@article{xuan_scheffer_lewis_cassel_liu_wiegmann_2023, title={The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics}, volume={184}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2023.107778}, abstractNote={Leaf-mining flies (Diptera: Agromyzidae) are a diverse clade of phytophagous Diptera known largely for their economic impact as leaf- or stem-miners on vegetable and ornamental plants. Higher-level phylogenetic relationships of Agromyzidae have remained uncertain because of challenges in sampling of both taxa and characters for morphology and PCR-based Sanger-era molecular systematics. Here, we used hundreds of orthologous single-copy nuclear loci obtained from anchored hybrid enrichment (AHE) to reconstruct phylogenetic relationships among the major lineages of leaf-mining flies. The resulting phylogenetic trees are highly congruent and well-supported, except for a few deep nodes, when using different molecular data types and phylogenetic methods. Based on divergence time dating using a relaxed clock model-based analysis, leaf-mining flies are shown to have diversified in multiple lineages since the early Paleocene, approximately 65 million years ago. Our study not only reveals a revised classification system of leaf-mining flies, but also provides a new phylogenetic framework to understand their macroevolution.}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Xuan, Jing-Li and Scheffer, Sonja J. and Lewis, Matt and Cassel, Brian K. and Liu, Wan-Xue and Wiegmann, Brian M.}, year={2023}, month={Jul} }
 @article{xuan_scheffer_lonsdale_cassel_lewis_eiseman_liu_wiegmann_2022, title={A genome-wide phylogeny and the diversification of genus Liriomyza (Diptera: Agromyzidae) inferred from anchored phylogenomics}, volume={9}, ISSN={["1365-3113"]}, DOI={10.1111/syen.12569}, abstractNote={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.}, journal={SYSTEMATIC ENTOMOLOGY}, author={Xuan, Jing-Li and Scheffer, Sonja J. and Lonsdale, Owen and Cassel, Brian K. and Lewis, Matthew L. and Eiseman, Charles S. and Liu, Wan-Xue and Wiegmann, Brian M.}, year={2022}, month={Sep} }
 @article{winkler_kirk-spriggs_bayless_soghigian_meier_pape_yeates_carvalho_copeland_wiegmann_2022, title={Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae}, volume={17}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0274292}, abstractNote={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.}, number={10}, journal={PLOS ONE}, author={Winkler, Isaac S. and Kirk-Spriggs, Ashley H. and Bayless, Keith M. and Soghigian, John and Meier, Rudolf and Pape, Thomas and Yeates, David K. and Carvalho, A. Bernardo and Copeland, Robert S. and Wiegmann, Brian M.}, year={2022}, month={Oct} }
 @article{bayless_trautwein_meusemann_shin_petersen_donath_podsiadlowski_mayer_niehuis_peters_et al._2021, title={Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics}, volume={19}, ISSN={["1741-7007"]}, DOI={10.1186/s12915-020-00944-8}, abstractNote={Abstract 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.}, number={1}, journal={BMC BIOLOGY}, author={Bayless, Keith M. and Trautwein, Michelle D. and Meusemann, Karen and Shin, Seunggwan and Petersen, Malte and Donath, Alexander and Podsiadlowski, Lars and Mayer, Christoph and Niehuis, Oliver and Peters, Ralph S. and et al.}, year={2021}, month={Feb} }
 @article{meredith_kularatna_nagaro_nagahawatte_bodinayake_kurukulasooriya_wijesingha_harden_piyasiri_hammouda_et al._2021, title={Colonization with multidrug-resistant Enterobacteriaceae among infants: an observational study in southern Sri Lanka}, volume={10}, ISSN={["2047-2994"]}, DOI={10.1186/s13756-021-00938-3}, abstractNote={Abstract Background The timing of and risk factors for intestinal colonization with multidrug-resistant Enterobacteriaceae (MDRE) are still poorly understood in areas with high MDRE carriage. We determined the prevalence, timing, and risk factors associated with MDRE intestinal colonization among infants in southern Sri Lanka. Methods Women and their newborn children were enrolled within 48 h after delivery in southern Sri Lanka. Rectal swabs were collected from women and infants at enrollment and 4–6 weeks later. Enterobacteriaceae were isolated and identified as MDRE (positive for extended-spectrum β-lactamases or carbapenem resistant) using standard microbiologic procedures. We used exact methods (Fisher’s exact and Kruskal–Wallis tests) and multivariable logistic regression to identify sociodemographic and clinical features associated with MDRE intestinal colonization. Whole-genome sequencing was performed on selected MDRE isolates to identify phylogroups and antibiotic resistance-encoding genes were identified with NCBI’s AMRfinder tool. Results Overall, 199 post-partum women and 199 infants were enrolled; 148/199 (74.4%) women and 151/199 (75.9%) infants were reassessed later in the community. Twenty-four/199 (12.1%) women and 3/199 (1.5%) infants displayed intestinal colonization with MDRE at enrollment, while 26/148 (17.6%) women and 24/151 (15.9%) infants displayed intestinal colonization with MDRE at the reassessment. While there were no risk factors associated with infant colonization at enrollment, multivariable analysis indicated that risk factors for infant colonization at reassessment included mother colonized at enrollment (aOR = 3.62) or reassessment (aOR = 4.44), delivery by Cesarean section (aOR = 2.91), and low birth weight (aOR = 5.39). Of the 20 MDRE isolates from infants that were sequenced, multilocus sequence typing revealed that 6/20 (30%) were clustered on the same branch as MDRE isolates found in the respective mothers. All sequenced isolates for mothers (47) and infants (20) had at least one ESBL-producing gene. Genes encoding fosfomycin resistance were found in 33/47 (70%) of mothers’ isolates and 16/20 (80%) of infants’ isolates and genes encoding resistance to colistin were found in one (2%) mother’s isolate. Conclusions Our results suggest that a substantial proportion of infants undergo MDRE intestinal colonization within 6 weeks of birth, potentially due to postnatal rather than intranatal transmission.}, number={1}, journal={ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL}, author={Meredith, Hannah R. and Kularatna, Sarath and Nagaro, Kristin and Nagahawatte, Ajith and Bodinayake, Champica and Kurukulasooriya, Ruvini and Wijesingha, Nishadhi and Harden, Lyndy B. and Piyasiri, Bhagya and Hammouda, Amr and et al.}, year={2021}, month={Apr} }
