 offspring and 40.97 d, in the case of E. aeneus and 0.05 (d⁻¹), 1.05 (d⁻¹), 23.13 offspring and 59.23 d, in the case of E. tenax. These results indicate that the current rearing system is more efficient for E. aeneus, which displays a faster population growth. However, some modifications need to be implemented to improve the production of E. tenax.     

Phylogenetic relationships of antlered flies, Phytalmia Gerstaecker (Diptera: Tephritidae): the evolution of antler shape and mating behaviour

Abstract  The genus Phytalmia (antlered flies, Diptera: Tephritidae) contains remarkable flies with elaborate male head projections known as antlers. The antlers are used in antagonistic intraspecific interactions between males competing to occupy oviposition sites. Phylogenetic relationships between the seven known species of Phytalmia were chosen to be investigated in order to determine the current monophyly of the genus and to assess the evolution of secondary sexual characters and associated behaviours, especially male antlers, fore-femoral, spines and stilting. A phylogenetic analysis of Phytalmia was conducted using two closely related species from the same tribe (Phytalmiini): Sessilina nigrilinea (Walker) and Diplochorda minor Malloch, and one species from a different tribe (Dacini): the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) as outgroups. A total of 1259 base pairs of mitochondrial DNA (COII and 16S) and 35 morphological characters were included in the analysis, using parsimony and maximum likelihood inference methods. A phylogenetic tree generated from combined data was used to infer the evolution of antler shapes and associated behaviours in the genus. The results of this paper support the monophyly of Phytalmia , with P. cervicornis Gerstaecker the sister group of the remaining species. The phylogeny suggests a general decrease in antler complexity over evolutionary time; however, the behavioural sequence of male flies becomes more complex over time, with steps (e.g. stilting) being added to the repertoire during antagonistic encounters. Finally, there are strong correlations between functionally constrained morphological and behavioural characters, therefore allowing the authors to make predications for species whose behaviours are unknown based on morphological attributes and the authors' hypothesised evolution of Phytalmia .     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

Pollination of the orchidEpipactis thunbergii by syrphid flies (Diptera: Syrphidae)

The behavior of visitors to the flowers of the orchidEpipactis thunbergii was studied, with special attention to the role of the epichile in the pollination process. Only four species of syrphid flies legitimately pollinated the flower, among whichSphaerophoria macrogaster was regarded as the most effective pollinator. The movable epichile, possessing a furrow at its base, played a critical role in the pollination process: it threw the syrphid fly onto the stigmatic surface when both sides of the basal slanting surface of the furrow were presumably pressed in the direction of the hypochile by the fore (and middle) legs of the retreating syrphid fly. At this moment, the fly received a set of pollinia on the thorax.     

Phylogenetic relationships of the Sparidae (Teleostei: Percoidei) and implications for convergent trophic evolution

A phylogenetic analysis of the majority of sparid genera and representatives of the sparoid families Centracanthidae, Lethrinidae and Nemipteridae is presented using 87 predominately osteological characters. The Sparidae constitute a monophyletic grouping, with the inclusion of the centracanthid Spicara smaris , which nests deep within the ingroup. The phylogeny was then used to investigate agreement with the most recent molecular study, taxonomic stability of subfamilial classification and the evolution of feeding strategies. Results show that the incongruence between morphological and molecular data appears largely to be an artifact of errors in rooting. However, there appears to be real and substantial conflict between the molecular tree and the morphological data, which is not attributable to the different positions of the least congruent taxa. The data support the molecular hypothesis that none of the subfamilial classification, based on dentition and trophic specialization, is monophyletic, and should be rejected pending further taxonomic revision. The phylogeny supports multiple independent origins of trophic types and it is suggested that the evolutionary plasticity of the oral teeth of sparids has been fundamental to the adaptive radiation of this family compared to their closest allies. ©2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76 , 269–301.     

Comparative characteristics of the wing apparatus and flight of Syrphid flies (Diptera: Syrphidae)

Comparative analysis of the wing apparatus and flight in nine species of flower flies (Syrphidae) has been performed. Data on the flight velocity, aerodynamic force, wing-beat frequency, stroke amplitude and stroke plane angle, wing area, body mass and volume, as well as correlations between these parameters at the intraspecific and family levels, have been obtained. Based on the obtained data, the subfamilies Syrphinae and Eristalinae have been compared.     

