Gregory W. Courtney

Episodic radiations in the fly tree of life

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation—lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)—and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y.

Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes

Abstract Relationships among families of the lower Diptera (formerly suborder ‘Nematocera’) have been exceptionally difficult to resolve. Multiple hypotheses based on morphology have been proposed to identify the earliest lineages of flies and place the phylogenetic origin of the higher flies (Brachycera), but convincing support is limited. Here we resolve relationships among the major groups of lower Diptera using sequence data from four nuclear markers, including both ribosomal (28S rDNA) and protein‐coding (CAD, TPI and PGD) genes. Our results support both novel and traditional arrangements. Most unexpectedly, the small, highly‐specialized family Deuterophlebiidae appears to be sister to all remaining Diptera. Other results include the resolution of the traditional infra‐orders Culicomorpha (including a novel superfamily Simulioidea = Thaumaleidae + Simuliidae), Tipulomorpha (Tipulidae sensu lato + Trichoceridae) and Bibionomorpha sensu lato. We find support for a limited Psychodomorpha (Blephariceridae, Tanyderidae and Psychodidae) and Ptychopteromorpha (Ptychopteridae), whereas the placement of several enigmatic families (Nymphomyiidae, Axymyiidae and Perissommatidae) remains ambiguous. According to genetic data, the infra‐order Bibionomorpha is sister to the Brachycera. Much of the phylogenetic signal for major lineages was found in the 28S rDNA gene, whereas protein‐coding genes performed variably at different levels. In addition to elucidating relationships, we also estimate the age of major lower dipteran clades, based on molecular divergence time estimates using relaxed‐clock Bayesian methods and fossil calibration points.

The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence

Members of the megadiverse insect order Diptera (flies) have successfully colonized all continents and nearly all habitats. There are more than 154 000 described fly species, representing 10–12% of animal species. Elucidating the phylogenetic relationships of such a large component of global biodiversity is challenging, but significant advances have been made in the last few decades. Since Hennig first discussed the monophyly of major groupings, Diptera has attracted much study, but most researchers have used non‐numerical qualitative methods to assess morphological data. More recently, quantitative phylogenetic methods have been used on both morphological and molecular data. All previous quantitative morphological studies addressed narrower phylogenetic problems, often below the suborder or infraorder level. Here we present the first numerical analysis of phylogenetic relationships of the entire order using a comprehensive morphological character matrix. We scored 371 external and internal morphological characters from larvae, pupae and adults for 42 species, representing all infraorders selected from 42 families. Almost all characters were obtained from previous studies but required revision for this ordinal‐level study, with homology assessed beyond their original formulation and across all infraorders. We found significant support for many major clades (including the Diptera, Culicomorpha, Bibionomorpha, Brachycera, Eremoneura, Cyclorrhapha, Schizophora, Calyptratae and Oestroidea) and we summarize the character evidence for these groups. We found low levels of support for relationships between the infraorders of lower Diptera, lower Brachycera and major lineages of lower Cyclorrhapha, and this is consistent with findings from molecular studies. These poorly supported areas of the tree may be due to periods of rapid radiation that left few synapomorphies in surviving lineages.

Global diversity of dipteran families (Insecta Diptera) in freshwater (excluding Simulidae, Culicidae, Chironomidae, Tipulidae and Tabanidae)

Today’s knowledge of worldwide species diversity of 19 families of aquatic Diptera in Continental Waters is presented. Nevertheless, we have to face for certain in most groups a restricted knowledge about distribution, ecology and systematic, particularly in the tropical environments. At the same time we realize a dramatically decline or even lack of specialists being able, having the time or the opportunity to extend or even secure the present information. The respective families with approximate numbers of aquatic species are: Blephariceridae (308), Deuterophlebiidae (14), Nyphomyiidae (7), Psychodidae (∼2.000), Scatopsidae (∼5), Tanyderidae (41), Ptychopteridae (69), Dixidae (173), Corethrellidae (97), Chaoboridae (∼50), Thaumaleidae (∼170), Ceratopogonidae (∼6.000), Stratiomyidae (∼43), Empididae (∼660), Lonchopteridae (2), Syrphidae (∼1.080), Sciomyzidae (∼190), Ephydridae (∼1.500), Muscidae (∼870). Numbers of aquatic species will surely increase with increased ecological and taxonomical efforts.