 @article{justi_soghigian_pecor_caicedo-quiroga_rutvisuttinunt_li_stevens_dorn_wiegmann_linton_2021, title={From e-voucher to genomic data: Preserving archive specimens as demonstrated with medically important mosquitoes (Diptera: Culicidae) and kissing bugs (Hemiptera: Reduviidae)}, volume={16}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0247068}, abstractNote={Scientific collections such as the U.S. National Museum (USNM) are critical to filling knowledge gaps in molecular systematics studies. The global taxonomic impediment has resulted in a reduction of expert taxonomists generating new collections of rare or understudied taxa and these large historic collections may be the only reliable source of material for some taxa. Integrated systematics studies using both morphological examinations and DNA sequencing are often required for resolving many taxonomic issues but as DNA methods often require partial or complete destruction of a sample, there are many factors to consider before implementing destructive sampling of specimens within scientific collections. We present a methodology for the use of archive specimens that includes two crucial phases: 1) thoroughly documenting specimens destined for destructive sampling—a process called electronic vouchering, and 2) the pipeline used for whole genome sequencing of archived specimens, from extraction of genomic DNA to assembly of putative genomes with basic annotation. The process is presented for eleven specimens from two different insect subfamilies of medical importance to humans: Anophelinae (Diptera: Culicidae)—mosquitoes and Triatominae (Hemiptera: Reduviidae)—kissing bugs. Assembly of whole mitochondrial genome sequences of all 11 specimens along with the results of an ortholog search and BLAST against the NCBI nucleotide database are also presented.}, number={2}, journal={PLOS ONE}, author={Justi, Silvia Andrade and Soghigian, John and Pecor, David B. and Caicedo-Quiroga, Laura and Rutvisuttinunt, Wiriya and Li, Tao and Stevens, Lori and Dorn, Patricia L. and Wiegmann, Brian and Linton, Yvonne-Marie}, year={2021}, month={Feb} }
 @article{norrbom_muller_gangadin_sutton_rodriguez_savaris_lampert_rodriguez clavijo_steck_moore_et al._2021, title={New species and host plants of Anastrepha (Diptera: Tephritidae) primarily from Suriname and Para, Brazil}, volume={5044}, ISSN={["1175-5334"]}, DOI={10.11646/zootaxa.5044.1.1}, abstractNote={Seventeen new species of Anastrepha, primarily from Suriname, French Guiana and Par, Brazil, are described and illustrated: A. aithogaster Norrbom from Brazil (Par), 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 Martn), and Suriname; A. fuscoalata Norrbom from Brazil (Par), French Guiana, and Suriname; A. gangadini Norrbom from Suriname; A. juxtalanceola Norrbom from Brazil (Par) and Suriname; A. microstrepha Norrbom from Brazil (Bahia) and Suriname; A. mitaraka Norrbom from French Guiana; A. neptis Norrbom from Brazil (Par), Ecuador (Orellana), Peru (Loreto) and Suriname; A. sobrina Norrbom from Brazil (Par), French Guiana, and Suriname; A. surinamensis Norrbom from Suriname; A. tenebrosa Norrbom from Brazil (Par) 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).}, number={1}, journal={ZOOTAXA}, author={Norrbom, Allen L. and Muller, Alies and Gangadin, Anielkoemar and Sutton, Bruce D. and Rodriguez, Erick J. and Savaris, Marcoandre and Lampert, Silvana and Rodriguez Clavijo, Pedro A. and Steck, Gary J. and Moore, Matthew R. and et al.}, year={2021}, month={Sep}, pages={1–74} }
 @article{li_teasdale_bayless_ellis_wiegmann_lamas_lambkin_evenhuis_nicholls_hartley_et al._2021, title={Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)}, volume={37}, ISSN={["1096-0031"]}, DOI={10.1111/cla.12436}, abstractNote={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.}, number={3}, journal={CLADISTICS}, author={Li, Xuankun and Teasdale, Luisa C. and Bayless, Keith M. and Ellis, Allan G. and Wiegmann, Brian M. and Lamas, Carlos Jose E. and Lambkin, Christine L. and Evenhuis, Neal L. and Nicholls, James A. and Hartley, Diana and et al.}, year={2021}, month={Jun}, pages={276–297} }
 @article{grzywacz_trzeciak_wiegmann_cassel_pape_walczak_bystrowski_nelson_piwczynski_2021, title={Towards a new classification of Muscidae (Diptera): a comparison of hypotheses based on multiple molecular phylogenetic approaches}, volume={46}, ISSN={["1365-3113"]}, DOI={10.1111/syen.12473}, abstractNote={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.}, number={3}, journal={SYSTEMATIC ENTOMOLOGY}, author={Grzywacz, Andrzej and Trzeciak, Paulina and Wiegmann, Brian M. and Cassel, Brian K. and Pape, Thomas and Walczak, Kinga and Bystrowski, Cezary and Nelson, Leanne and Piwczynski, Marcin}, year={2021}, month={Jul}, pages={508–525} }
 @article{buenaventura_szpila_cassel_wiegmann_pape_2020, title={Anchored hybrid enrichment challenges the traditional classification of flesh flies (Diptera: Sarcophagidae)}, volume={45}, ISSN={["1365-3113"]}, DOI={10.1111/syen.12395}, abstractNote={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.}, number={2}, journal={SYSTEMATIC ENTOMOLOGY}, author={Buenaventura, Eliana and Szpila, Krzysztof and Cassel, Brian K. and Wiegmann, Brian M. and Pape, Thomas}, year={2020}, month={Apr}, pages={281–301} }
 @article{seger_drummond_delgado_day_sither_soghigian_wiegmann_reiskind_ellis_byrd_2019, title={FIRST RECORD OF MANSONIA DYARI FROM SAINT CROIX, UNITED STATES VIRGIN ISLANDS}, volume={35}, ISSN={["1943-6270"]}, DOI={10.2987/19-6859.1}, abstractNote={ABSTRACT The first report of Mansonia dyari on Saint Croix, United States Virgin Islands (USVI), is confirmed. Adult and larval specimens were collected in 2018 and 2019 through adult surveillance and larval collections. Specimens were identified by microscopic methods, and a representative specimen was confirmed by DNA sequencing (mitochondrial cytochrome c oxidase subunit I). Morphological features are reviewed and compared with Mansonia flaveola, a species previously reported in the USVI. Notes are provided on the locations, collection methods, and mosquito associates found with Ma. dyari in the USVI.}, number={3}, journal={JOURNAL OF THE AMERICAN MOSQUITO CONTROL ASSOCIATION}, author={Seger, Krystal R. and Drummond, Aubrey, II and Delgado, David and Day, Corey A. and Sither, Charles B. and Soghigian, John and Wiegmann, Brian M. and Reiskind, Michael H. and Ellis, Brett R. and Byrd, Brian D.}, year={2019}, month={Sep}, pages={214–216} }
