Phylogenomics reveals the history of host use in mosquitoes.

Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: 188-250 MYA]), considerably older than previous estimates. Moreover, we utilize an extensive database of host associations for mosquitoes to show that mosquitoes have shifted to feeding upon the blood of mammals numerous times, and that mosquito diversification and host-use patterns within major lineages appear to coincide in earth history both with major continental drift events and with the diversification of vertebrate classes.

Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae.

The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. An extraordinary diversity in life histories, feeding habits and morphology are a hallmark of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm placement of Cryptochetidae as sister taxon to a large clade containing both Drosophilidae and Braulidae-the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.

Similar pattern, different paths: tracing the biogeographical history of Megaloptera (Insecta: Neuropterida) using mitochondrial phylogenomics.

The sequential breakup of the supercontinent Pangaea since the Middle Jurassic is one of the crucial factors that has driven the biogeographical patterns of terrestrial biotas. Despite decades of effort searching for concordant patterns between diversification and continental fragmentation among taxonomic groups, increasing evidence has revealed more complex and idiosyncratic scenarios resulting from a mixture of vicariance, dispersal and extinction. Aquatic insects with discreet ecological requirements, low vagility and disjunct distributions represent a valuable model for testing biogeographical hypotheses by reconstructing their distribution patterns and temporal divergences. Insects of the order Megaloptera have exclusively aquatic larvae, their adults have low vagility, and the group has a highly disjunct geographical distribution. Here we present a comprehensive phylogeny of Megaloptera based on a large-scale mitochondrial genome sequencing of 99 species representing >90% of the world genera from all major biogeographical regions. Molecular dating suggests that the deep divergence within Megaloptera pre-dates the breakup of Pangaea. Subsequently, the intergeneric divergences within Corydalinae (dobsonflies), Chauliodinae (fishflies) and Sialidae (alderflies) might have been driven by both vicariance and dispersal correlated with the shifting continent during the Cretaceous, but with strikingly different and incongruent biogeographical signals. The austral distribution of many corydalids appears to be a result of colonization from Eurasia through southward dispersal across Europe and Africa during the Cretaceous, whereas a nearly contemporaneous dispersal via northward rafting of Gondwanan landmasses may account for the colonization of extant Eurasian alderflies from the south.

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.

Discovery of Lebambromyia in Myanmar Cretaceous Amber: Phylogenetic and Biogeographic Implications (Insecta, Diptera, Phoroidea).

Lebambromyia sacculifera sp. nov. is described from Late Cretaceous amber from Myanmar, integrating traditional observation techniques and X-ray phase contrast microtomography. Lebambromyia sacculifera is the second species of Lebambromyia after L. acrai Grimaldi and Cumming, described from Lebanese amber (Early Cretaceous), and the first record of this taxon from Myanmar amber, considerably extending the temporal and geographic range of this genus. The new specimen bears a previously undetected set of phylogenetically relevant characters such as a postpedicel sacculus and a prominent clypeus, which are shared with Ironomyiidae and Eumuscomorpha. Our cladistic analyses confirmed that Lebambromyia represented a distinct monophyletic lineage related to Platypezidae and Ironomyiidae, though its affinities are strongly influenced by the interpretation and coding of the enigmatic set of features characterizing these fossil flies.

Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics.

BACKGROUND: The most species-rich radiation of animal life in the 66 million years following the Cretaceous extinction event is that of schizophoran flies: a third of fly diversity including Drosophila fruit fly model organisms, house flies, forensic blow flies, agricultural pest flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these flies. We use protein encoding sequence data from transcriptomes, including 3145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge. RESULTS: Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea stat. rev. as successive sister groups to the remaining Schizophora. Ephydroidea, Drosophila's superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroborated by morphological traits, the 'Modified Oviscapt Clade' containing Tephritoidea, Nerioidea, and other families, and the 'Cleft Pedicel Clade' containing Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multispecies coalescent approaches. Rogue taxon removal was effective in increasing support values compared with strategies that maximise gene coverage or minimise missing data. CONCLUSIONS: Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.

Revision of the Australian bee fly genus Meomyia Evenhuis, 1983, with description of three new species (Bombyliidae, Bombyliinae, Bombyliini).

The endemic Australian bee fly genus Meomyia Evenhuis is revised, including six described species and three newly described: Meomyia hortorum sp. nov., Meomyia kochae sp. nov., Meomyia melanocincta sp. nov. Bombylius tetratrichus Walker is excluded from Meomyia and placed in Dissodesma Bowden Li. Meomyia is characterised by the slender and elongate antennal flagellum, and the black abdominal band and dense black tuft on apex of abdomen. A key to species of Meomyia is provided. Species are found in southern Australia.

A minimum reporting standard for multiple sequence alignments.

Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.

Sand wasp (Hymenoptera: Crabronidae) parasites emerging from mud wasp nests (Hymenoptera: Sphecidae)-a reliable host record of Thraxan Yeates amp; Lambkin (Diptera: Bombyliidae: Anthracinae) with description of the pupal exuviae of three Thraxan species.

