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.T he history of life is often portrayed as an ongoing series of evolutionary bursts, with each representing the origin and diversification of unique life forms with different and ecologically significant adaptations. Although the radiations of some groups, such as cichlid fishes of the lakes of East Africa or Darwin's finches, are well documented (1), the big radiations that account for most of the diversity of life on Earth have been more challenging to explore. To understand these radiations, we must resolve the relationships among major taxa, date the origin of these lineages (many of them ancient), and then explicitly consider whether the diversification events are really pulse-like adaptive radiations or, more simply, the result of nonadaptive, or even random, neutral processes.Although the paradigm of adaptive radiation has been applied to every level of biological classification, the large-scale macroevolutionary pattern expected from ancient repeated episodes of adaptive radiation is unclear. It has been predicted that at this scale, ecologically driven diversification may result in (i) significant variation in clade size, uncorrelated to the age of the clade (2), and (ii) shifts in average diversification rate coincident with major shifts in morphology, life history, or ecology (3). Another macroevolutionary prediction of repeated adaptive radiation is the widespre...

Background: Evolutionary relationships among the 11 extant orders of insects that undergo complete metamorphosis, called Holometabola, remain either unresolved or contentious, but are extremely important as a context for accurate comparative biology of insect model organisms. The most phylogenetically enigmatic holometabolan insects are Strepsiptera or twisted wing parasites, whose evolutionary relationship to any other insect order is unconfirmed. They have been controversially proposed as the closest relatives of the flies, based on rDNA, and a possible homeotic transformation in the common ancestor of both groups that would make the reduced forewings of Strepsiptera homologous to the reduced hindwings of Diptera. Here we present evidence from nucleotide sequences of six singlecopy nuclear protein coding genes used to reconstruct phylogenetic relationships and estimate evolutionary divergence times for all holometabolan orders.

Sarcophagidae is one of the most species‐rich families within the superfamily Oestroidea. This diversity is usually represented by three lineages: Miltogramminae, Paramacronychiinae and Sarcophaginae. Historically, the phylogenetic relationships among these lineages have been elusive, due to poorly supported hypotheses or small taxon sets, or both. This study provides a dramatic increase in molecular data, more balanced sampling of all three lineages from all biogeographical regions and a reassessment of morphological characters using scanning electron microscopy in the most comprehensive assessment of subfamily‐level phylogeny in Sarcophagidae to date. This analysis of the largest molecular dataset ever produced for a phylogenetic analysis of a fly lineage, with 950 loci from anchored hybrid enrichment comprising 435 930 bp from 101 species, revealed Paramacronychiinae as sister to Miltogramminae, not to Sarcophaginae, as suggested by adult morphology. Maximum likelihood analysis produced a well‐supported topology, with 91% of the nodes receiving strong bootstrap proportions (> 97%). In contrast to the molecular data, three out of nine morphological characters studied point to a sister‐group relationship of (Sarcophaginae + Paramacronychiinae) and the remaining six characters are either silent on subfamily relationships or in need of further study. Re‐examination of morphological structures provides new insights into the evolution of male genitalic traits within Sarcophagidae and highlights their convergence producing conflicting phylogenetic signal. Our phylogeny reconciles older and widely used systems of classification with tree‐based thinking and sets up a classification of flesh flies that is more aligned with their evolutionary history.

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Muscidae are a megadiverse dipteran family that exhibits extraordinary diversity in morphology and life history as both immatures and adults. The classification of Muscidae has been long debated, and most higher‐level relationships remain unknown. In this study, we used multilocus Sanger sequencing (mS‐seq), anchored hybrid enrichment (AHE) and restriction‐site associated DNA sequencing (RAD‐seq) approaches to examine relationships within Muscidae. The results from AHE and RAD‐seq largely correspond to those obtained from mS‐seq in terms of overall topology, yet phylogenomic approaches received much higher nodal support. The results from all molecular approaches contradict the traditional classification based predominantly on adult morphology, but provide an opportunity to re‐interpret the morphology of immature stages. Rearrangements in Muscidae classification are proposed as follows: (i) Mesembrina Meigen and Polietes Rondani are transferred from Muscinae to Azeliinae; (ii) Reinwardtiinae stat. rev. is resurrected as a subfamily distinct from Azeliinae; (iii) Eginia Robineau‐Desvoidy, Neohelina Malloch, Syngamoptera Schnabl and Xenotachina Malloch are transferred to Reinwardtiinae stat. rev.