 @article{kutty_meusemann_bayless_marinho_pont_zhou_misof_wiegmann_yeates_cerretti_et al._2019, title={Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera}, volume={35}, ISSN={["1096-0031"]}, DOI={10.1111/cla.12375}, abstractNote={The Calyptratae, one of the most species-rich fly clades, only originated and diversified after the Cretaceous–Palaeogene extinction event and yet exhibit high species diversity and a diverse array of life history strategies including predation, phytophagy, saprophagy, haematophagy and parasitism. We present the first phylogenomic analysis of calyptrate relationships. The analysis is based on 40 species representing all calyptrate families and on nucleotide and amino acid data for 1456 single-copy protein-coding genes obtained from shotgun sequencing of transcriptomes. Topologies are overall well resolved, robust and largely congruent across trees obtained with different approaches (maximum parsimony, maximum likelihood, coalescent-based species tree, four-cluster likelihood mapping). Many nodes have 100% bootstrap and jackknife support, but the true support varies by more than one order of magnitude [Bremer support from 3 to 3427; random addition concatenation analysis (RADICAL) gene concatenation size from 10 to 1456]. Analyses of a Dayhoff-6 recoded amino acid dataset also support the robustness of many clades. The backbone topology Hippoboscoidea+(Fanniidae+(Muscidae+((Anthomyiidae–Scathophagidae)+Oestroidea))) is strongly supported and most families are monophyletic (exceptions: Anthomyiidae and Calliphoridae). The monotypic Ulurumyiidae is either alone or together with Mesembrinellidae as the sister group to the rest of Oestroidea. The Sarcophagidae are sister to Mystacinobiidae+Oestridae. Polleniinae emerge as sister group to Tachinidae and the monophyly of the clade Calliphorinae+Luciliinae is well supported, but the phylogenomic data cannot confidently place the remaining blowfly subfamilies (Helicoboscinae, Ameniinae, Chrysomyinae). Compared to hypotheses from the Sanger sequencing era, many clades within the muscoid grade are congruent but now have much higher support. Within much of Oestroidea, Sanger era and phylogenomic data struggle equally with regard to finding well-supported hypotheses.}, number={6}, journal={CLADISTICS}, author={Kutty, Sujatha Narayanan and Meusemann, Karen and Bayless, Keith M. and Marinho, Marco A. T. and Pont, Adrian C. and Zhou, Xin and Misof, Bernhard and Wiegmann, Brian M. and Yeates, David and Cerretti, Pierfilippo and et al.}, year={2019}, month={Dec}, pages={605–622} }
 @article{adedipe_grubbs_coates_wiegmman_lorenzen_2019, title={Structural and functional insights into the Diabrotica virgifera virgifera ATP-binding cassette transporter gene family}, volume={20}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-019-6218-8}, DOI={10.1186/s12864-019-6218-8}, abstractNote={Abstract Background The western corn rootworm, Diabrotica virgifera virgifera , is a pervasive pest of maize in North America and Europe, which has adapted to current pest management strategies. In advance of an assembled and annotated D. v. virgifera genome, we developed transcriptomic resources to use in identifying candidate genes likely to be involved in the evolution of resistance, starting with members of the ATP-binding cassette (ABC) transporter family. Results In this study, 65 putative D. v. virgifera ABC ( Dvv ABC) transporters were identified within a combined transcriptome assembly generated from embryonic, larval, adult male, and adult female RNA-sequence libraries. Phylogenetic analysis placed the deduced amino-acid sequences of the Dvv ABC transporters into eight subfamilies (A to H). To supplement our sequence data with functional analysis, we identified orthologs of Tribolium castaneum ABC genes which had previously been shown to exhibit overt RNA interference (RNAi) phenotypes. We identified eight such D. v. virgifera genes, and found that they were functionally similar to their T. castaneum counterparts. Interestingly, depletion of DvvABCB_39715 and DvvABCG_3712 transcripts in adult females produced detrimental reproductive and developmental phenotypes, demonstrating the potential of these genes as targets for RNAi-mediated insect control tactics. Conclusions By combining sequence data from four libraries covering three distinct life stages, we have produced a relatively comprehensive de novo transcriptome assembly for D. v. virgifera . Moreover, we have identified 65 members of the ABC transporter family and provided the first insights into the developmental and physiological roles of ABC transporters in this pest species.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Adedipe, Folukemi and Grubbs, Nathaniel and Coates, Brad and Wiegmman, Brian and Lorenzen, Marcé}, year={2019}, month={Nov} }
 @article{gillung_winterton_bayless_khouri_borowiec_yeates_kimsey_misof_shing_zhou_et al._2018, title={Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids}, volume={128}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2018.08.007}, abstractNote={The onset of phylogenomics has contributed to the resolution of numerous challenging evolutionary questions while offering new perspectives regarding biodiversity. However, in some instances, analyses of large genomic datasets can also result in conflicting estimates of phylogeny. Here, we present the first phylogenomic scale study of a dipteran parasitoid family, built upon anchored hybrid enrichment and transcriptomic data of 240 loci of 43 ingroup acrocerid taxa. A new hypothesis for the timing of spider fly evolution is proposed, wielding recent advances in divergence time dating, including the fossilized birth-death process to show that the origin of Acroceridae is younger than previously proposed. To test the robustness of our phylogenetic inferences, we analyzed our datasets using different phylogenetic estimation criteria, including supermatrix and coalescent-based approaches, maximum-likelihood and Bayesian methods, combined with other approaches such as permutations of the data, homogeneous versus heterogeneous models, and alternative data and taxon sets. Resulting topologies based on amino acids and nucleotides are both strongly supported but critically discordant, primarily in terms of the monophyly of Panopinae. Conflict was not resolved by controlling for compositional heterogeneity and saturation in third codon positions, which highlights the need for a better understanding of how different biases affect different data sources. In our study, results based on nucleotides were both more robust to alterations of the data and different analytical methods and more compatible with our current understanding of acrocerid morphology and patterns of host usage.}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Gillung, Jessica P. and Winterton, Shaun L. and Bayless, Keith M. and Khouri, Ziad and Borowiec, Marek L. and Yeates, David and Kimsey, Lynn S. and Misof, Bernhard and Shing, Seunggwan and Zhou, Xin and et al.}, year={2018}, month={Nov}, pages={233–245} }