Two female Thraxan sp. (Diptera: Bombyliidae: Anthracinae) emerged from parasitised Pison simillimum Smith (Hymenoptera: Crabronidae) larvae found inside a Sceliphron formosum Smith (Hymenoptera: Sphecidae) mud wasps nest. Thraxan sp. larvae are endoparasites of P. simillimum larvae. The endoparasite pupates inside the host larva, kills it, and emerges free of the host body. We describe and illustrate the pupal exuviae of the newly found species and two known species, T. luteus Yeates Lambkin and T. misatulus Yeates Lambkin, and we compare these pupal exuviae to those of Anthrax Scopoli.

Revision of the Australian bee fly genus Sisyromyia White, 1916 (Bombyliidae, Bombyliinae, Acrophthalmydini).

We review Sisyromyia White (Bombyliidae, Bombyliinae), a remarkable Australian endemic bee fly genus, which includes 11 species, including six species we describe as new here: Sisyromyia albisquama sp. nov., Sisyromyia angustivitta sp. nov., Sisyromyia elongata sp. nov., Sisyromyia maculipennis sp. nov., Sisyromyia umbra sp. nov., Sisyromyia vittata sp. nov. The genus can be easily distinguished from other Australian genera in the subfamily by having a one-segmented antennal flagellum, subapex of flagellum with some long hairs; a pale median stripe present on the abdomen consisting of dense, decumbent short scales, cell r5 open; cell br nearly as long as cell bm, crossvein m-m located on base of cell dm; crossvein m-m long, nearly as long as crossvein r-m. We also recognized one new synonym, and propose a new combination for Sisyromyia binghi Evenhuis. A key to species of Sisyromyia is provided, and we extensively illustrate their internal and external morphology.

Revision of the Australian bee fly genus Pilosia Hull, 1973 (Bombyliidae, Bombyliinae) from Western Australia.

A restricted Western Australia bee fly genus Pilosia Hull (Bombyliidae, Bombyliinae) is reviewed with the description of two new species, Pilosia incana Bowden Li sp. nov. and Pilosia flava Li Yeates sp. nov., and the type species, Pilosia flavopilosa Hull, 1973 is identified as a new junior synonym of Pilosia immutatus (Walker, 1849). This genus can easily be distinguished from other Australian genera in the subfamily by having a three-segmented antennal flagellum, a closed cell cup and a haired mediotergite. A recent morphological phylogeny of Australian Bombyliinae suggested Pilosia is sister to all the remaining Bombyliinae genera (Li Yeates, 2018). A key to all three known species of Pilosia is provided.

One hundred years of solitude ended: A second species of Marmasoma White, 1916 (Diptera, Bombyliidae, Bombyliinae, Eclimini) from Australia.

Known as a monotypic genus for over a century, Marmasoma White, 1916 is an endemic Australian bee fly genus belonging to the tribe Eclimini of the subfamily Bombyliinae. A new species: Marmasoma hortorum sp. nov. is described based on a series of specimens from Western Australia and South Australia. This new species can be easily distinguished from the congener by the inconspicuous pale wing markings and mostly white to pale yellow scales on the body, as well as characters of both male and female genitalia. M. sumptuosum is found in south-eastern Australia, including Tasmania, and some specimens have been collected on Kangaroo Island, South Australia. M. hortorum sp. nov. occurs in south Western Australia, and a pair of specimens has been taken just north of Port Augusta in South Australia. A key to species of Marmasoma is provided.

Entomo-venomics: The evolution, biology and biochemistry of insect venoms.

The insects are a hyperdiverse class containing more species than all other animal groups combined-and many employ venom to capture prey, deter predators and micro-organisms, or facilitate parasitism or extra-oral digestion. However, with the exception of those made by Hymenoptera (wasps, ants and bees), little is known about insect venoms. Here, we review the current literature on insects that use venom for prey capture and predator deterrence, finding evidence for fourteen independent origins of venom usage among insects, mostly among the hyperdiverse holometabolan orders. Many lineages, including the True Bugs (Heteroptera), robber flies (Asilidae), and larvae of many Neuroptera, Coleoptera and Diptera, use mouthpart-associated venoms to paralyse and pre-digest prey during hunting. In contrast, some Hymenoptera and larval Lepidoptera, and one species of beetle, use non-mouthpart structures to inject venom in order to cause pain to deter potential predators. Several recently published insect venom proteomes indicate molecular convergence between insects and other venomous animal groups, with all insect venoms studied so far being potently bioactive cocktails containing both peptides and larger proteins, including novel peptide and protein families. This review summarises the current state of the field of entomo-venomics.

Immature stages of the Australian flower-loving fly Apiocera striativentris (Diptera: Apioceridae).

