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.

Where do the Neotropical Empidini lineages (Diptera: Empididae: Empidinae) fit in a worldwide context?

The tribe Empidini (Diptera: Empididae: Empidinae) is a diverse group with fourteen genera, seven of which are exclusive to the Neotropical region: Bolrhamphomyia Rafael, Chilerhamphomyia Rafael, Hystrichonotus Collin, Lamprempis Wheeler and Melander, Macrostomus Wiedemann, Opeatocerata Melander and Porphyrochroa Melander. Although Empidini itself is likely paraphyletic, many presumably monophyletic genera and species groups are recognized. Here, we apply DNA sequences from multiple genes to infer the phylogeny of Empidini, focusing on placing the Neotropical lineages within the entire tribe and identifying monophyletic groups. We included 98 Empidini taxa along with 18 outgrous terminals, spanning the diversity within the group. The results from the analyses performed are largely similar, with major groupings of genera in common. Specifically, the analyses recovered a monophyletic Hilarini and a paraphyletic Empidini. Most species from Chile and Argentina (Andean region) are found to belong to an early branching lineage within Empidinae, and are not monophyletic with other Empidini. A large portion of the remaining Neotropical Empidini (not Andean) comprises a single clade that includes four endemic genera and a number of Neotropical Empis Linneaus species. Macrostomus and Porphyrochroa each recovered as monophyletic and sister to one another, although generic placement of a few taxa remains uncertain due to conflicting morphological features. Lamprempis+Opeatocerata are also found to be sister-taxa in most analyses. Several large genera were found to be polyphyletic or paraphyletic including Empis and Rhamphomyia Meigen. We evaluate our findings and discuss them in light of current Empidinae taxonomy.

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

Molecular phylogenetic studies at all taxonomic levels often infer rapid radiation events based on short, poorly resolved internodes. While such rapid episodes of diversification are an important and widespread evolutionary phenomenon, much of this poor phylogenetic resolution may be attributed to the continuing widespread use of "traditional" markers (mitochondrial, ribosomal, and some nuclear protein-coding genes) that are often poorly suited to resolve difficult, higher-level phylogenetic problems. Here we reconstruct phylogenetic relationships among a representative set of taxa of the parasitoid fly family Tachinidae and related outgroups of the superfamily Oestroidea. The Tachinidae are one of the most species rich, yet evolutionarily recent families of Diptera, providing an ideal case study for examining the differential performance of loci in resolving phylogenetic relationships and the benefits of adding more loci to phylogenetic analyses. We assess the phylogenetic utility of nine genes including both traditional genes (e.g., CO1 mtDNA, 28S rDNA) and nuclear protein-coding genes newly developed for phylogenetic analysis. Our phylogenetic findings, based on a limited set of taxa, include: a close relationship between Tachinidae and the calliphorid subfamily Polleninae, monophyly of Tachinidae and the subfamilies Exoristinae and Dexiinae, subfamily groupings of Dexiinae+Phasiinae and Tachininae+Exoristinae, and robust phylogenetic placement of the somewhat enigmatic genera Strongygaster, Euthera, and Ceracia. In contrast to poor resolution and phylogenetic incongruence of "traditional genes," we find that a more selective set of highly informative genes is able to more precisely identify regions of the phylogeny that experienced rapid radiation of lineages, while more accurately depicting their phylogenetic context. Although much expanded taxon sampling is necessary to effectively assess the monophyly of and relationships among major tachinid lineages and their relatives, we show that a small number of well-chosen nuclear protein-coding genes can successfully resolve even difficult phylogenetic problems.

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.

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.

Repeated climate-linked host shifts have promoted diversification in a temperate clade of leaf-mining flies.

A central but little-tested prediction of "escape and radiation" coevolution is that colonization of novel, chemically defended host plant clades accelerates insect herbivore diversification. That theory, in turn, exemplifies one side of a broader debate about the relative influence on clade dynamics of intrinsic (biotic) vs. extrinsic (physical-environmental) forces. Here, we use a fossil-calibrated molecular chronogram to compare the effects of a major biotic factor (repeated shift to a chemically divergent host plant clade) and a major abiotic factor (global climate change) on the macroevolutionary dynamics of a large Cenozoic radiation of phytophagous insects, the leaf-mining fly genus Phytomyza (Diptera: Agromyzidae). We find one of the first statistically supported examples of consistently elevated net diversification accompanying shift to new plant clades. In contrast, we detect no significant direct effect on diversification of major global climate events in the early and late Oligocene. The broader paleoclimatic context strongly suggests, however, that climate change has at times had a strong indirect influence through its effect on the biotic environment. Repeated rapid Miocene radiation of these flies on temperate herbaceous asterids closely corresponds to the dramatic, climate-driven expansion of seasonal, open habitats.

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

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