 @misc{wiegmann_richards_2018, title={Genomes of Diptera}, volume={25}, ISSN={["2214-5753"]}, DOI={10.1016/j.cois.2018.01.007}, abstractNote={Diptera (true flies) are among the most diverse holometabolan insect orders and were the first eukaryotic order to have a representative genome fully sequenced. 110 fly species have publically available genome assemblies and many hundreds of population-level genomes have been generated in the model organisms Drosophila melanogaster and the malaria mosquito Anopheles gambiae. Comparative genomics carried out in a phylogenetic context is illuminating many aspects of fly biology, providing unprecedented insight into variability in genome structure, gene content, genetic mechanisms, and rates and patterns of evolution in genes, populations, and species. Despite the rich availability of genomic resources in flies, there remain many fly lineages to which new genome sequencing efforts should be directed. Such efforts would be most valuable in fly families or clades that exhibit multiple origins of key fly behaviors such as blood feeding, phytophagy, parasitism, pollination, and mycophagy.}, journal={CURRENT OPINION IN INSECT SCIENCE}, author={Wiegmann, Brian M. and Richards, Stephen}, year={2018}, month={Feb}, pages={116–124} }
 @article{shin_bayless_winterton_dikow_lessard_yeates_wiegmann_trautwein_2018, title={Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)}, volume={43}, ISSN={["1365-3113"]}, DOI={10.1111/syen.12275}, number={2}, journal={SYSTEMATIC ENTOMOLOGY}, author={Shin, Seunggwan and Bayless, Keith M. and Winterton, Shaun L. and Dikow, Torsten and Lessard, Bryan D. and Yeates, David K. and Wiegmann, Brian M. and Trautwein, Michelle D.}, year={2018}, month={Apr}, pages={277–289} }
 @article{kjer_borowiec_frandsen_ware_wiegmann_2016, title={Advances using molecular data in insect systematics}, volume={18}, ISSN={["2214-5753"]}, DOI={10.1016/j.cois.2016.09.006}, abstractNote={The size of molecular datasets has been growing exponentially since the mid 1980s, and new technologies have now dramatically increased the slope of this increase. New datasets include genomes, transcriptomes, and hybrid capture data, producing hundreds or thousands of loci. With these datasets, we are approaching a consensus on the higher level insect phylogeny. Huge datasets can produce new challenges in interpreting branch support, and new opportunities in developing better models and more sophisticated partitioning schemes. Dating analyses are improving as we recognize the importance of careful fossil calibration selection. With thousands of genes now available, coalescent methods have come of age. Barcode libraries continue to expand, and new methods are being developed for incorporating them into phylogenies with tens of thousands of individuals.}, journal={CURRENT OPINION IN INSECT SCIENCE}, author={Kjer, Karl and Borowiec, Marek L. and Frandsen, Paul B. and Ware, Jessica and Wiegmann, Brian M.}, year={2016}, month={Dec}, pages={40–47} }
 @article{young_lemmon_skevington_mengual_stahls_reemer_jordaens_kelso_lemmon_hauser_et al._2016, title={Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)}, volume={16}, ISSN={["1471-2148"]}, DOI={10.1186/s12862-016-0714-0}, abstractNote={Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.}, journal={BMC EVOLUTIONARY BIOLOGY}, author={Young, Andrew Donovan and Lemmon, Alan R. and Skevington, Jeffrey H. and Mengual, Ximo and Stahls, Gunilla and Reemer, Menno and Jordaens, Kurt and Kelso, Scott and Lemmon, Emily Moriarty and Hauser, Martin and et al.}, year={2016}, month={Jun} }
 @article{courtney_wiegmann_2016, title={Editorial overview: Insect phylogenetics: an expanding toolbox to resolve evolutionary questions}, volume={18}, ISSN={2214-5745}, url={http://dx.doi.org/10.1016/J.COIS.2016.11.001}, DOI={10.1016/J.COIS.2016.11.001}, journal={Current Opinion in Insect Science}, publisher={Elsevier BV}, author={Courtney, Gregory W and Wiegmann, Brian M}, year={2016}, month={Dec}, pages={93–95} }
 @article{schreeg_marr_tarigo_cohn_bird_scholl_levy_wiegmann_birkenheuer_2016, title={Mitochondrial Genome Sequences and Structures Aid in the Resolution of Piroplasmida phylogeny}, volume={11}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84994744879&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0165702}, abstractNote={The taxonomy of the order Piroplasmida, which includes a number of clinically and economically relevant organisms, is a hotly debated topic amongst parasitologists. Three genera (Babesia, Theileria, and Cytauxzoon) are recognized based on parasite life cycle characteristics, but molecular phylogenetic analyses of 18S sequences have suggested the presence of five or more distinct Piroplasmida lineages. Despite these important advancements, a few studies have been unable to define the taxonomic relationships of some organisms (e.g. C. felis and T. equi) with respect to other Piroplasmida. Additional evidence from mitochondrial genome sequences and synteny should aid in the inference of Piroplasmida phylogeny and resolution of taxonomic uncertainties. In this study, we have amplified, sequenced, and annotated seven previously uncharacterized mitochondrial genomes (Babesia canis, Babesia vogeli, Babesia rossi, Babesia sp. Coco, Babesia conradae, Babesia microti-like sp., and Cytauxzoon felis) and identified additional ribosomal fragments in ten previously characterized mitochondrial genomes. Phylogenetic analysis of concatenated mitochondrial and 18S sequences as well as cox1 amino acid sequence identified five distinct Piroplasmida groups, each of which possesses a unique mitochondrial genome structure. Specifically, our results confirm the existence of four previously identified clades (B. microti group, Babesia sensu stricto, Theileria equi, and a Babesia sensu latu group that includes B. conradae) while supporting the integration of Theileria and Cytauxzoon species into a single fifth taxon. Although known biological characteristics of Piroplasmida corroborate the proposed phylogeny, more investigation into parasite life cycles is warranted to further understand the evolution of the Piroplasmida. Our results provide an evolutionary framework for comparative biology of these important animal and human pathogens and help focus renewed efforts toward understanding the phylogenetic relationships within the group.}, number={11}, journal={PLOS ONE}, author={Schreeg, Megan E. and Marr, Henry S. and Tarigo, Jaime L. and Cohn, Leah A. and Bird, David M. and Scholl, Elizabeth H. and Levy, Michael G. and Wiegmann, Brian M. and Birkenheuer, Adam J.}, year={2016}, month={Nov} }
