Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae)

First Molecular Diagnosis of Oestrus ovis (Linnaeus, 1758) Larvae Causing Conjunctival Ophthalmomyiasis in Mexico City, Mexico

PURPOSE

Human ophthalmomyiasis is a rare ocular parasitosis that results from the accidental infestation of dipteran larvae of several species, including Oestrus ovis (Linnaeus, 1758). This study aims to present the fourth documented human case of ophthalmomyiasis in Mexico, identifying the etiological agent through morphological and molecular analyses. Additionally, we investigated the phylogenetic position and genetic distances among different specimens globally characterized based on mitochondrial Cox1 sequences.

METHODS

A total of five larval specimens were extracted from the patient's eye, with two specimens allocated for identification based on morphological features using a stereomicroscope, and the remaining three preserved in absolute ethanol, one of them used for subsequent analysis using molecular methods. The mitochondrial Cox1 region was amplified and sequenced using automated Sanger sequencing. The resulting sequence was deposited in GenBank under accession number OR440699 and subjected to BlastN analysis against 35 other Cox1 sequences of O. ovis from GenBank. The identity and phylogenetic position of the strains were further explored using parsimony and maximum likelihood phylogenetic methods.

RESULTS

Morphological examination of the larval specimens extracted from the patient's eye unequivocally identified them as O. ovis species. BlastN analysis and comprehensive phylogenetic investigations involving a total of 36 Cox1 sequences confirmed the taxonomic identity of the larvae. Notably, our sequence was positioned within the cluster formed by the Brazilian and two Iranian samples. This finding underscores a shared genetic ancestry among these distinct geographical isolates and provides valuable insights into the evolutionary relationships within O. ovis populations.

CONCLUSION

The presence of O. ovis infestation in Mexico City suggests potential shifts in environmental conditions favoring fly proliferation, highlighting the need for vigilance in urban healthcare settings.

Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

Unusual rearrangements of mitogenomes in Diptera revealed by comparative analysis of 135 tachinid species (Insecta, Diptera, Tachinidae)

The Tachinidae is one of the most speciose families in Diptera, and the exclusively parasitoid species play an important role in regulating populations of many herbivorous insects in ecosystems, including many agricultural pests. To better comprehend the characteristics and evolution of the mitochondrial genome for the Tachinidae, we are adding a massive amount of new molecular data by assembling the mitogenomes for 71 genera and 135 species from all four tachinid subfamilies through next-generation sequencing, and we are presenting the most comprehensive mitogenomic phylogenetic analysis of this family so far. Extensive rearrangements observed in the mitogenome of Admontia podomyia (Exoristinae) are unique for the entire suborder Cyclorrhapha. The rearrangement pattern suggests that the process involved a tandem duplication of the complete mitogenome, followed by both random and nonrandom loss of one copy of each gene. Additionally, five minor mitogenome rearrangements are discovered and described in three subfamilies. We present the largest species-level phylogenetic hypothesis for Tachinidae to date, based on mitogenomes of 152 species of Tachinidae, representing all four subfamilies and with five non-tachinid outgroups. Our analyses support the monophyly of the Tachinidae and most tribes and genera were recovered with good support, but the higher-level phylogenetic relationships within Tachinidae were poorly resolved, indicating that mitogenome data alone are not enough to unambiguously resolve the deeper phylogenetic relationships within Tachinidae.

UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics

Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a primer design program called UPrimer that can quickly design clade-specific NPCL amplification primers based on genome data, without requiring manual intervention. Unlike other available primer design programs, UPrimer uses a nested-PCR strategy that greatly improves the amplification success rate of the designed primers. We examined all available metazoan genome data deposited in NCBI and developed NPCL primer sets for 21 metazoan groups with UPrimer, covering a wide range of taxa, including arthropods, mollusks, cnidarians, echinoderms, and vertebrates. On average, each clade-specific NPCL primer set comprises ∼1,000 NPCLs. PCR amplification tests were performed in 6 metazoan groups, and the developed primers showed a PCR success rate exceeding 95%. Furthermore, we demonstrated a phylogenetic case study in Lepidoptera, showing how NPCL primers can be used for phylogenomic analyses with amplicon capture. Our results indicated that using 100 NPCL probes recovered robust high-level phylogenetic relationships among butterflies, highlighting the utility of the newly designed NPCL primer sets for phylogenetic studies. We anticipate that the automated tool UPrimer and the developed NPCL primer sets for 21 metazoan groups will enable researchers to obtain phylogenomic data more efficiently and cost-effectively and accelerate the resolution of various parts of the Tree of Life.

