Morphology versus molecules: the phylogenetic relationships of Sepsidae (Diptera: Cyclorrhapha) based on morphology and DNA sequence data from ten genes

The first mitochondrial genome of Meroplius fukuharai (Diptera: Sepsidae)

Meroplius fukuharai is an important sanitary and ecological resource insect. We sequenced and annotated the mitogenome of Meroplius fukuharai which is the first representative of the genus Meroplius with nearly complete mitochondrial data. This mitogenome is 14,803 bp long, which consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), and two ribosomal RNA genes. All genes have a conservational arrangement with other published species of Sepsidae. Our results also supported the monophyly of Sepsidae, and the genus Meroplius is more closely related to genus Sepsis, Microsepsis, and Archisepsis.

Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species

The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species. We investigate signals of admixture between allopatric and sympatric populations of the two closely related European dung fly species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). Based on microsatellite genotypes, we first inferred a baseline demographic history using Approximate Bayesian Computation. We then used genomic data from pooled DNA of natural and laboratory populations to test for past interspecific gene flow based on allelic configurations discordant with the inferred population tree (ABBA-BABA test with D-statistic). Comparing the detected signals of gene flow with the contemporary geographic relationship among interspecific pairs of populations (sympatric vs. allopatric), we made two contrasting observations. At one site in the French Cevennes, we detected an excess of past interspecific gene flow, while at two sites in Switzerland we observed lower signals of past microsatellite genotypes gene flow among populations in sympatry compared to allopatric populations. These results suggest that the species boundaries between these two species depend on the past and/or present eco-geographic context in Europe, which indicates that there is no uniform link between contemporary geographic proximity and past interspecific gene flow in natural populations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11692-023-09612-5.

The first comprehensive, multigene molecular phylogeny for big-headed flies (Diptera: Pipunculidae)

The first comprehensive molecular phylogeny of Pipunculidae (Diptera) is inferred from analyses of 6963 bp of DNA sequence data from the following five loci: cytochrome c oxidase subunit I (COI), cytochrome b (Cytb), 12S ribosomal DNA, carbamoyl phosphate synthetase region of CAD (CAD) and alanyl-tRNA synthetase (AATS). The monophyly of Pipunculidae and most known subfamilies, including Chalarinae, Nephrocerinae, Pipunculinae and Protonephrocerinae, are well supported, as are most existing generic concepts. Molecular analysis reveals that Nephrocerinae, either with or without Protonephrocerinae, depending on analytical method, is sister to the rest of the family. Within Pipunculinae, Cephalopsini is synonymized with Pipunculini (synon. nov.) and Eudorylini with Tomosvaryellini (synon. nov.), leaving Pipunculinae with three tribes: Microcephalopsini, Pipunculini and Tomosvaryellini. Jassidophaga is proposed as a synonym of Verrallia (synon. nov.). Beckerias, Cephalops s.s., Cephalosphaera s.s., Neocephalosphaera, Parabeckerias and Semicephalops are all raised to generic status (stat. nov.). Eudorylas fusculus and E. vineti are transferred to Clistoabdominalis (comb. nov.) and Clistoabdominalis ruralis and C. doczkali to Eudorylas (comb. nov.). We provide evidence for four new genera of Pipunculidae, one of which is described herein (Tricosus gen. nov.; Australia: New South Wales, contains two new combinations, Tricosus cyclohirtus and Tricosus anorhaebus).