Phylogenetic analysis of the Blephariceromorpha, with special reference to mountain midges (Diptera: Deuterophlebiidae)

Abstract. A cladistic analysis of the Blephariceromorpha (here including the Nymphomyiidae, Deuterophlebiidae and Blephariceridae) and related Diptera provides a test of the phylogenetic hypotheses of Rohdendorf (1964, 1974), Hennig (1973), Wood & Borkent (1989) and Courtney (1990a). In particular, monophyly of the Blephariceroidea and Blephariceromorpha (sensu Wood & Borkent), and their relationship to other Diptera, is tested. Evaluation of larval, pupal and adult characters supports the hypothesis of Wood & Borkent, as modified by Courtney. Four larval features suggest that the Blephariceromorpha + Psychodomorpha form a monophyletic group, although an alternate hypothesis predicting that the Blephariceromorpha is the sister group of the Psychodomorpha + (Ptychopteromorpha + Culicomorpha), is discussed. Monophyly of the Blephariceromorpha (Nymphomyioidea + Blephariceroidea) is supported by one adult and five larval characters. Monophyly of the Blephariceroidea (Deuterophlebiidae + Blephariceridae) is supported by thirteen synapotypies, including features of the larva (six), pupa (three) and adult (four). Nineteen, nineteen and nine hypothesized synapotypies support monophyly of the Nymphomyiidae, Deuterophlebiidae and Blephariceridae, respectively.

Phylogenetic synthesis of morphological and molecular data reveals new insights into the higher-level classification of Tipuloidea (Diptera)

Tipuloidea, the crane flies, are a diverse lineage of true flies (Insecta: Diptera) whose phylogenetic classification and taxonomy remain a challenge. Here we present the results of a quantitative phylogenetic analysis of Tipuloidea based on combined morphological characters (adult, larvae and pupae) and nuclear gene sequence data (28S rDNA and CAD). Forty‐five species, from 44 genera and subgenera, were sampled, representing the four putative families of Tipuloidea (Cylindrotomidae, Limoniidae, Pediciidae and Tipulidae sensu stricto). Analyses of individual datasets, although differing in overall topology, support the monophyly of several major lineages within Tipuloidea. Parsimony and Bayesian analyses using individual morphological and molecular datasets resulted in incongruent topologies. Increased resolution and tree support was obtained when both datasets (morphology and genes) were combined, in both combined evidence parsimony and Bayesian analyses, than when analysed separately. The recovered consensus phylogeny was not consistent with any previously proposed Tipuloidea classification, with previous importance assigned to character states shown here to represent losses and reversals seen as a major factor influencing erroneous classification. The results provided here, together with evidence from previous analyses, were used to append the Tipuloidea classification to supported evolutionary lineages. Tipuloidea is presented as two families: Pediciidae and Tipulidae. Pediciidae is recovered as the sister group to all remaining Tipuloidea. Our current phylogenetic hypothesis is not consistent with the existing subfamilial classification of the ‘Limoniidae’, which is paraphyletic with respect to a well‐supported Tipulinae + Cylindrotominae clade, whereas the three ‘limoniid’ subfamilies are para‐ or polyphyletic. The recognition of ‘Limoniidae’ as a valid monophyletic family is discouraged and the subfamilies of ‘Limoniidae’ are amended and placed within Tipulidae. A revised phylogenetic classification is proposed for the crane flies based on a synthesis of evidence from multiple genes and morphology.

Next-Generation Field Guides

To conserve species, we must first identify them. Field researchers, land managers, educators, and citizen scientists need up-to-date and accessible tools to identify organisms, organize data, and share observations. Emerging technologies complement traditional, book-form field guides by providing users with a wealth of multimedia data. We review technical innovations of next-generation field guides, including Web-based and stand-alone applications, interactive multiple-access keys, visual-recognition software adapted to identify organisms, species checklists that can be customized to particular sites, online communities in which people share species observations, and the use of crowdsourced data to refine machine-based identification algorithms. Next-generation field guides are user friendly; permit quality control and the revision of data; are scalable to accommodate burgeoning data; protect content and privacy while allowing broad public access; and are adaptable to ever-changing platforms and browsers. These tools have great potential to engage new audiences while fostering rigorous science and an appreciation for nature.