First phylogenetic analysis of the Nearctic madicolous midges of the genus Androprosopa Mik (Diptera: Thaumaleidae)

Molecular phylogenetic analyses were conducted to infer relationships between the eastern and western Nearctic Androprosopa Mik and amongst the considerably more diverse western Nearctic species. Fresh, molecular-grade material was obtained for all Nearctic Androprosopa species except two Mexican species, An. sonorensis (Arnaud & Boussy) and An. zempoala Sinclair & Huerta, that eluded capture. Molecular sequences from two nuclear protein-coding genes, big zinc finger (BZF) and molybdenum cofactor sulfurase (MCS), were sampled from representatives of several outgroup and ingroup taxa and analyzed phylogenetically using maximum likelihood criteria to confirm identifications of females and immatures using a barcoding approach, test species boundaries among morphologically similar species, and infer relationships among more morphologically disparate groups. Resulting phylogenies suggest the following with significant node (bootstrap) support: (1) the eastern Nearctic Androprosopa species form the sister group to the lineage comprised of all sampled Palearctic thaumaleids, i.e., An. larvata (Mik), An. striata (Okada), and Thaumalea testacea Ruthe; (2) the aforementioned lineage is the sister group to the clade comprised of western Nearctic Androprosopa species; (3) the western Nearctic Androprosopa species form three multispecies lineages, two of which can be further divided into three or more well founded species groups. Our results suggest that Androprosopa as currently defined is paraphyletic. Additionally, we propose several new species groups within the western Nearctic Androprosopa based on molecular and morphological data.

Phylogenetic relationships of the woodlouse flies (Diptera: Rhinophorinae) and the cluster flies (Diptera: Polleniidae)

Phylogenetic relationships within the oestroid subclades Rhinophorinae (Calliphoridae) and Polleniidae were reconstructed for the first time, applying a Sanger sequencing approach using the two protein-coding nuclear markers CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase; 1794 bp) and MCS (molybdenum cofactor sulfurase; 2078 bp). Three genera of Polleniidae and nineteen genera of Rhinophorinae were analyzed together with a selection of taxa representing the major lineages of Oestroidea (non-rhinophorine Calliphoridae, Oestridae, Sarcophagidae, Tachinidae). The selected markers provide good resolution and moderate to strong support of the distal branches, but weak support for several deeper nodes. Polleniidae (cluster flies) emerge as monophyletic and their sister-group relationship to Tachinidae is confirmed. Morinia Robineau-Desvoidy as currently circumscribed emerges as paraphyletic with regard to Melanodexia Williston, and Pollenia Robineau-Desvoidy is the sister taxon of the Morinia-Melanodexia clade. We propose a classification with two subfamilies, Moriniinae Townsend (including Morinia, Melanodexia, and Alvamaja Rognes), and Polleniinae Brauer & Bergenstamm (including Pollenia, Dexopollenia Townsend, and Xanthotryxus Aldrich). Anthracomyza Malloch and Nesodexia Villeneuve are considered as Oestroidea incertae sedis pending further study. Rhinophorinae (woodlouse flies) emerge as monophyletic and sister to a clade composed of (Ameniinae + (Ameniinae + Phumosiinae)), and a tribal classification is proposed with the subfamily divided into Rhinophorini Robineau-Desvoidy, 1863 and Phytonini Robineau-Desvoidy, 1863 (the Stevenia-group and the Phyto-group of authors, respectively). Oxytachina Brauer & Bergenstamm, 1891, stat. rev. is resurrected to contain nine Afrotropical rhinophorine species currently assigned to genus Rhinomorinia Brauer & Bergenstamm, 1891: Oxytachina approximata (Crosskey, 1977) comb. nov., O. atra (Bischof, 1904) comb. nov., O. bisetosa (Crosskey, 1977) comb. nov., O. capensis (Brauer & Bergenstamm, 1893) comb. nov., O. scutellata (Crosskey, 1977) comb. nov., O. setitibia (Crosskey, 1977) comb. nov., O. verticalis (Crosskey, 1977) comb. nov., O. vittata Brauer & Bergenstamm, 1891, and O. xanthocephala (Bezzi, 1908) comb. nov.

From bites to barcodes: uncovering the hidden diversity of black flies (Diptera: Simuliidae) in Vietnam

BACKGROUND

Prompt and precise identification of black flies (Simuliidae) is crucial, given their biting behaviour and significant impact on human and animal health. To address the challenges presented by morphology and chromosomes in black fly taxonomy, along with the limited availability of molecular data pertaining to the black fly fauna in Vietnam, this study employed DNA-based approaches. Specifically, we used mitochondrial and nuclear-encoded genes to distinguish nominal species of black flies in Vietnam.

METHODS

In this study, 135 mitochondrial cytochrome c oxidase subunit I (COI) sequences were established for 45 species in the genus Simulium in Vietnam, encompassing three subgenera (Gomphostilbia, Nevermannia, and Simulium), with 64 paratypes of 27 species and 16 topotypes of six species. Of these COI sequences, 71, representing 27 species, are reported for the first time.

RESULTS

Combined with GenBank sequences of specimens from Malaysia, Myanmar, Thailand, and Vietnam, a total of 234 DNA barcodes of 53 nominal species resulted in a 71% success rate for species identification. Species from the non-monophyletic Simulium asakoae, S. feuerborni, S. multistriatum, S. striatum, S. tuberosum, and S. variegatum species groups were associated with ambiguous or incorrect identifications. Pairwise distances, phylogenetics, and species delimitation analyses revealed a high level of cryptic diversity, with discovery of 15 cryptic taxa. The current study also revealed the limited utility of a fast-evolving nuclear gene, big zinc finger (BZF), in discriminating closely related, morphologically similar nominal species of the S. asakoae species group.