Seventeen new species of Anastrepha, primarily from Suriname, French Guiana and Pará, Brazil, are described and illustrated: A. aithogaster Norrbom from Brazil (Pará), French Guiana, and Suriname; A. aliesae Norrbom from Suriname; A. brownsbergiensis Norrbom from Suriname; A. crassaculeus Norrbom & Rodriguez Clavijo from Colombia (Magdalena, Norte de Santander) and Suriname; A. curvivenis Norrbom from Brazil (Amazonas), Ecuador (Zamora-Chinchipe), Peru (San Martín), and Suriname; A. fuscoalata Norrbom from Brazil (Pará), French Guiana, and Suriname; A. gangadini Norrbom from Suriname; A. juxtalanceola Norrbom from Brazil (Pará) and Suriname; A. microstrepha Norrbom from Brazil (Bahia) and Suriname; A. mitaraka Norrbom from French Guiana; A. neptis Norrbom from Brazil (Pará), Ecuador (Orellana), Peru (Loreto) and Suriname; A. sobrina Norrbom from Brazil (Pará), French Guiana, and Suriname; A. surinamensis Norrbom from Suriname; A. tenebrosa Norrbom from Brazil (Pará) and Peru (Loreto); A. triangularis Norrbom from Suriname; A. wachiperi Norrbom from French Guiana and Peru (Cusco); and A. wittiensis Norrbom from Suriname. The following host plant records are reported: A. aithogaster from fruit of Parahancornia fasciculata (Poir.) Benoist (Apocynaceae); A. aliesae from fruit of Passiflora coccinea Aubl. and P. glandulosa Cav. (Passifloraceae); A. crassaculeus from fruit of an undetermined species of Pouteria (Sapotaceae); A. fuscoalata from fruit of Trymatococcus oligandrus (Benoist) Lanj. (Moraceae); A. sobrina from fruit of Eugenia lambertiana DC. (Myrtaceae); and A. wittiensis from fruit of Manilkara bidentata (A. DC.) A. Chev. (Sapotaceae).

Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of viruses and pathogens. Because mosquitoes are also highly diverse and globally widespread, their phylogeny has remained either little known or difficult to discern. Here, we used phylogenomic analysis of 709 orthologous nuclear gene sequences 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 tree supports an origin of mosquitoes in the early Triassic (~217 mya) with species diversification and host-use patterns within major lineages coinciding in earth history both with major geologic events and with the diversification of vertebrate classes.

The genus Liriomyza Mik (Diptera: Agromyzidae) is a diverse and globally distributed group of acalyptrate flies. Phylogenetic relationships among Liriomyza species have remained incompletely investigated and have never been fully addressed using molecular data. Here, we reconstruct the phylogeny of the genus Liriomyza using various phylogenetic methods (maximum likelihood, Bayesian inference, and gene tree coalescence) on target-capture-based phylogenomic datasets (nucleotides and amino acids) obtained from anchored hybrid enrichment (AHE). We have recovered tree topologies that are nearly congruent across all data types and methods, and individual clade support is strong across all phylogenetic analyses. Moreover, defined morphological species groups and clades are well-supported in our best estimates of the molecular phylogeny. Liriomyza violivora (Spencer) is a sister group to all remaining sampled Liriomyza species, and the well-known polyphagous vegetable pests [L. huidobrensis (Blanchard), L. langei Frick, L. bryoniae. (Kaltenbach), L. trifolii (Burgess), L. sativae Blanchard, and L. brassicae (Riley)].belong to multiple clades that are not particularly closely related on the trees. Often, closely related Liriomyza species feed on distantly related host plants. We reject the hypothesis that cophylogenetic processes between Liriomyza species and their host plants drive diversification in this genus. Instead, Liriomyza exhibits a widespread pattern of major host shifts across plant taxa. Our new phylogenetic estimate for Liriomyza species provides considerable new information on the evolution of host-use patterns in this genus. In addition, it provides a framework for further study of the morphology, ecology, and diversification of these important flies.