 @article{morita_bayless_yeates_wiegmann_2016, title={Molecular phylogeny of the horse flies: a framework for renewing tabanid taxonomy}, volume={41}, ISSN={["1365-3113"]}, DOI={10.1111/syen.12145}, abstractNote={Horse flies, family Tabanidae, are the most diverse family-level clade of bloodsucking insects, but their phylogeny has never been thoroughly explored using molecular data. Most adult female Tabanidae feed on nectar and on the blood of various mammals. Traditional horse fly classification tends towards large heterogeneous taxa, which impede much-needed taxonomic work. To guide renewed efforts in the systematics of horse flies and their relatives, we assembled a dataset of 110 exemplar species using nucleotide data from four genes—mitochondrial CO1, and nuclear 28S, CAD and AATS. All commonly recognized tribes in Tabanidae are represented, along with outgroups in Tabanomorpha. The phylogeny is reconstructed using Bayesian inference, and divergence times are estimated using Bayesian relaxed clock methods with time constraints from tabanid fossils. Our results show Athericidae strongly supported as the lineage most closely related to Tabanidae, and Pangoniinae and Tabaninae as monophyletic lineages. However, Chrysopsinae is nonmonophyletic, with strong support for both a nonmonophyletic Bouvieromyiini and for Rhinomyzini as sister to Tabaninae. Only the tribes Philolichini, Chrysopsini, Rhinomyzini and Haematopotini are recovered as monophyletic, although Scionini is monophyletic with exclusion of the peculiar genus Goniops Aldrich. Mycteromyia Philippi and Adersia Austen, two enigmatic genera sometimes placed in separate family-level groups, are recovered inside Pangoniini and Chrysopsini, respectively. Several species-rich genera are not recovered as monophyletic, including Esenbeckia Rondani, Silvius Meigen, Dasybasis Macquart and Tabanus L. Tabanidae likely originated in the Cretaceous, and all major extant groups were present by the early Palaeogene. This newly revised phylogenetic framework for Tabanidae forms the basis for a new assessment of tabanid diversification and provides context for understanding the evolution of trophic specialization in horse flies.}, number={1}, journal={SYSTEMATIC ENTOMOLOGY}, author={Morita, Shelah I. and Bayless, Keith M. and Yeates, David K. and Wiegmann, Brian M.}, year={2016}, month={Jan}, pages={56–72} }
 @article{yeates_meusemann_trautwein_wiegmann_zwick_2016, title={Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution}, volume={13}, ISSN={["2214-5753"]}, DOI={10.1016/j.cois.2015.10.007}, abstractNote={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.}, journal={CURRENT OPINION IN INSECT SCIENCE}, author={Yeates, David K. and Meusemann, Karen and Trautwein, Michelle and Wiegmann, Brian and Zwick, Andreas}, year={2016}, month={Feb}, pages={16–23} }
 @article{winterton_hardy_gaimari_hauser_hill_holston_irwin_lambkin_metz_turco_et al._2016, title={The phylogeny of stiletto flies (Diptera: Therevidae)}, volume={41}, ISSN={["1365-3113"]}, DOI={10.1111/syen.12147}, abstractNote={The therevoid clade represents a group of four families (Apsilocephalidae, Evocoidae, Scenopinidae and Therevidae) of lower brachyceran Diptera in the superfamily Asiloidea. The largest of these families is that of the stiletto flies (Therevidae). A large-scale (i.e. supermatrix) phylogeny of Therevidae is presented based on DNA sequence data from seven genetic loci (16S, 18S and 28S ribosomal DNA and four protein-encoding genes: elongation factor 1-alpha, triose phosphate isomerase, short-wavelength rhodopsin and the CPSase region of carbamoyl-phosphate synthase-aspartate transcarbamoylase-dihydroorotase). Results are presented from Bayesian phylogenetic analyses of approximately 8.7 kb of sequence data for 204 taxa representing all subfamilies and genus groups of Therevidae. Our results strongly support the sister-group relationship between Therevidae and Scenopinidae, with Apsilocephalidae as sister to Evocoidae. Previous estimates of stiletto fly phylogeny based on morphology or DNA sequence data, or supertree analysis, have failed to find significant support for relationships among subfamilies. We report for the first time strong support for the placement of the subfamily Phycinae as sister to the remaining Therevidae, originating during the Mid Cretaceous. As in previous studies, the sister-group relationship between the species-rich subfamilies Agapophytinae and Therevinae is strongly supported. Agapophytinae are recovered as monophyletic, inclusive of the Taenogera group. Therevinae comprise the bulk of the species richness in the family and appear to be a relatively recent and rapid radiation originating in the southern hemisphere (Australia + Antarctica + South America) during the Late Cretaceous. Genus groups are defined for all subfamilies based on these results.}, number={1}, journal={SYSTEMATIC ENTOMOLOGY}, author={Winterton, Shaun L. and Hardy, Nate B. and Gaimari, Stephen D. and Hauser, Martin and Hill, Hilary N. and Holston, Kevin C. and Irwin, Michael E. and Lambkin, Christine L. and Metz, Mark A. and Turco, Federica and et al.}, year={2016}, month={Jan}, pages={144–161} }
 @article{watts_winkler_daugeron_carvalho_turner_wiegmann_2016, title={Where do the Neotropical Empidini lineages (Diptera: Empididae: Empidinae) fit in a worldwide context?}, volume={95}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2015.10.019}, abstractNote={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.}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Watts, Mirian and Winkler, Isaac S. and Daugeron, Christophe and Carvalho, Claudio J. B. and Turner, Steven P. and Wiegmann, Brian M.}, year={2016}, month={Feb}, pages={67–78} }
 @article{kjer_ware_rust_wappler_lanfear_jermiin_zhou_aspock_aspock_beutel_et al._2015, title={Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution"}, volume={349}, number={6247}, journal={Science}, author={Kjer, K. M. and Ware, J. L. and Rust, J. and Wappler, T. and Lanfear, R. and Jermiin, L. S. and Zhou, X. and Aspock, H. and Aspock, U. and Beutel, R. G. and et al.}, year={2015} }
 @article{haseyama_wiegmann_almeida_carvalho_2015, title={Say goodbye to tribes in the new house fly classification: A new molecular phylogenetic analysis and an updated biogeographical narrative for the Muscidae (Diptera)}, volume={89}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2015.04.006}, abstractNote={House flies are one of the best known groups of flies and comprise about 5000 species worldwide. Despite over a century of intensive taxonomic research on these flies, classification of the Muscidae is still poorly resolved. Here we brought together the most diverse molecular dataset ever examined for the Muscidae, with 142 species in 67 genera representing all tribes and all biogeographic regions. Four protein coding genes were analyzed: mitochondrial CO1 and nuclear AATS, CAD (region 4) and EF1-α. Maximum likelihood and Bayesian approaches were used to analyze five different partitioning schemes for the alignment. We also used Bayes factors to test monophyly of the traditionally accepted tribes and subfamilies. Most subfamilial taxa were not recovered in our analyses, and accordingly monophyly was rejected by Bayes factor tests. Our analysis consistently found three main clades of Muscidae and so we propose a new classification with only three subfamilies without tribes. Additionally, we provide the first timeframe for the diversification of all major lineages of house flies and examine contemporary biogeographic hypotheses in light of this timeframe. We conclude that the muscid radiation began in the Paleocene to Eocene and is congruent with the final stages of the breakup of Gondwana, which resulted in the complete separation of Antarctica, Australia, and South America. With this newly proposed classification and better understanding of the timing of evolutionary events, we provide new perspectives for integrating morphological and ecological evolutionary understanding of house flies, their taxonomy, phylogeny, and biogeography.}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Haseyama, Kirstern L. F. and Wiegmann, Brian M. and Almeida, Eduardo A. B. and Carvalho, Claudio J. B.}, year={2015}, month={Aug}, pages={1–12} }