CONCLUSION

This study represents the first comprehensive molecular genetic analysis of the black fly fauna in Vietnam to our knowledge, providing a foundation for future research. DNA barcoding exhibits varying levels of differentiating efficiency across species groups but is valuable in the discovery of cryptic diversity.

Cephenemyia stimulator (Diptera: Oestridae) myiasis in a roe deer (Capreolus capreolus) from Portugal

Herein we present a nasopharyngeal myiasis case by Cephenemyia stimulator in a roe deer hunted in Trás-os-Montes (NE Portugal). Preliminary inspection showed one larva sorting through the nostrils and the examination of the nasopharyngeal cavity showed more than 15 larvae in the glottis and retropharyngeal recesses. Four larvae were collected and stored into 70% ethanol for morphological and molecular identification. Three of the larvae were identified as third instars and the other one as a prepupa of Cephenemyia stimulator, being the first confirmation of this species in roe deer from Portugal. C. stimulator is currently widely distributed in roe deer from central and northern Spain so, the transboundary natural dispersal of these cervids would explain the introduction of this myiasis in Portugal. Further studies are needed to monitor the spreading of this infection in the westernmost populations of European roe deer.

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.

Molecular Analysis of Parasitoid Flies Tachinidae

The parasitoids from Tachinidae family have important role in biological control; nevertheless, the phylogenetic relationships of supra genera groups are poorly studied. Here, we present phylogenetic analyses of the family based on molecular data. 73 species of parasitoid flies belonging to 30 tachinid genera, including the four currently recognized subfamilies (Dexiinae, Exoristinae, Phasiinae, Tachininae) and 20 tribes were analyzed in the molecular study. The Tachinidae are reconstructed as a monophyletic assemblage based on morphological data and with four nonhomoplasious apomorphies (synapomorphies). Monophyly is well supported by a bootstrap value. Our morphological analysis generally supports the subfamily grouping Dexiinae + Phasiinae, while Tachininae + Exoristinae is not supported as one group, and with only the Exoristinae and the Phasiinae reconstructed as monophyletic assemblages. The Dexiinae, which were previously considered a wellestablished monophyletic assemblage (except for few studies), are reconstructed as polyparaphyletic with respect to the Phasiinae. The Tachininae are reconstructed as a paraphyletic grade, while monophyly of Exoristinae was recovered except genus Admontia Brauer Bergenstamm, which arose within subfamily Tachininae. In contrast to molecular analysis, all subfamilies are polyparaphyletic groups in which they interact with each other, with the exception of Phasiinae, which includes most of its taxa in a monophyletic group.

Characterization and Comparative Analysis of Mitochondrial Genomes Among the Calliphoridae (Insecta: Diptera: Oestroidea) and Phylogenetic Implications

The Calliphoridae (blowflies) are significant for forensic science, veterinary management, medical science, and economic issues. However, the phylogenetic relationships within this family are poorly understood and controversial, and the status of the Calliphoridae has been a crucial problem for understanding the evolutionary relationships of the Oestroidea these years. In the present study, seven mitochondrial genomes (mitogenomes), including six calliphorid species and one Polleniidae species, were sequenced and annotated. Then a comparative mitochondrial genomic analysis among the Calliphoridae is presented. Additionally, the phylogenetic relationship of the Calliphoridae within the larger context of the other Oestroidea was reconstructed based on the mitogenomic datasets using maximum likelihood (ML) and Bayesian methods (BI). The results suggest that the gene arrangement, codon usage, and base composition are conserved within the calliphorid species. The phylogenetic analysis based on the mitogenomic dataset recovered the Calliphoridae as monophyletic and inferred the following topology within Oestroidea: (Oestridae (Sarcophagidae (Calliphoridae + (Polleniidae + (Mesembrinellidae + Tachinidae))))). Although the number of exemplar species is limited, further studies are required. Within the Calliphoridae, the Chrysomyinae were recovered as sister taxon to Luciliinae + Calliphorinae. Our analyses indicated that mitogenomic data have the potential for illuminating the phylogenetic relationships in the Oestroidea as well as for the classification of the Calliphoridae.

Monophyletic blowflies revealed by phylogenomics

BACKGROUND

Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification.

RESULTS

We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature.

CONCLUSIONS

Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.

Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)

Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the main lineages in our AHE tree to build a data set with more genes (550 loci versus 216 loci) and higher support levels. Our overall results show strong congruence with the current classification of the family, with 11 out of 14 included subfamilies recovered as monophyletic. Heterotropinae and Mythicomyiinae are successive sister groups to the remainder of the family. We examined the evolution of key morphological characters through our phylogenetic hypotheses and show that neither the "sand chamber subfamilies" nor the "Tomophthalmae" are monophyletic in our phylogenomic analyses. Based on our results, we reinstate two tribes at the subfamily level (Phthiriinae stat. rev. and Ecliminae stat. rev.) and we include the genus Sericosoma Macquart (previously incertae sedis) in the subfamily Oniromyiinae, bringing the total number of bee fly subfamilies to 19. Our dating analyses indicate a Jurassic origin of the family (165-194 Ma), with the sand chamber evolving early in bee fly evolution, in the late Jurassic or mid-Cretaceous (100-165 Ma). We hypothesize that the angiosperm radiation and the hothouse climate established during the late Cretaceous accelerated the diversification of bee flies, by providing an expanded range of resources for the parasitoid larvae and nectarivorous adults.