Phylogenetic relationships and classification of the Chloropinae of the world (Diptera: Chloropidae)

The Chloropidae is a species-rich family of flies with about 3000 species in four subfamilies. The Chloropinae is the second most species-rich subfamily with almost 1000 described species in 75 accepted genera. There is agreement about the monophyly of the subfamily; however, the relationships among the genera are still poorly understood and some genera are clearly paraphyletic. Thus, the interpretation of the evolution of morphological traits, such as male terminalia sclerites, remains challenging. This is the first phylogenetic study of the Chloropinae using a formal analytical approach, including representatives of 73 genera of the subfamily and 124 morphological characters. The monophyly of the Chloropinae is corroborated. Chloropella is sister to the remainder of the subfamily. Slightly different analytical procedures show stable clades and rogue taxa. We propose a system for the subfamily with ten tribes, three of which are newly proposed here—Chloropellini trib. nov., Chloropini, Chloropsinini trib. nov., Diplotoxini, Eurinini stat. nov., Lasiosinini, Mepachymerini, Meromyzini, Mindini and Pseudothaumatomyini. Eight genera are kept incertae sedis and two new genera are erected. There is compelling evidence that Chlorops and Ectecephalina are paraphyletic.

Hidden in the urban parks of New York City: Themira lohmanus, a new species of Sepsidae described based on morphology, DNA sequences, mating behavior, and reproductive isolation (Sepsidae, Diptera)

New species from well-studied taxa such as Sepsidae (Diptera) are rarely described from localities that have been extensively explored and one may think that New York City belongs to this category. Yet, a new species of Themira (Diptera: Sepsidae) was recently discovered which is currently only known to reside in two of New York City's largest urban parks. Finding a new species of Themira in these parks was all the more surprising because the genus was revised in 1998 and is not particularly species-rich (13 species). Its status is confirmed as a new species based on morphology, DNA sequences, and reproductive isolation tests with a closely related species, and is described as Themira lohmanus Ang, sp. n. The species breeds on waterfowl dung and it is hypothesized that this makes the species rare in natural environments. However, it thrives in urban parks where the public feeds ducks and geese. The mating behavior of Themira lohmanus was recorded and is similar to the behavior of its closest relative T. biloba.

Evolutionary analysis identifies multiple genome expansions and contractions in Sepsidae (Diptera) and suggests targets for future genomic research

We here argue that data from comparative studies of genome size and karyotypes provide important information for planning comparative research on genome evolution. We document for 39 species of sepsids that there is a four-fold difference in genome size (151-618 Mbp). Mapping genome sizes onto a phylogenetic hypothesis identifies that this range is the result of five genome expansions and four genome contractions that we here define as changes in genome size of more than 50 Mbp. We then generate karyotype data for 10 species and find no changes in chromosome number. The study reveals that the "Oriental" clade of sepsids is a promising system for studying genome evolution because it has experienced three genome expansion events. These events can be compared with an expansion in the "Neotropical" clade in order to reveal the mechanisms that underlie genome expansion in Sepsidae. A review of the literature on genome sizes and karyotypes reveals that they have been poorly documented in Metazoa. This means that researchers interested in the evolution of genome expansions and contractions are currently not being able to identify appropriate target taxa for genome sequencing. We thus argue for more comparative research on genome sizes and karyotypes and point out that historically species were chosen for genome sequencing for reasons not related to genome evolution (e.g. small genome size, model species status, phylogenetic position, interesting phenotypes). We believe that it is now time to use a more genome-centric selection criterion, where species for whole genome sequencing are selected based on their importance for understanding genome evolution.

A new species of Docosia Winnertz from Central Europe, with DNA barcoding based on four gene markers (Diptera, Mycetophilidae)

A new species of Docosia Winnertz, Docosia dentata sp. n., is described and illustrated, based on a single male specimen collected in Muránska planina National Park in Central Slovakia. DNA sequences (COI, COII, CytB, and ITS2) are included and compared for 13 species of Docosia. There was found only little congruence between the molecular results and previous scarce data about interspecific relationships based on morphology. The COI and CytB gene markers showed the highest interspecific gene distances while ITS2 showed the lowest ones. An updated key to the 23 Central European species of Docosia is also presented.

Across the Baltic: a new record for an enigmatic black scavenger fly, Zuskamira inexpectata (Pont, 1987) (Sepsidae) in Finland

Specimens of the enigmatic, monotypic European genus Zuskamira Pont, 1987 (Sepsidae) were initially collected only from the lower central Swedish provinces of Darlana, Uppland and Västmanland. However, the same species was subsequently found much more south in Lower-Saxony and Schleswig-Holstein although Germany is overall well sampled for sepsid flies. Here we report a further (longitudinal) range expansion based on new localities in Southern Finland. New localities for Finland and Sweden are here added and we discuss briefly the habitat requirements of the species.