Phylogenetic relationships within the leaf-mining flies (Diptera: Agromyzidae) inferred from sequence data from multiple genes

The leaf-mining flies (Diptera: Agromyzidae) are a diverse group whose larvae feed internally in leaves, stems, flowers, seeds, and roots of a wide variety of plant hosts. The systematics of agromyzids has remained poorly known due to their small size and morphological homogeneity. We investigated the phylogenetic relationships among genera within the Agromyzidae using parsimony and Bayesian analyses of 2965 bp of DNA sequence data from the mitochondrial COI gene, the nuclear ribosomal 28S gene, and the single copy nuclear CAD gene. We included 86 species in 21 genera, including all but a few small genera, and spanning the diversity within the family. The results from parsimony and Bayesian analyses were largely similar, with major groupings of genera in common. Specifically, both analyses recovered a monophyletic Phytomyzinae and a monophyletic Agromyzinae. Within the subfamilies, genera found to be monophyletic given our sampling include Agromyza, Amauromyza, Calycomyza, Cerodontha, Liriomyza, Melanagromyza, Metopomyza, Nemorimyza, Phytobia, and Pseudonapomyza. Several genera were found to be polyphyletic or paraphyletic including Aulagromyza, Chromatomyia, Phytoliriomyza, Phytomyza, and Ophiomyia. We evaluate our findings and discuss host-use evolution in light of current agromyzid taxonomy and two recent hypotheses of relationships based on morphological data.     

Phylogenetic relationships of the genus Cheilosia and the tribe Rhingiini (Diptera, Syrphidae) based on morphological and molecular characters

The phylogenetic relationships of the tribe Rhingiini and the genus Cheilosia (Diptera, Syrphidae) were investigated using morphological and molecular characters. The genus Cheilosia is one of the most diverse lineages of hoverflies (Syrphidae). The mitochondrial protein coding gene cytochrome c oxidase subunit I (COI), and the D2‐3 region of the nuclear 28S rRNA gene were chosen for sequencing, and morphological characters were scored for both adults and immature stages. The combined dataset included 56 ingroup taxa. The datasets were analyzed separately and in conjunction, using both static and dynamic alignment under the parsimony criterion. The aim of the study was to assess the phylogenetic relationships of the tribe Rhingiini, and to explore if the subgenera of Cheilosia were supported as monophyletic clades. Results showed that the monophyly of subtribes of Rhingiini remained ambiguous, especially due to unstable phylogenetic placements of the genera Portevinia and Rhingia. We recovered most subgenera of Cheilosia as monophyletic clades. Dynamic alignment, using the optimization alignment program POY, always recovered more parsimonious topologies under all parameter weighting schemes, than did parsimony analyses using static alignment and analyzed with NONA.     

Phylogenetic relationships of flesh flies in the subfamily Sarcophaginae based on three mtDNA fragments (Diptera: Sarcophagidae)

In an effort to improve our knowledge of the phylogenetic relationships among species and genera of the subfamily Sarcophaginae, we analysed data from three mitochondrial gene fragments. Sequence data for portions of the genes cytochrome oxidase I (COI), cytochrome oxidase II (COII) and dehydrogenase subunit 4 (ND4) were obtained from 43 species of Sarcophagidae representing 15 genera. We used a Bayesian approach to simultaneously choose how best to partition the data and which substitution model to apply to each partition. Phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods. Our results are consistent with monophyly of the subfamily Sarcophaginae (posterior probability 1; bootstrap support 93%), as well as with monophyly of several genera within the Sarcophaginae (including Sarcophaga s.l.; posterior probability 1; bootstrap support 97%). We found support for a sister‐group relationship between Ravinia Robineau‐Desvoidy and Oxysarcodexia Townsend, which has been hypothesised by past authors on the basis of morphological similarities, although this was supported only in the Bayesian analyses (posterior probability 0. 81–0. 98), and for some novel supra‐generic clades. Contrary to a recent morphological hypothesis, we do not find Helicobia Coquillett to be nested within Sarcophaga Meigen; our data suggest, but do not strongly support, a hypothesis that Peckia Robineau‐Desvoidy is the sister group to Sarcophaga.     

Carmine cochineal killers: the flower fly genus Eosalpingogaster Hull (Diptera: Syrphidae) revised

The flower fly genus Eosalpingogaster Hull, predator of the carminic acid producer cochineal (Dactylopiidae), is revised. Two new species are described (knutsoni sp.n. and umbra sp.n. ) and an identification key is provided for all known species. Diagnoses, illustrations, synonymies and distributional and biological data are given. Three new synonyms are proposed [texana Curran as jun.syn. of cochenillivora (Guérin‐Méneville); liposeta Fluke and dactylopianus Blanchard as jun.syn. of nigriventris (Bigot)] and two lectotypes are designated for cochenillivora (Guérin‐Méneville) and nigriventris (Bigot). Eosalpingogaster is elevated to full generic status based on adult morphological characters, biological data and a new phylogenetic analysis of molecular characters with genes 28S, 18S and cytochrome c oxidase subunit I. All data, images and drawings are available online as an example of the utility of international standards for biodiversity informatics.     