The world Polleniidae (Diptera, Oestroidea): key to genera and checklist of species

A key to the world genera and a checklist of the world species for the family Polleniidae, including distributions, are provided. The following taxonomic and nomenclatural changes are proposed: Nitellia hermoniella Lehrer, 2007 = Pollenia mediterranea Grunin, 1966, syn. nov., Pollenia bentalia Lehrer, 2007 = Pollenia semicinerea Villeneuve, 1911, syn. nov., Dasypoda angustifrons Jacentkovský, 1941 = Pollenia tenuiforceps Séguy, 1928, syn. nov.; Anthracomyza Malloch, 1928, resurrected name (monotypic; type species Anthracomyia atratula Malloch) is considered a valid name and tentatively assigned to Polleniidae, giving Anthracomyza atratula (Malloch, 1927) as a resurrected combination; Morinia crassitarsis (Villeneuve, 1936), stat. rev. is considered a valid species, and Micronitellia Enderlein, 1936, stat. nov. is considered an available name.

Optimizing the widely used nuclear protein-coding gene primers in beetle phylogenies and their application in the genus Sasajiscymnus Vandenberg (Coleoptera: Coccinellidae)

Advances in genomic biology and the increasing availability of genomic resources allow developing hundreds of nuclear protein-coding (NPC) markers, which can be used in phylogenetic research. However, for low taxonomic levels, it may be more practical to select a handful of suitable molecular loci for phylogenetic inference. Unfortunately, the presence of degenerate primers of NPC markers can be a major impediment, as the amplification success rate is low and they tend to amplify nontargeted regions. In this study, we optimized five NPC fragments widely used in beetle phylogenetics (i.e., two parts of carbamoyl-phosphate synthetase: CADXM and CADMC, Topoisomerase, Wingless and Pepck) by reducing the degenerate site of primers and the length of target genes slightly. These five NPC fragments and 6 other molecular loci were amplified to test the monophyly of the coccinellid genus Sasajiscymnus Vandenberg. The analysis of our molecular data set clearly supported the genus Sasajiscymnus may be monophyletic but confirmation with an extended sampling is required. A fossil-calibrated chronogram was generated by BEAST, indicating an origin of the genus at the end of the Cretaceous (77.87 Myr). Furthermore, a phylogenetic informativeness profile was generated to compare the phylogenetic properties of each gene more explicitly. The results showed that COI provides the strongest phylogenetic signal among all the genes, but Pepck, Topoisomerase, CADXM and CADMC are also relatively informative. Our results provide insight into the evolution of the genus Sasajiscymnus, and also enrich the molecular data resources for further study.

The world woodlouse flies (Diptera, Rhinophoridae)

The world Rhinophoridae are catalogued, recognising 33 genera and 177 species. Nomenclatural information is provided for all genus-group and species-group names, including lists of synonyms and name-bearing type data. Species distributions are recorded by country. A key to the world genera is presented. Four new genera are erected to accommodate five new species, which do not fit within any of the current generic concepts in Rhinophoridae, according to the results of a morphology-based phylogenetic analysis: Marshallicona Cerretti & Pape with type species Marshallicona quitu Cerretti & Pape, gen. et sp. nov. (Ecuador); Maurhinophora Cerretti & Pape with type species Maurhinophora indoceanica Cerretti & Pape, gen. et sp. nov. (Mauritius); Neotarsina Cerretti & Pape with type species Neotarsina caraibica Cerretti & Pape, gen. et sp. nov. (Trinidad and Tobago) and Neotarsina andina Cerretti & Pape, sp. nov. (Peru); Kinabalumyia Cerretti & Pape with type species Kinabalumyia pinax Cerretti & Pape, gen. et sp. nov. (Malaysia, Sabah). The genus Aporeomyia Pape & Shima (type species Aporeomyia antennalis Pape & Shima), originally assigned to Tachinidae, is here reassigned to Rhinophoridae based on a reassessment of the homologies of the male terminalia. The following five species-group names, which were previously treated as junior synonyms or nomina dubia, are recognised as valid species names: Acompomintho caucasica (Villeneuve, 1908), stat. rev. [from nomen dubium to valid species]; Acompomintho sinensis (Villeneuve, 1936), stat. rev. [from nomen dubium to valid species]; Stevenia bertei (Rondani, 1865), stat. rev. [from nomen dubium to valid species]; Stevenia sardoa Villeneuve, 1920, stat. rev. [from junior synonym of Rhinophora deceptoria Loew, 1847 to valid species]; Stevenia subalbida (Villeneuve, 1911), stat. rev. [from junior synonym of Rhinophora deceptoria Loew, 1847 to valid species]. Reversal of precedence is invoked for the following case of subjective synonymy to promote stability in nomenclature: Rhinophora lepida (Meigen, 1824), nomen protectum, and Musca parcus Harris, 1780: 144, nomen oblitum. New generic and specific synonymies are proposed for the following two names: Mimodexia Rohdendorf, 1935, junior synonym of Tromodesia Rondani, 1856, syn. nov. and Ptilocheta tacchetti Rondani, 1865, junior synonym of Stevenia obscuripennis (Loew, 1847), syn. nov. The following new combinations are proposed: Acompomintho sinensis (Villeneuve, 1936), comb. nov. [transferred from Tricogena Robineau-Desvoidy, 1830]; Tromodesia guzari (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia intermedia (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia lindneriana (Rohdendorf, 1961), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia magnifica (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia obscurior (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia pallidissima (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia setiventris (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935] and Tromodesia shachrudi (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935].