 @article{tothova_rozkosny_knutson_kutty_wiegmann_meier_2013, title={A phylogenetic analysis of Sciomyzidae (Diptera) and some related genera}, volume={29}, ISSN={["1096-0031"]}, DOI={10.1111/cla.12002}, abstractNote={Sciomyzidae is a family of acalyptrate flies with 546 species in 61 genera that is among the most extensively studied groups of higher Diptera. Most of the known larvae are obligate enemies of Gastropoda. Hundreds of studies published over the past 50 years have resulted in detailed information concerning morphology of adults and immature stages, biology, development, behaviour, phenology and distribution. However, studies of phylogenetic relationships are based almost exclusively on morphological characters of adults, and no comprehensive molecular analysis across the family has been published. Here we fill this void by generating and analysing molecular data for 54 species of Sciomyzidae (22 genera), including Phaeomyiidae (one genus), and seven representative species of five other families of Sciomyzoidea (Coelopidae, Dryomyzidae, Helcomyzidae, Heteromyzidae and Huttoninidae) as outgroups. The reconstruction is based on morphological characters as well as nucleotide sequences for genes from the mitochondrial (12S, 16S, COI, COII, Cytb) and nuclear genome (28S, EF1α). The results are compared with recent morphological analyses. Our analyses support the monophyly of Sciomyzidae + Phaeomyiidae, and place Phaeomyiinae as a unique lineage within Sciomyzidae. A modified classification comprising three subfamilies is proposed. The major subfamily, Sciomyzinae, consists of two monophyletic and well separated groups, the tribes Sciomyzini and Tetanocerini.}, number={4}, journal={CLADISTICS}, author={Tothova, Andrea and Rozkosny, Rudolf and Knutson, Lloyd and Kutty, Sujatha Narayanan and Wiegmann, Brian M. and Meier, Rudolf}, year={2013}, month={Aug}, pages={404–415} }
 @article{kirk-spriggs_wiegmann_2013, title={A revision of Afrotropical Quasimodo flies (Diptera: Schizophora; Curtonotidae). Part IV-the continental Afrotropical species of Curtonotum Macquart, with descriptions of thirteen new species and a combined phylogenetic analysis of the Curtonotidae}, volume={3684}, DOI={10.11646/zootaxa.3684.1.1}, abstractNote={A first comprehensive phylogeny of the entire family Curtonotidae is generated from molecular markers and morphology. The molecular data set comprises 33 taxa (30 in-group Curtonotidae; three out-groups: Camilla, Diastata, Drosophila) and 4 gene regions from 3 genes: 2 non-contiguous fragments from the CPSase (carbamoylphosphate synthetase) domain of the nuclear protein coding gene CAD (= CAD1 and CAD3); a fragment from the coding region of TPI (triosephosophate isomerase); and a fragment of the mitochondrial gene CO1 (cytochrome oxidase 1). We performed Bayesian like-lihood analyses in the program MrBayes 3.2; maximum likelihood analyses in the program Garli 2.0; and parsimony analysis in TNT on the concatenated genetic dataset. A data matrix of 62 discrete, morphological features of imagines was compiled from 75 taxa (70 in-group Curtonotidae taxa and five out-group exemplars: Amiota, Camilla, Diastata, Drosophila, Stegana), and these data are presented as Appendix II. For the combined morphological and molecular data a Bayes-ian likelihood analysis in the program MrBayes 3.2 and a parsimony analysis in TNT were performed, and for the morphological dataset a parsimony analysis was carried out in TNT. Results of the molecular and morphological analyses attest to the monophyly of the Curtonotidae and clearly indicate two primary clades, with Axinota + Curtonotum being sister to the remainder of the Curtonotidae. Curtonotum sensu stricto (sensu Klymko and Marshall 2011) is here adopted and ten newly-defined species-groups of the genus Curtonotum are recognised the: anus; boeny; campsiphallum; gonzo; platyphallum; rinhatinana; saheliense; striatifrons; stuckenbergi; and uncinatum species-groups. The following nomenclatorial changes are proposed: Cyrtona appendiculata Séguy, 1938 is formally reinstated as a valid species and is re-moved as a junior synonym of Cyrtona pictipennis (Thomson, 1869). The former variety name sublineata (Duda, 1939) is upgraded to a specific name, as Parapsinota sublineata (Duda, 1939). The continental Afrotropical fauna of the genus Curtonotum Macquart, 1844 is revised and a diagnosis of the genus is provided. Known biology, behaviour and published information on immature stages of the genus are briefly reviewed. Type material of 12 of the 13 named species (C. angolense Tsacas, C. campsiphallum Tsacas, C. cuthbertsoni Duda, C. herrero Tsacas, C. pauliani Tsacas, C. platyphallum Tsacas, C. quinquevittatum Curran, C. saheliense Tsacas, C. sao Tsacas, C. simile Tsacas, C. striatifrons Malloch and C. tigrinum Séguy), was studied and errors in previous interpretations and designation of type specimens are resolved. Curtonotum pauliani is the only species occurring on both the continental African mainland and Madagascar. The type spec-imen of C. maculiventris (Enderlein) is lost and a neotype is here designated. One species synonymy is proposed: C. tigrinum Séguy, 1933 = C. maculiventris (Enderlein, 1917), syn. n. Additional material of the aforementioned species is noted, substantially increasing their known distributions. Thirteen species are described as new, namely: C. bicuspis Kirk- Spriggs, sp. n., C. cimbebas Kirk-Spriggs, sp. n., C. constance Kirk-Spriggs, sp. n., C. freidberg Kirk-Spriggs, sp. n., C. gonzo Kirk-Spriggs, sp. n., C. hay Kirk-Spriggs, sp. n., C. litoralis Kirk-Spriggs, sp. n., C. marriott Kirk-Spriggs, sp. n., C. mcgregor Kirk-Spriggs, sp. n., C. moffatt Kirk-Spriggs, sp. n., C. tsacas Kirk-Spriggs, sp. n., C. uncinatum Kirk- Spriggs, sp. n. and C. unicuspis Kirk-Spriggs, sp. n. The head and thorax, frons, wing, fifth sternite and hypandrium of the male of the 25 named species are illustrated for the first time, as well as the highly diagnostic male phallus, from both the right and left sides laterally. A key to species based on male characters is provided, and species distributions are mapped and interpreted according to major vegetation types, topography and humidity zones. The biogeographical signif-icance of the continental Afrotropical species is discussed. Co-ordinates used to plot maps and a list of Major Habitat Types and Vegetation Types in which species occur are provided as Appendix III.}, number={1}, journal={Zootaxa}, author={Kirk-Spriggs, A. H. and Wiegmann, Brian M}, year={2013}, pages={1-} }