Life history patterns of nearctic mountain midges diptera deuterophlebiidae

Mountain midges (Diptera:Deuterophlebiidae) are widespread and seasonally abundant in streams of western North America. As part of a comprehensive systematic investigation of the Deuterophlebiidae, I examined the life histories of all Nearctic species, including aspects of habitat, reproductive biology, and phenology. Collection techniques were also evaluated. This paper is based on qualitative data obtained during a seven-year period (1981-1988) and from more than 500 collection sites, and on a quantitative phenological study in 1986 of 17 populations from the Pacific Northwest. Deuterophlebiids generally are considered stenobionts, requiring cold, mountain streams; however, many species inhabit a diversity of stream types, from small, high-gradient creeks to large, low-gradient rivers. The immature stages of all species are restricted to riffle habitats where current velocities typically exceed 1 m/s. Adult mountain midges exhibit marked diel synchrony, with emergence, flight, and mating during only the early morning. Flight behaviour of the short-lived adults is distinct and includes formation of male swarms. Field and laboratory observations show that females shed their wings and select oviposition sites underwater. Asynchronous life histories are typical of Nearctic species, with egg-hatching and adult emergence usually extending 2-3 mo. This strategy is adaptive for populations in the Pacific Northwest, where unpredictable spring spates may scour substrates and cause correspondingly high mortality of stream benthos. Univoltine life histories are typical of Nearctic mountain midges, though variation from this pattern was seen in three populations. Temporal, habitat and/or reproductive isolation of sympatric deuterophlebiids, blepharicerids, and other torrenticolous insects was evident in many streams.

Revision of Nearctic mountain midges (Diptera : Deuterophlebiidae

Previously undescribed character systems are evaluated and incorporated in a redescription of the genus Deuterophlebia Edwards (Diptera: Deuterophlebiidae). Nearctic species of mountain midges are revised to include six species, two of which are new. Deuterophlebia personata sp. nov. is widespread in the mountains of western North America, with northern populations apparently parthenogenetic. Deuterophlebia vernalis sp. nov. occurs only in south-central Washington state. A lectotype and paralectotype are designated for D. coloradensis Pennak, and distributional data are given for all North American species. Also provided are keys to larvae, pupae, and adults of Nearctic species, and a discussion of character variation in mountain midges, with particular reference to problematic populations from Oregon and California.

First μ‐CT‐based 3d reconstruction of a dipteran larva—the head morphology of protanyderus (tanyderidae) and its phylogenetic implications

The larval head of Protanyderus was examined and documented using innovative techniques, with emphasis on internal structures. A chart listing all head muscles of dipteran larvae and other holometabolan groups is presented in the Supporting Information. The results are compared to conditions found in other nematoceran lineages. The larval head of Protanyderus is characterized mainly by plesiomorphic character states such as the complete and largely exposed head capsule, the long coronal suture, V‐shaped frontal sutures, lateral antennal insertion areas, a transverse labrum, a nearly horizontal plane of mandibular movements, mandibles lacking a movable distal part, a mesal hook and mesal or distal combs, separated maxillary endite lobes, a comparatively complete array of muscles, and a brain only partly located within the head capsule. An anteriorly toothed hypostomal plate and dense labral brushes of microtrichiae are also likely groundplan features of Diptera. The pharyngeal filter is a possible apomorphy of Diptera excl. Deuterophlebiidae (or Deuterophlebiidae + Nymphomyiidae). The messors have also likely evolved early in the dipteran crown group but are absent in the groundplan. The phylogenetic interpretation of externolateral plates with growth lines is ambiguous. Autapomorphies of Tanyderidae are differences between the third and fourth instar larvae, the roof‐like extension above the antennal insertion area, the dorsal endocarina, and the posterodorsal internal ridge. The phylogenetic position of Tanyderidae is controversial, but features of the larval head do not support a proposed sistergroup relationship between Tanyderidae and Psychodidae. Both groups differ in many features of the larval head, and we did not identify a single potential synapomorphy. Larval characters alone are insufficient for a reliable phylogenetic reconstruction, though they vary greatly and apparently contain phylogenetic information. The evaluation of these features in the context of robust molecular phylogenies will be a sound basis for the reconstruction of complex evolutionary scenarios for the megadiverse Diptera. Diptera. J. Morphol. 2012.