Molecular phylogeny and evolution of world Tachinidae (Diptera)

We reconstructed phylogenetic relationships within the diverse parasitoid fly family Tachinidae using four nuclear loci (7800 bp) and including an exceptionally large sample of more than 500 taxa from around the world. The position of the earthworm-parasitizing Polleniinae (Calliphoridae s.l.) as sister to Tachinidae is strongly supported. Our analyses recovered each of the four tachinid subfamilies and most recognized tribes, with some important exceptions in the Dexiinae and Tachininae. Most notably, the tachinine tribes Macquartiini and Myiophasiini form a clade sister to all other Tachinidae, and a clade of Palpostomatini is reconstructed as sister to Dexiinae + Phasiinae. Although most nodes are well-supported, relationships within several lineages that appear to have undergone rapid episodes of diversification (basal Dexiinae and Tachininae, Blondeliini) were poorly resolved. Reconstructions of host use evolution are equivocal, but generally support the hypothesis that the ancestral host of tachinids was a beetle and that subsequent host shifts to caterpillars may coincide with accelerated diversification. Evolutionary reconstructions of reproductive strategy using alternative methods were incongruent, however it is most likely that ancestral tachinids possessed unincubated, thick shelled eggs from which incubated eggs evolved repeatedly, potentially expanding available host niches. These results provide a broad foundation for understanding the phylogeny and evolution of this important family of parasitoid insects. We hope it will serve as a framework to be used in concert with morphology and other sources of evidence to revise the higher taxonomic classification of Tachinidae and further explore their evolutionary history and diversification.

The endemic Cladophorales (Ulvophyceae) of ancient Lake Baikal represent a monophyletic group of very closely related but morphologically diverse species

Lake Baikal, the oldest lake in the world, is home to spectacular biodiversity and extraordinary levels of endemism. While many of the animal species flocks from Lake Baikal are famous examples of evolutionary radiations, the lake also includes a wide diversity of endemic algae that are not well investigated with regards to molecular-biological taxonomy and phylogeny. The endemic taxa of the green algal order Cladophorales show a range of divergent morphologies that led to their classification in four genera in two families. We sequenced partial large- and small-subunit rDNA as well as the internal transcribed spacer region of 14 of the 16 described endemic taxa to clarify their phylogenetic relationships. One endemic morphospecies, Cladophora kusnetzowii, was shown to be conspecific with the widespread Aegagropila linnaei. All other endemic morphospecies formed a monophyletic group nested within the genus Rhizoclonium (Cladophoraceae), a very surprising result, in stark contrast to their morphological affinities. The Baikal clade represents a species flock of closely related taxa with very low genetic differentiation. Some of the morphospecies were congruent with lineages recovered in the phylogenies, but due to the low phylogenetic signal in the rDNA sequences the relationships within the Baikal clade were not all well resolved. The Baikal clade appears to represent a recent radiation, based on the low molecular divergence within the group, and it is hypothesized that the large morphological variation results from diversification in sympatry from a common ancestor in Lake Baikal.

First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences

Calyptrate flies include about 22,000 extant species currently classified into Hippoboscoidea (tsetse, louse, and bat flies), the muscoid grade (house flies and relatives) and the Oestroidea (blow flies, bot flies, flesh flies, and relatives). Calyptrates are abundant in nearly all terrestrial ecosystems, often playing key roles as decomposers, parasites, parasitoids, vectors of pathogens, and pollinators. For oestroids, the most diverse group within calyptrates, definitive fossils have been lacking. The first unambiguous fossil of Oestroidea is described based on a specimen discovered in amber from the Dominican Republic. The specimen was identified through digital dissection by CT scans, which provided morphological data for a cladistic analysis of its phylogenetic position among extant oestroids. The few known calyptrate fossils were used as calibration points for a molecular phylogeny (16S, 28S, CAD) to estimate the timing of major diversification events among the Oestroidea. Results indicate that: (a) the fossil belongs to the family Mesembrinellidae, and it is identified and described as Mesembrinella caenozoica sp. nov.; (b) the mesembrinellids form a sister clade to the Australian endemic Ulurumyia macalpinei (Ulurumyiidae) (McAlpine's fly), which in turn is sister to all remaining oestroids; (c) the most recent common ancestor of extant Calyptratae lived just before the K-Pg boundary (ca. 70 mya); and (d) the radiation of oestroids began in the Eocene (ca. 50 mya), with the origin of the family Mesembrinellidae dated at ca. 40 mya. These results provide new insight into the timing and rate of oestroid diversification and highlight the rapid radiation of some of the most diverse and ecologically important families of flies. ZooBank accession number-urn:lsid:zoobank.org:pub:0DC5170B-1D16-407A-889E-56EED3FE3627.