 @article{wiegmann_2013, title={Flies: The Natural History and Diversity of Diptera. By Stephen A. Marshall. Buffalo (New York): Firefly Books. $125.00. 616 p.; ill.; index. ISBN: 978-1-77085-100-9. 2012.}, volume={88}, ISSN={0033-5770 1539-7718}, url={http://dx.doi.org/10.1086/673828}, DOI={10.1086/673828}, abstractNote={Previous articleNext article No AccessReviews and Brief NoticesFlies: The Natural History and Diversity of Diptera. By Stephen A. Marshall. Buffalo (New York): Firefly Books. $125.00. 616 p.; ill.; index. ISBN: 978-1-77085-100-9. 2012.Brian M. WiegmannBrian M. WiegmannEntomology, North Carolina State University, Raleigh, North Carolina Search for more articles by this author PDFPDF PLUSFull Text Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by The Quarterly Review of Biology Volume 88, Number 4December 2013 Published in association with Stony Brook University Article DOIhttps://doi.org/10.1086/673828 Views: 38Total views on this site Copyright © 2013 by The University of Chicago Press. All rights reserved.PDF download Crossref reports no articles citing this article.}, number={4}, journal={The Quarterly Review of Biology}, publisher={University of Chicago Press}, author={Wiegmann, Brian M.}, year={2013}, month={Dec}, pages={359–359} }
 @article{lessard_cameron_bayless_wiegmann_yeates_2013, title={The evolution and biogeography of the austral horse fly tribe Scionini (Diptera: Tabanidae: Pangoniinae) inferred from multiple mitochondrial and nuclear genes}, volume={68}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2013.04.030}, abstractNote={Phylogenetic relationships within the Tabanidae are largely unknown, despite their considerable medical and ecological importance. The first robust phylogenetic hypothesis for the horse fly tribe Scionini is provided, completing the systematic placement of all tribes in the subfamily Pangoniinae. The Scionini consists of seven mostly southern hemisphere genera distributed in Australia, New Guinea, New Zealand and South America. A 5757 bp alignment of 6 genes, including mitochondrial (COI and COII), ribosomal (28S) and nuclear (AATS and CAD regions 1, 3 and 4) genes, was analysed for 176 taxa using both Bayesian and maximum likelihood approaches. Results indicate the Scionini are strongly monophyletic, with the exclusion of the only northern hemisphere genus Goniops. The South American genera Fidena, Pityocera and Scione were strongly monophyletic, corresponding to current morphology-based classification schemes. The most widespread genus Scaptia was paraphyletic and formed nine strongly supported monophyletic clades, each corresponding to either the current subgenera or several previously synonymised genera that should be formally resurrected. Molecular results also reveal a newly recognised genus endemic to New Zealand, formerly placed within Scaptia. Divergence time estimation was employed to assess the global biogeographical patterns in the Pangoniinae. These analyses demonstrated that the Scionini are a typical Gondwanan group whose diversification was influenced by the fragmentation of that ancient land mass. Furthermore, results indicate that the Scionini most likely originated in Australia and subsequently radiated to New Zealand and South American by both long distance dispersal and vicariance. The phylogenetic framework of the Scionini provided herein will be valuable for taxonomic revisions of the Tabanidae.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Lessard, B. D. and Cameron, S. L. and Bayless, K. M. and Wiegmann, B. M. and Yeates, D. K.}, year={2013}, month={Sep}, pages={516–540} }
 @misc{lambkin_sinclair_pape_courtney_skevington_meier_yeates_blagoderov_wiegmann_2013, title={The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence}, volume={38}, ISSN={["1365-3113"]}, DOI={10.1111/j.1365-3113.2012.00652.x}, abstractNote={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.}, number={1}, journal={SYSTEMATIC ENTOMOLOGY}, author={Lambkin, Christine L. and Sinclair, Bradley J. and Pape, Thomas and Courtney, Greg W. and Skevington, Jeffrey H. and Meier, Rudolf and Yeates, David K. and Blagoderov, Vladimir and Wiegmann, Brian M.}, year={2013}, month={Jan}, pages={164–179} }
 @article{trautwein_wiegmann_beutel_kjer_yeates_2012, title={Advances in Insect Phylogeny at the Dawn of the Postgenomic Era}, volume={57}, ISSN={["1545-4487"]}, DOI={10.1146/annurev-ento-120710-100538}, abstractNote={Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).}, journal={ANNUAL REVIEW OF ENTOMOLOGY, VOL 57}, author={Trautwein, Michelle D. and Wiegmann, Brian M. and Beutel, Rolf and Kjer, Karl M. and Yeates, David K.}, year={2012}, pages={449-+} }
 @article{yeates_wiegmann_2012, title={The impact of the Manual of Nearctic Diptera on phylogenetic dipterology}, volume={144}, ISSN={["1918-3240"]}, DOI={10.4039/tce.2012.22}, abstractNote={Abstract Our knowledge of the phylogenetic relationships of Diptera advanced through the 20th century at an unprecedented rate; the two crowning achievements of the century were Hennig's magnum opus – the Handbuch der Zoologie treatment of the order and Volume 3 of the Manual of Nearctic Diptera series, edited by McAlpine and Wood. The Manual is outstanding because of its scope and rigorous, consistent approach, treating the relationships of the entire order at family level using Hennigian argumentation. Synapomorphic characters from all life stages were identified using outgroup comparison and monophyletic taxa were established using synapomorphies mapped onto nodes. The Manual chapters energized a generation of students to publish rigorous, quantitative cladistic phylogenetic treatments of many dipteran groups. The chapters also acted as an authoritative scaffold for the development of dipteran molecular systematics in the 1990s. No other megadiverse insect order has had such an influential phylogenetic springboard into the 21st century.}, number={2}, journal={CANADIAN ENTOMOLOGIST}, author={Yeates, David K. and Wiegmann, Brian M.}, year={2012}, month={Apr}, pages={197–205} }
 @article{wiegmann_trautwein_winkler_barr_kim_lambkin_bertone_cassel_bayless_heimberg_et al._2011, title={Episodic radiations in the fly tree of life}, volume={108}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1012675108}, DOI={10.1073/pnas.1012675108}, abstractNote={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.}, number={14}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Wiegmann, B. M. and Trautwein, M. D. and Winkler, I. S. and Barr, N. B. and Kim, J.-W. and Lambkin, C. and Bertone, M. A. and Cassel, B. K. and Bayless, K. M. and Heimberg, A. M. and et al.}, year={2011}, month={Mar}, pages={5690–5695} }