'Direct PCR' optimization yields a rapid, cost-effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction

Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately, obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short cut to DNA barcoding, that is, a nondestructive PCR method that skips DNA extraction ('direct PCR') and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of nonbiting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g. details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (i) tissue quantity, (ii) body part, (iii) primer pair and (iv) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g. Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands.

Analysing small insect glands with UV-LDI MS: high-resolution spatial analysis reveals the chemical composition and use of the osmeterium secretion in Themira superba (Sepsidae: Diptera)

For many insect species, pheromones are important communication tools, but chemical analysis and experimental study can be technically challenging because they require the detection and handling of complex chemicals in small quantities. One drawback of traditional mass spectrometry methods such as gas chromatography mass spectrometry is that whole-body extractions from one to several hundred individuals are required, with the consequence that intra- and interindividual differences cannot be detected. Here, we used the recently introduced UV-LDI MS (ultraviolet laser desorption/ionization mass spectrometry) to profile the 'osmeterium' of the sepsid fly Themira superba that is located on the edge of the hind tibia of males. Based on analyses of individual legs, we established that the gland produced a secretion that consisted of oxygenated hydrocarbons and putative isoprenoids. The secretion was first detected 24 h after eclosion, and its transfer to the wings of females during mating was demonstrated using UV-LDI MS. We then tested whether the secretion had an anti-aphrodisiac function, but experimental transfer of the secretion to virgin females did not affect mating success or copulation duration. Throughout the study, UV-LDI MS proved invaluable, because it allowed tracking the natural and experimental transfer of small quantities of pheromones to specific body parts of small flies.

Genetic data confirm the species status of Sepsis nigripes Meigen (Diptera : Sepsidae) and adds one species to the Alpine fauna while questioning the synonymy of Sepsis helvetica Munari

Due to their interesting biology, conspicuous sexual dimorphism and the ability to conduct experiments on species that breed under laboratory condition, sepsid flies (Diptera : Sepsidae) are becoming increasingly important model organisms in evolutionary biology. Accurate species boundaries and well supported phylogenetic hypotheses are thus of interest to many biologists. Here we resolve the conflict surrounding the taxonomic status of the European Sepsis nigripes Meigen, 1826, which is shown to be a valid species using morphological and molecular data applied to multiple species concepts. The species is also placed onto a phylogenetic tree for the genus Sepsis that includes most European and North American species. In addition, we assess the genetic variability between two populations of the Holarctic Sepsis luteipes Melander & Spuler, 1917 from Europe and North America and find conflicting evidence between morphology and DNA sequences. Different species concepts here yield different inferences, and if two species were to be accepted based on molecular data, Sepsis helvetica Munari, 1985 from Europe would have to be resurrected from synonymy. We provide high-resolution images for all species in order to aid in accurate identification. Both species are also added to Sepsidnet, the digital reference collection for Sepsidae (http://sepsidnet-rmbr.nus.edu.sg). Lastly, we discuss a field site in the Swiss Alps where 12 species of Sepsis occur sympatrically on the same pasture.

Does better taxon sampling help? A new phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha) based on 50 new taxa and the same old mitochondrial and nuclear markers