Molecular phylogenetic relationships reveal contrasting evolutionary patterns in Gorgoniidae (Octocorallia) in the Eastern Pacific

The description and delimitation of species in an evolutionary framework is essential for understanding patterns of biodiversity and distribution, and in the assessment of conservation strategies for natural resources. This study seeks to clarify the evolutionary history and genetic variation within and between closely related octocoral species that are fundamental to benthic marine ecosystems for harbouring a high diversity of associated fauna. For our study system, we focused on members of the Gorgoniidae family in the Eastern Pacific, particularly of the Ecuadorian littoral, a less studied marine ecosystem. According to our results, the diagnosis of the genus Pacifigorgia is here amended to include species previously considered in the genus Leptogorgia. The genera Leptogorgia and Eugorgia are included within a single clade, and neither are recovered as monophyletic. In this case, according to the priority rule of the International Code of Zoological Nomenclature (ICZN), our proposal is to include the species considered in these two genera in Leptogorgia. In addition, we found evidence of interesting speciation patterns: morphological differentiation with no apparent genetic differentiation (in Pacifigorgia), and inconsistencies between mitochondrial and nuclear data that suggest a hybridisation phenomenon (in Leptogorgia). In the first case, recent radiation, ancient hybridisation, sympatric speciation, and in the second, reticulate evolution may have contributed to the evolutionary history of the studied taxa. Therefore, incongruences observed between morphological and molecular evidences in these octocorals, and in corals in general, may reveal the types of events/patterns that have influenced their evolution.

DNA Barcodes for the Northern European Tachinid Flies (Diptera: Tachinidae)

This data release provides COI barcodes for 366 species of parasitic flies (Diptera: Tachinidae), enabling the DNA based identification of the majority of northern European species and a large proportion of Palearctic genera, regardless of the developmental stage. The data will provide a tool for taxonomists and ecologists studying this ecologically important but challenging parasitoid family. A comparison of minimum distances between the nearest neighbors revealed the mean divergence of 5.52% that is approximately the same as observed earlier with comparable sampling in Lepidoptera, but clearly less than in Coleoptera. Full barcode-sharing was observed between 13 species pairs or triplets, equaling to 7.36% of all species. Delimitation based on Barcode Index Number (BIN) system was compared with traditional classification of species and interesting cases of possible species oversplits and cryptic diversity are discussed. Overall, DNA barcodes are effective in separating tachinid species and provide novel insight into the taxonomy of several genera.

Molecular phylogeny of the megadiverse insect infraorder Bibionomorpha sensu lato (Diptera)

The phylogeny of the insect infraorder Bibionomorpha (Diptera) is reconstructed based on the combined analysis of three nuclear (18S, 28S, CAD) and three mitochondrial (12S, 16S, COI) gene markers. All the analyses strongly support the monophyly of Bibionomorpha in both the narrow (sensu stricto) and the broader (sensu lato) concepts. The major lineages of Bibionomorpha sensu lato (Sciaroidea, Bibionoidea, Anisopodoidea, and Scatopsoidea) and most of the included families are supported as monophyletic groups. Axymyiidae was not found to be part of Bibionomorpha nor was it found to be its sister group. Bibionidae was paraphyletic with respect to Hesperinidae and Keroplatidae was paraphyletic with respect to Lygistorrhinidae. The included Sciaroidea incertae sedis (except Ohakunea Edwards) were found to belong to one clade, but the relationships within this group and its position within Sciaroidea require further study.

Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles

Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

Annotated catalogue of the Tachinidae (Insecta, Diptera) of the Afrotropical Region, with the description of seven new genera