Phylogenetic relationships of the Australian lomatiines (Diptera: Bombyliidae)

Cladistic analysis is used to isolate the monophyletic group of genera that comprise the Australian Lomatiinae and to investigate the relationships between the Australian genera. Cladograms of genera in the Australian Tomophthalmae and Lomatiinae are presented. Myonema Roberts and Neosardus Roberts are placed in the Cylleniinae, Antonia Loew remains in the Antoniinae and Petrorossia Bezzi is placed in the Anthracinae. The relationship of the Australian lomatiines to the world fauna is discussed, as are the relationships between the Australian genera. Docidomyia White is included in the Lomatiinae and is the sister group of all other genera of the subfamily: Comptosia Macquart sens.lat.; Doddosia Edwards, Oncodosia Edwards and Paramonovomyia Evenhuis. The current diagnosis of the Lomatiinae is changed to reflect the inclusion of Docidomyia. The two subgenera of Comptosia sensu Edwards, Aleucosia Edwards and Comptosia , were not each others' closest relatives in the strict consensus tree. Thus Comptosia as currently recognized is paraphyletic and the two subgenera are treated as genera, Aleucosia stat.nov. and Comptosia stat.nov.     

Phylogenetic relationships of corallinaceae (Corallinales,Rhodophyta): taxonomic implications for reef‐building corallines

A new, more complete, five‐marker (SSU, LSU, psbA, COI, 23S) molecular phylogeny of the family Corallinaceae, order Corallinales, shows a paraphyletic grouping of seven well‐supported monophyletic clades. The taxonomic implications included the amendment of two subfamilies, Neogoniolithoideae and Metagoniolithoideae, and the rejection of Porolithoideae as an independent subfamily. Metagoniolithoideae contained Harveylithon gen. nov., with H. rupestre comb. nov. as the generitype, and H. canariense stat. nov., H. munitum comb. nov., and H. samoënse comb. nov. Spongites and Pneophyllum belonged to separate clades. The subfamily Neogoniolithoideae included the generitype of Spongites, S. fruticulosus, for which an epitype was designated. Pneophyllum requires reassesment. The generitype of Hydrolithon, H. reinboldii, was a younger heterotypic synonym of H. boergesenii. The evolutionary novelty of the subfamilies Hydrolithoideae, Metagoniolithoideae, and Lithophylloideae was the development of tetra/bisporangial conceptacle roofs by filaments surrounding and interspersed among the sporangial initials.     

Phylogenetic and taxonomic relationships of the Polypedates leucomystax complex (Amphibia)

Kuraishi, N., Matsui, M., Hamidy, A., Belabut, D. M., Ahmad, N., Panha, S., Sudin, A., Yong, H. S., Jiang, J.‐P., Ota, H., Thong, H. T. & Nishikawa, K. (2012). Phylogenetic and taxonomic relationships of the Polypedates leucomystax complex (Amphibia). —Zoologica Scripta, 42, 54–70. We investigated the phylogenetic and taxonomic relationships and estimated the history of species diversification and biogeography in the Asian rhacophorid genus Polypedates, focusing on the Polypedates leucomystax complex, whose members are notoriously difficult to classify. We first estimated phylogenetic relationships within the complex using 2005‐bp sequences of the mitochondrial 12S rRNA, tRNA^val and 16S rRNA genes with maximum parsimony, maximum likelihood (ML) and Bayesian methods of inference. Polypedates exhibits well‐supported monophyly, with distinct clades for P. otilophus, P. colletti, P. maculatus and the P. leucomystax complex, consisting of P. macrotis, and the Malay (Polypedates sp. from Malay Peninsula), North China (P. braueri), South China (Polypedates cf. mutus 1), Indochina (P. megacephalus), Sunda (P. leucomystax) and Laos (Polypedates cf. mutus 2) clades. In a subsequent phylogenetic analysis of 4696‐bp sequences of the nuclear brain‐derived neurotrophic factor (BDNF), sodium/calcium exchanger 1 (NCX), POMC, Rag‐1, Rhod and Tyr genes using Bayesian methods of inference, all of these clades were recovered. Some clades of the P. leucomystax complex occur sympatrically and show high genetic diversity or morphological and acoustic differences. Similar tendencies were observed between some allopatric clades. Therefore, we consider each of these groups to be distinct specifically. We also estimated absolute divergence times within the genus using Bayesian methods. Divergence in Polypedates began with the divergence of a primarily South Asian Clade from the common ancestor of secondarily South‐East Asia P. maculatus and South‐East Asian members. The divergence between the latter occurred much later. The P. leucomystax complex diverged in the Pliocene, much later than other congeners, and seems to have been greatly affected by human‐related dispersal after the Pleistocene.     