The Apioceridae (Diptera) are relatively large asiloid flies with just over 140 described species worldwide. They are closely related to both Mydidae and Asilidae, and most species are found in Australia and North America, however a handful are found in both southern Africa and southern South America. The immature stages of only one species is known, the Australian beach dune inhabiting species Apiocera maritima Hardy. Like most asiloid larvae, apiocerid larvae are assumed to be predators of other soft-bodied invertebrates in the soil. Anatomically the larvae and pupae are similar to those of closely related families. The larvae are elongate, cream-coloured, subcylindrical and with a small, well-sclerotised head capsule. The pupa has a number of robust processes and spines on the head capsule and rows of distinctive bristles on the abdominal tergites. These spines and bristles are used by the pupa to drill upwards out of the soil prior to adult emergence. Here we describe the late instar larva and pupa of the Australian species A. striativentris Paramonov and compare them to the larva and pupa of the previously described species. Apiocerid larvae have distinctive, rounded abdominal segments 2-5 that may be diagnostic for the family.

Parallel evolution of mound-building and grass-feeding in Australian nasute termites.

Termite mounds built by representatives of the family Termitidae are among the most spectacular constructions in the animal kingdom, reaching 6-8 m in height and housing millions of individuals. Although functional aspects of these structures are well studied, their evolutionary origins remain poorly understood. Australian representatives of the termitid subfamily Nasutitermitinae display a wide variety of nesting habits, making them an ideal group for investigating the evolution of mound building. Because they feed on a variety of substrates, they also provide an opportunity to illuminate the evolution of termite diets. Here, we investigate the evolution of termitid mound building and diet, through a comprehensive molecular phylogenetic analysis of Australian Nasutitermitinae. Molecular dating analysis indicates that the subfamily has colonized Australia on three occasions over the past approximately 20 Myr. Ancestral-state reconstruction showed that mound building arose on multiple occasions and from diverse ancestral nesting habits, including arboreal and wood or soil nesting. Grass feeding appears to have evolved from wood feeding via ancestors that fed on both wood and leaf litter. Our results underscore the adaptability of termites to ancient environmental change, and provide novel examples of parallel evolution of extended phenotypes.

Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections.

Museums and herbaria represent vast repositories of biological material. Until recently, working with these collections has been difficult, due to the poor condition of historical DNA. However, recent advances in next-generation sequencing technology, and subsequent development of techniques for preparing and sequencing historical DNA, have recently made working with collection specimens an attractive option. Here we describe the unique technical challenges of working with collection specimens, and innovative molecular methods developed to tackle them. We also highlight possible applications of collection specimens, for taxonomy, ecology and evolution. The application of next-generation sequencing methods to museum and herbaria collections is still in its infancy. However, by giving researchers access to billions of specimens across time and space, it holds considerable promise for generating future discoveries across many fields.

Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution.

Our understanding on the phylogenetic relationships of insects has been revolutionised in the last decade by the proliferation of next generation sequencing technologies (NGS). NGS has allowed insect systematists to assemble very large molecular datasets that include both model and non-model organisms. Such datasets often include a large proportion of the total number of protein coding sequences available for phylogenetic comparison. We review some early entomological phylogenomic studies that employ a range of different data sampling protocols and analyses strategies, illustrating a fundamental renaissance in our understanding of insect evolution all driven by the genomic revolution. The analysis of phylogenomic datasets is challenging because of their size and complexity, and it is obvious that the increasing size alone does not ensure that phylogenetic signal overcomes systematic biases in the data. Biases can be due to various factors such as the method of data generation and assembly, or intrinsic biological feature of the data per se, such as similarities due to saturation or compositional heterogeneity. Such biases often cause violations in the underlying assumptions of phylogenetic models. We review some of the bioinformatics tools available and being developed to detect and minimise systematic biases in phylogenomic datasets. Phylogenomic-scale data coupled with sophisticated analyses will revolutionise our understanding of insect functional genomics. This will illuminate the relationship between the vast range of insect phenotypic diversity and underlying genetic diversity. In combination with rapidly developing methods to estimate divergence times, these analyses will also provide a compelling view of the rates and patterns of lineagenesis (birth of lineages) over the half billion years of insect evolution.

First crane fly from the Upper Jurassic of Australia (Diptera: Limoniidae).

The first crane fly (Diptera: Tipuloidea) fossil discovered in the Upper Jurassic Talbragar Fish Bed in Australia is described and illustrated. Eotipula grangeri sp. nov., described from a single specimen, is assigned to the family Limoniidae based primarily on the conformation of wing veins. It is the second and oldest record of Limoniidae from Australia, and the first of Jurassic age from the southern hemisphere.

A new species, new immature stages, and new synonymy in Australian Dasybasis flies (Diptera: Tabanidae: Diachlorini).

Australian beach sand is a productive habitat for lower brachyceran fly larvae but often overlooked by collectors. We collected two species of tabanid larvae from coastal beach sand in southern New South Wales in August 2013. Both species belong to the Dasybasis macrophthalma species-group of Mackerras (1959), one a new species, and the other D. exulans (Erichson, 1842). We describe both new immature stages and the new species adult as Dasybasis rieki sp. nov. (Diptera: Tabanidae: Diachlorini). Trojan (1994b) elevated the D. macrophthalma species group to the genus Sznablius. We review the evidence for the generic status of Sznablius, and synonymize it with Dasybasis.