The Tachinidae of the Afrotropical Region are catalogued and seven genera and eight species are newly described. There are 237 genera and 1126 species recognized, of which 101 genera and 1043 species are endemic to the region. The catalogue is based on examination of the primary literature comprising about 525 references as well as numerous name-bearing types and other specimens housed in collections. Taxa are arranged hierarchically and alphabetically under the categories of subfamily, tribe, genus, subgenus (where recognized), species, and rarely subspecies. Nomenclatural information is provided for all genus-group and species-group names, including lists of synonyms (mostly restricted to Afrotropical taxa) and name-bearing type data. Species distributions are recorded by country within the Afrotropical Region and by larger geographical divisions outside the region. Additional information is given in the form of notes, numbering about 300 in the catalogue section. Seven genera and eight species are described as new: Afrophylax Cerretti & O'Hara with type species Sturmia aureiventris Villeneuve, 1910, gen. n. (Exoristinae, Eryciini); Austrosolieria Cerretti & O'Hara with type species Austrosolieria londti Cerretti & O'Hara, gen. n. and sp. n. (South Africa) and Austrosolieria freidbergi Cerretti & O'Hara, sp. n. (Malawi) (Tachininae, Leskiini); Carceliathrix Cerretti & O'Hara with type species Phorocera crassipalpis Villeneuve, 1938, gen. n. (Exoristinae, Eryciini); Filistea Cerretti & O'Hara with type species Viviania aureofasciata Curran, 1927, gen. n. and Filistea verbekei Cerretti & O'Hara, sp. n. (Cameroon, D.R. Congo, Uganda) (Exoristinae, Blondeliini); Mesnilotrix Cerretti & O'Hara with type species Dexiotrix empiformis Mesnil, 1976, gen. n. (Dexiinae, Dexiini); Myxophryxe Cerretti & O'Hara with type species Phorocera longirostris Villeneuve, 1938, gen. n., Myxophryxe murina Cerretti & O'Hara, sp. n. (South Africa), Myxophryxe regalis Cerretti & O'Hara, sp. n. (South Africa), and Myxophryxe satanas Cerretti & O'Hara, sp. n. (South Africa) (Exoristinae, Goniini); and Stiremania Cerretti & O'Hara with type species Stiremania karoo Cerretti & O'Hara, gen. n. and sp. n. (South Africa), and Stiremania robusta Cerretti & O'Hara, sp. n. (South Africa) (Exoristinae, Goniini). Paraclara Bezzi, 1908 is transferred from the Cylindromyiini to the Hermyini, comb. n. Sarrorhina Villeneuve, 1936 is transferred from the Minthoini to the Graphogastrini, comb. n. Three genera are newly recorded from the Afrotropical Region: Madremyia Townsend, 1916 (Eryciini); Paratrixa Brauer & Bergenstamm, 1891 (Blondeliini); and Simoma Aldrich, 1926 (Goniini). Three genera previously recorded from the Afrotropical Region are no longer recognized from the region: Calozenillia Townsend, 1927 (Palaearctic, Oriental and Australasian regions); Eurysthaea Robineau-Desvoidy, 1863 (Palaearctic, Oriental and Australasian regions); and Trixa Meigen, 1824 (Palaearctic and Oriental regions). Two species are newly recorded from the Afrotropical Region: Amnonia carmelitana Kugler, 1971 (Ethiopia, Kenya); and Simoma grahami Aldrich, 1926 (Namibia). Three species previously recorded from the Afrotropical Region are no longer recognized from the region: Euthera peringueyi Bezzi, 1925 (Oriental Region); Hamaxia incongrua Walker, 1860 (Palaearctic, Oriental and Australasian regions); Leucostoma tetraptera (Meigen, 1824) (Palaearctic Region). New replacement names are proposed for five preoccupied names of Afrotropical species: Billaea rubida O'Hara & Cerretti for Phorostoma rutilans Villeneuve, 1916, preoccupied in the genus Billaea Robineau-Desvoidy, 1830 by Musca rutilans Fabricius, 1781, nom. n.; Cylindromyia braueri O'Hara & Cerretti for Ocyptera nigra Villeneuve, 1918, preoccupied in the genus Cylindromyia Meigen, 1803 by Glossidionophora nigra Bigot, 1885, nom. n.; Cylindromyia rufohumera O'Hara & Cerretti for Ocyptera scapularis Villeneuve, 1944, preoccupied in the genus Cylindromyia Meigen, 1803 by Ocyptera scapularis Loew, 1845, nom. n.; Phytomyptera longiarista O'Hara & Cerretti for Phytomyzoneura aristalis Villeneuve, 1936, preoccupied in the genus Phytomyptera Rondani, 1845 by Phasiostoma aristalis Townsend, 1915, nom. n.; and Siphona (Siphona) pretoriana O'Hara & Cerretti for Siphona laticornis Curran, 1941, preoccupied in the genus Siphona Meigen, 1803 by Actia laticornis Malloch, 1930, nom. n. New type species fixations are made under the provisions of Article 70.3.2 of the ICZN Code for two genus-group names: Lydellina Villeneuve, 1916, type species newly fixed as Lydellina villeneuvei Townsend, 1933 (valid genus name); and Sericophoromyia Austen, 1909, type species newly fixed as Tachina quadrata Wiedemann, 1830 (synonym of Winthemia Robineau-Desvoidy, 1830). Lectotypes are designated for the following nine nominal species based on examination of one or more syntypes of each: Degeeria crocea Villeneuve, 1950; Degeeria semirufa Villeneuve, 1950; Erycia brunnescens Villeneuve, 1934; Exorista oculata Villeneuve, 1910; Kiniatilla tricincta Villeneuve, 1938; Myxarchiclops caffer Villeneuve, 1916; Ocyptera linearis Villeneuve, 1936; Peristasisea luteola Villeneuve, 1934; and Phorocera crassipalpis Villeneuve, 1938. The following four genus-group names that were previously treated as junior synonyms or subgenera are recognized as valid generic names: Bogosiella Villeneuve, 1923, status revived; Dyshypostena Villeneuve, 1939, status revived; Perlucidina Mesnil, 1952, status revived; and Thelymyiops Mesnil, 1950, status n. The following six species-group names that were previously treated as junior synonyms are recognized as valid species names: Besseria fossulata Bezzi, 1908, status revived; Degeeria cinctella Villeneuve, 1950, status revived (as Medina cinctella (Villeneuve)); Nemoraea miranda intacta Villeneuve, 1916, status revived (as Nemoraea intacta Villeneuve); Succingulum exiguum Villeneuve, 1935, status revived (as Trigonospila exigua (Villeneuve)); Wagneria rufitibia abbreviata Mesnil, 1950, status n. (as Periscepsia abbreviata (Mesnil)); and Wagneria rufitibia nudinerva Mesnil, 1950, status n. (as Periscepsia nudinerva (Mesnil)). The following 25 new or revived combinations are proposed: Afrophylax aureiventris (Villeneuve, 1910), comb. n.; Blepharella orbitalis (Curran, 1927), comb. n.; Bogosiella pomeroyi Villeneuve, 1923, comb. revived; Brachychaetoides violacea (Curran, 1927), comb. n.; Carceliathrix crassipalpis (Villeneuve, 1938), comb. n.; Charitella whitmorei (Cerretti, 2012), comb. n.; Dyshypostena edwardsi (van Emden, 1960), comb. n.; Dyshypostena tarsalis Villeneuve, 1939, comb. revived; Estheria buccata (van Emden, 1947), comb. n.; Estheria surda (Curran, 1933), comb. n.; Filistea aureofasciata (Curran, 1927), comb. n.; Madremyia setinervis (Mesnil, 1968), comb. n.; Mesnilotrix empiformis (Mesnil, 1976), comb. n.; Myxophryxe longirostris (Villeneuve, 1938), comb. n.; Nealsomyia chloronitens (Mesnil, 1977), comb. n.; Nealsomyia clausa (Curran, 1940), comb. n.; Nilea longicauda (Mesnil, 1970), comb. n.; Paratrixa aethiopica Mesnil, 1952, comb. revived; Paratrixa stammeri Mesnil, 1952, comb. revived; Perlucidina africana (Jaennicke, 1867), comb. n.; Perlucidina perlucida (Karsch, 1886), comb. revived; Prolophosia retroflexa (Villeneuve, 1944), comb. n.; Sturmia profana (Karsch, 1888), comb. n.; additionally, Ceromasia rufiventris Curran, 1927 is treated as an unplaced species of Goniini, comb. n. and Hemiwinthemia stuckenbergi Verbeke, 1973 is treated as an unplaced species of Leskiini, comb. n. New or revived generic and specific synonymies are proposed for the following nine names: Afrosturmia Curran, 1927 with Blepharella Macquart, 1851, syn. n.; Archiphania van Emden, 1945 with Catharosia Rondani, 1868, syn. revived; Besseria longicornis Zeegers, 2007 with Besseria fossulata Bezzi, 1908 (current name Besseria fossulata), syn. n.; Dexiomera Curran, 1933 with Estheria Robineau-Desvoidy, 1830, syn. n.; Hemiwinthemia francoisi Verbeke, 1973 with Nemoraea capensis Schiner, 1868 (current name Smidtia capensis), syn. n.; Kinangopana van Emden, 1960 with Dyshypostena Villeneuve, 1939, syn. n.; Metadrinomyia Shima, 1980 with Charitella Mesnil, 1957, syn. n.; Phorocera majestica Curran, 1940 with Phorocera longirostris Villeneuve, 1938 (current name Myxophryxe longirostris), syn. n.; and Podomyia discalis Curran, 1939 with Antistasea fimbriata Bischof, 1904 (current name Antistasea fimbriata), syn. n.