We here present a phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha), a group of schizophoran flies with ca. 320 described species that is widely used in sexual selection research. The hypothesis is based on five nuclear and five mitochondrial markers totaling 8813 bp for ca. 30% of the diversity (105 sepsid taxa) and - depending on analysis - six or nine outgroup species. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian inferences (BI) yield overall congruent, well-resolved, and supported trees that are largely unaffected by three different ways to partition the data in BI and ML analyses. However, there are also five areas of uncertainty that affect suprageneric relationships where different analyses yield alternate topologies and MP and ML trees have significant conflict according to Shimodaira-Hasegawa tests. Two of these were already affected by conflict in a previous analysis that was based on the same genes and a subset of 69 species. The remaining three involve newly added taxa or genera whose relationships were previously resolved with low support. We thus find that the denser taxon sample in the present analysis does not reduce the topological conflict that had been identified previously. The present study nevertheless presents a significant contribution to the understanding of sepsid relationships in that 50 additional taxa from 18 genera are added to the Tree-of-Life of Sepsidae and that the placement of most taxa is well supported and robust to different tree reconstruction techniques.

A phylogenetic analysis of relationships among genera of Conopidae (Diptera) based on molecular and morphological data

Members of the family Conopidae (Diptera) have been the focus of little targeted phylogenetic research. The most comprehensive test of phylogenetic support for the present subfamily classification of Conopidae is presented here using 66 specimens, including 59 species of Conopidae and seven outgroup taxa. Relationships among subfamily clades are also explored. A total of 6824 bp of DNA sequence data from five gene regions (12S ribosomal DNA, cytochrome c oxidase subunit I, cytochrome b, 28S ribosomal DNA and alanyl-tRNA synthetase) are combined with 111 morphological characters in a combined analysis using both parsimony and Bayesian methods. Parsimony analysis recovers three shortest trees. Bayesian analysis recovers a nearly identical tree. Five monophyletic subfamilies of Conopidae are recovered. The rarely acknowledged Zodioninae is restored, including the genera Zodion and Parazodion. The genus Sicus is removed from Myopinae. Morphological synapomorphies are discussed for each subfamily and inter-subfamily clade, including a comprehensive review of the character interpretaions of previous authors. Included are detailed comparative illustrations of male and female genitalia of representatives of all five subfamilies with new morphological interpretation.

Deciphering the evolutionary history and developmental mechanisms of a complex sexual ornament: the abdominal appendages of Sepsidae (Diptera)

Male abdomen appendages are a novel trait found within Sepsidae (Diptera). Here we demonstrate that they are likely to have evolved once, were lost three times, and then secondarily gained in one lineage. The developmental basis of these appendages was investigated by counting the number of histoblast cells in each abdominal segment in four species: two that represented the initial instance of appendage evolution, one that has secondarily gained appendages, and one species that did not have appendages. Males of all species with appendages have elevated cell counts for the fourth segment, which gives rise to the appendages. In Perochaeta dikowi, which reacquired the trait, the females also have elevated cell count on the fourth segment despite the fact that females do not develop appendages. The species without appendages has similar cell counts in all segments regardless of sex. These results suggest that the basis for appendage development is shared in males across all species, but the sexual dimorphism is regulated differently in P. dikowi.

Molecular data sheds light on the classification of long-legged flies (Diptera:Dolichopodidae)

Dolichopodidae (long-legged flies) is the world’s fourth largest dipteran family, but a phylogeny based on a broad global taxon sample is still lacking. We present here a first molecular phylogenetic hypothesis for Dolichopodidae, based on 157 dolichopodid species in 68 genera and 15 subfamilies from the Old and New World, and seven empidoid species (Empididae, Hybotidae) as outgroups. Both relatively fast-evolving mitochondrial markers (COI, 12S, 16S) and a more conserved nuclear marker (18S) were used, the latter being widely employed to study the phylogeny at higher taxonomic levels. We present strong evidence for Microphorinae as sister group to Dolichopodidae sensu stricto, and for the monophyletic Parathalassiinae as part of Dolichopodidae sensu stricto. Monophyly of Achalcinae, Dolichopodinae, and Sciapodinae is supported and Stolidosomatinae are placed within Sympycninae. Diaphorinae, Medeterinae, Neurigoninae, Rhaphiinae, and Sympycninae are paraphyletic, and Hydrophorinae and Peloropeodinae polyphyletic. Our broad taxon sample allows us to gain new insights into the complex systematics of Dolichopodidae. Our results highlight several problems with the traditional classification, which have considerable consequences for the systematic status of some taxa. The poor resolution observed in deep divergences supports previous hypotheses suggesting a rapid early radiation of Dolichopodidae.