辽宁食蚜蝇科昆虫名录(双翅目:食蚜蝇科)

本文报道了辽宁省食蚜蝇科昆29属53种的名录和分布。     

Field boundaries as barriers to movement of hover flies (Diptera: Syrphidae) in cultivated land

Field boundaries play an important role as refuges, food sources and corridors for invertebrates and vertebrates, and increasing farmland fragmentation impacts on these functions. However, hedgerows and other structures can also impede dispersal by flying insects. The current work uses the pollen of Phacelia tanacetifolia in hover fly guts as a marker to assess hover fly movement in farm landscapes. In the United Kingdom and New Zealand, Phacelia pollen was found in the guts of Ephisyrphus balteatus and Metasyrphus corollae (United Kingdom) and Melanostoma fasciatum (New Zealand) at distances up to 200 m from the source, when there were no barriers between the flowers and the traps used to catch the flies. The rate of decline over distance in the proportion of flies containing pollen was similar for the two countries. The extent to which four replicated field boundary types impeded hover fly movement was tested using post-and-wire fences, lines of poplars (Populus spp.) with gaps, dense poplars and controls (no potential barriers). Phacelia was planted on one side of each boundary, and along the centre of the control plots. The relative presence of the pollen in flies on both sides of the barriers showed that both types of poplar boundary restricted the movement of the flies, but the fence had no effect. In a separate experiment, gravid females of M. fasciatum were captured at a greater height on a shade-cloth fence than were non-gravid females and males. The implications of this work include the functioning and persistence of metapopulations and the influence of field boundaries on population recovery of beneficial invertebrates following pesticide-induced mortality. If field boundaries contribute to a temporal asynchrony between pest and natural enemy populations, this needs to be considered along with the well-established roles of boundaries as refugia for, and sources of, beneficial arthropods.     

The phylogenetic relationships of flies in the superfamily Empidoidea (Insecta: Diptera)

We conducted a molecular phylogenetic study of the Empidoidea, a diverse group of 10,000 species of true flies, with two major goals: to reconstruct a taxonomically complete and robustly supported phylogeny for the group and to use this information to assess several competing classifications for the clade. We amassed 3900+ nucleotides of coding data from the carbamoylphosphate synthase domain of the rudimentary locus (CAD) and 1200+ nucleotides from the large nuclear ribosomal subunit (28S) from 72 and 71 species, respectively, representing several orthorrhaphan and cyclorrhaphan families and all previously recognized empidoidean subfamilies. Independent and combined phylogenetic analyses of these data were conducted using parsimony, maximum likelihood, and Bayesian criteria. The combined matrix included 61 taxa for which both CAD and 28S sequences were obtained. Analyses of CAD first and second codon positions alone and when concatenated with 28S sequences yielded trees with similar and largely stable topologies. Analyses of 28S data alone supported many clades although resolution is limited by low sequence divergence. The following major empidoid clades were recovered with convincing support in a majority of analyses: Atelestidae, Empidoidea exclusive of Atelestidae, Hybotidae sensu lato, Dolichopodidae+Microphorinae (including Parathallassius), and Empididae sensu lato (including Brachystomatinae, Ceratomerinae, Clinocerinae, Empidinae, Hemerodromiinae, Oreogetoninae, and Trichopezinae). The branching arrangement among these four major clades was Atelestidae, Hybotidae, Dolichopodidae/Microphorinae, Empididae. Previously recognized subclades recovered with robust support included Hybotinae, Brachystomatinae, Tachydromiinae, Clinocerinae (in part), Hemerodromiinae, Empidinae, and Empidiini.     

Genome-wide acceleration of protein evolution in flies (Diptera)

Background

The rate of molecular evolution varies widely between proteins, both within and among lineages. To what extent is this variation influenced by genome-wide, lineage-specific effects? To answer this question, we assess the rate variation between insect lineages for a large number of orthologous genes.

Results

When compared to the beetle Tribolium castaneum, we find that the stem lineage of flies and mosquitoes (Diptera) has experienced on average a 3-fold increase in the rate of evolution. Pairwise gene comparisons between Drosophila and Tribolium show a high correlation between evolutionary rates of orthologous proteins.

Conclusion

Gene specific divergence rates remain roughly constant over long evolutionary times, modulated by genome-wide, lineage-specific effects. Among the insects analysed so far, it appears that the Tribolium genes show the lowest rates of divergence. This has the practical consequence that homology searches for human genes yield significantly better matches in Tribolium than in Drosophila. We therefore suggest that Tribolium is better suited for comparisons between phyla than the widely employed dipterans.