Redefining the generic limits of Winthemia (Diptera : Tachinidae)

One of the major problems hindering the systematic study of tachinid flies is that genera are often poorly defined, making it difficult to unambiguously assign species among closely related genera. Within the tribe Winthemiini, an example of this problem is represented by the unstable classification of the Afrotropical species most recently classified as Smidtia capensis (Schiner). This species has been previously assigned to four different genera on the basis of limited examination and evidence. Here, we evaluate the identity and phylogenetic affinities of this species and other members of the tribe Winthemiini using morphological and molecular phylogenetic analysis. We demonstrate that S. capensis actually belongs to the genus Winthemia Robineau-Desvoidy. We also find that Winthemia is paraphyletic with respect to two monotypic genera, Crypsina (type species Crypsina prima Brauer & Bergenstamm) and Hemiwinthemia (type species Hemiwinthemia calva Villeneuve). On the basis of morphological and genetic evidence, we propose to extend the generic limits of Winthemia to include W. londti, sp. nov. (South Africa), W. capensis (Schiner), comb. nov. (South Africa), W. prima (Brauer & Bergenstamm), comb. nov. (China, Japan, Australia) and W. calva (Villeneuve), comb. nov. (D.R. Congo), thus synonymising with Winthemia the generic names Crypsina, syn. nov. and Hemiwinthemia, syn. nov.