Five additions to the list of Sepsidae Diptera for Vietnam: Perochaeta cuirassa sp. n., Perochaeta lobo sp. n., Sepsis spura sp. n., Sepsis sepsi Ozerov, 2003 and Sepsis monostigma Thompson, 1869

A recent collecting trip to Vietnam yielded three new species and two new records of Sepsidae (Diptera) for the country. Here we describe two new species in the species-poor genus Perochaeta (Perochaeta cuirassasp. n. andPerochaeta lobosp. n.) and one to the largest sepsid genus Sepsis (Sepsis spurasp. n.) which is also found in Sumatra and Sulawesi. Two additional Sepsis species are new records for Vietnam (Sepsis sepsi Ozerov, 2003; Sepsis monostigma Thompson, 1869). We conclude with a discussion of the distribution of Perochaeta and the three Sepsis species.

Hennig's orphans revisited: testing morphological hypotheses in the "Opomyzoidea" (Diptera: Schizophora)

The acalyptrate fly superfamily Opomyzoidea, as currently recognized, is a poorly-known group of 14 families. The composition of this group and relationships among included families have been controversial. Furthermore, the delimitation of two opomyzoid families, Aulacigastridae and Periscelididae, has been unstable with respect to placement of the genera Stenomicra, Cyamops, and Planinasus. To test the monophyly of Opomyzoidea, previously proposed relationships between families, and the position of the three problematic genera, we sequenced over 3300bp of nucleotide sequence data from the 28S ribosomal DNA and CAD (rudimentary) genes from 29 taxa representing all opomyzoid families, as well as 13 outgroup taxa. Relationships recovered differed between analyses, and only branches supporting well-established monophyletic families were recovered with high support, with a few exceptions. Opomyzoidea and its included subgroup, Asteioinea, were found to be non-monophyletic. Stenomicra, Cyamops, and Planinasus group consistently with Aulacigastridae, contrary to recent classifications. Xenasteiidae and Australimyzidae, two small, monogeneric families placed in separate superfamilies, were strongly supported as sister groups.

Metamodels and phylogenetic replication: a systematic approach to the evolution of developmental pathways

Molecular genetic analysis of phenotypic variation has revealed many examples of evolutionary change in the developmental pathways that control plant and animal morphology. A major challenge is to integrate the information from diverse organisms and traits to understand the general patterns of developmental evolution. This integration can be facilitated by evolutionary metamodels-traits that have undergone multiple independent changes in different species and whose development is controlled by well-studied regulatory pathways. The metamodel approach provides the comparative equivalent of experimental replication, allowing us to test whether the evolution of each developmental pathway follows a consistent pattern, and whether different pathways are predisposed to different modes of evolution by their intrinsic organization. A review of several metamodels suggests that the structure of developmental pathways may bias the genetic basis of phenotypic evolution, and highlights phylogenetic replication as a value-added approach that produces deeper insights into the mechanisms of evolution than single-species analyses.

Conflict, convergent evolution, and the relative importance of immature and adult characters in endopterygote phylogenetics

We use two episodes from systematic history to illustrate how conflict between immature and adult data was important for the development of phylogenetic systematics. A reference search in Zoological Record reveals that most phylogenetic analyses of endopterygote insects continue to utilize morphological rather than DNA sequence data. However, the use of immature and adult data is established for only a few taxa. An assessment of the phylogenetic utility of 73 matrices with immature and adult data reveals that the immature partitions have fewer characters and that immature characters provide lower node support through homoplasy levels in immatures, and adult partitions are comparable. Despite much conflict, analyses based on all available evidence yield better tree resolution and higher support. We argue that DNA sequence-based matching of immature and adult stages will greatly help with the study of endopterygote immatures and facilitate the assembly of combined character matrices with data from all life-history stages.