 @article{wiegmann_trautwein_winkler_barr_kim_lambkin_bertone_cassel_bayless_heimberg_et al._2011, title={Episodic radiations in the fly tree of life}, volume={108}, number={14}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Wiegmann, B. M. and Trautwein, M. D. and Winkler, I. S. and Barr, N. B. and Kim, J. W. and Lambkin, C. and Bertone, M. A. and Cassel, B. K. and Bayless, K. M. and Heimberg, A. M. and et al.}, year={2011}, pages={5690–5695} }
 @article{copeland_kirk-spriggs_muteti_booth_wiegmann_2011, title={Rediscovery of the "terrible hairy fly", Mormotomyia hirsuta Austen (Diptera: Mormotomyiidae), in eastern Kenya, with notes on biology, natural history, and genetic variation of the Ukasi Hill population}, volume={52}, ISSN={["2305-2562"]}, DOI={10.5733/afin.052.0211}, abstractNote={ABSTRACT Sixty-two years since last observed alive, Mormotomyia hirsuta Austen, the “terrible hairy fly”, was found inside and outside a large, cave-like cleft boulder at the summit of Ukasi Hill in eastern Kenya, the type locality of the species. Adults were observed climbing the walls of the boulder and walking on thick layers of bat guano, in which larvae and puparia were also discovered. Large numbers of M. hirsuta were observed on and at the base of the northern side of the boulder, which at the time of capture experienced continuous shade during daylight hours. Only three individuals were observed at the southern opening, exposed to direct sunlight and hot, dry conditions. A collection of vertebrate bones and skulls from layers of guano both inside and outside the cleft revealed several vertebrate associates, including two species of Chiroptera, Chaerephon cf. bivittatus (Heuglin) and Tadarida aegyptiaca (E. Geoffroy), which are probably the two major guano-producing species responsible for the larv...}, number={2}, journal={AFRICAN INVERTEBRATES}, author={Copeland, Robert S. and Kirk-Spriggs, Ashley H. and Muteti, Samuel and Booth, Warren and Wiegmann, Brian M.}, year={2011}, month={Dec}, pages={363–390} }
 @article{trautwein_wiegmann_yeates_2010, title={A multigene phylogeny of the fly superfamily Asiloidea (Insecta): Taxon sampling and additional genes reveal the sister-group to all higher flies (Cyclorrhapha)}, volume={56}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2010.04.017}, abstractNote={Asiloidea are a group of 9 lower brachyceran fly families, considered to be the closest relative to the large Metazoan radiation Eremoneura (Cyclorrhapha + Empidoidea). The evidence for asiloid monophyly is limited, and few characters define the relationships between the families of Asiloidea and Eremoneura. Additionally, enigmatic genera, Hilarimorpha and Apystomyia, retain morphological characters of both asiloids and higher flies. We use the nuclear protein-coding gene CAD and 28S rDNA to test the monophyly of Asiloidea and to resolve its relationship to Eremoneura. We explore the effects of taxon sampling on support values and topological stability, the resolving power of additional genes, and hypothesis testing using four-cluster likelihood mapping. We find that: (1) the ‘asiloid’ genus Apystomyia is sister to Cyclorrhapha, (2) the remaining asiloids are monophyletic at the exclusion of the family Bombyliidae, and (3) our best estimate of relationships places the asiloid flies excluding Bombyliidae as the sister-group to Eremoneura, though high support is lacking.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Trautwein, Michelle D. and Wiegmann, Brian M. and Yeates, David K.}, year={2010}, month={Sep}, pages={918–930} }
 @misc{kutty_pape_wiegmann_meier_2010, title={Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly}, volume={35}, ISSN={["1365-3113"]}, DOI={10.1111/j.1365-3113.2010.00536.x}, abstractNote={The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well-known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher-level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree-based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).}, number={4}, journal={SYSTEMATIC ENTOMOLOGY}, author={Kutty, Sujatha Narayanan and Pape, Thomas and Wiegmann, Brian M. and Meier, Rudolf}, year={2010}, month={Oct}, pages={614–635} }
 @misc{winterton_hardy_wiegmann_2010, title={On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data}, volume={35}, ISSN={["1365-3113"]}, DOI={10.1111/j.1365-3113.2010.00521.x}, abstractNote={Neuropterida comprise the holometabolan orders Neuroptera (lacewings, antlions and relatives), Megaloptera (alderflies, dobsonflies) and Raphidioptera (snakeflies) as a monophyletic group sister to Coleoptera (beetles). The higher-level phylogenetic relationships among these groups, as well as the family-level hierarchy of Neuroptera, have to date proved difficult to reconstruct. We used morphological data and multi-locus DNA sequence data to infer Neuropterida relationships. Nucleotide sequences were obtained for fragments of two nuclear genes (CAD, 18S rDNA) and two mitochondrial genes (COI, 16S rDNA) for 69 exemplars representing all recently recognized families of Neuropterida as well as outgroup exemplars from Coleoptera. The joint posterior probability of phylogeny and divergence times was estimated using a Bayesian relaxed-clock inference method to establish a temporal sequence of cladogenesis for the group over geological time. Megaloptera were found to be paraphyletic with respect to the rest of Neuropterida, calling into question the validity of the ordinal status for Megaloptera as presently defined. Ordinal relationships were weakly supported, and monophyly of Megaloptera was not recovered in any total-evidence analysis; Corydalidae were frequently recovered as sister to Raphidioptera. Only in relaxed-clock inferences were Raphidioptera and a paraphyletic Megaloptera recovered with strong support as a monophyletic group sister to Neuroptera. A monophyletic Neuroptera diverged from a common Raphidioptera + ‘Megaloptera’ ancestor during the Late Carboniferous. Contrary to some previous hypotheses, Coniopterygidae, not Nevrorthidae, were recovered as sister to the rest of Neuroptera, with Nevrorthidae recovered with Osmylidae and Sisyridae. The monophyly of the universally recognized Myrmeleontiformia was confirmed, with an origin in the mid-Triassic, but a monophyletic Hemerobiiformia was not recovered in any analysis. Dilaridae were not closely related to the clade comprising Mantispidae and Berothidae, and diverged earlier than proposed previously. The phylogenetic status and taxonomic composition of Polystoechotidae and Ithonidae are in need of re-evaluation, as Oliarces Carpenter (presently Ithonidae) was placed well within the present circumscription of Polystoechotidae.}, number={3}, journal={SYSTEMATIC ENTOMOLOGY}, author={Winterton, Shaun L. and Hardy, Nate B. and Wiegmann, Brian M.}, year={2010}, month={Jul}, pages={349–378} }
 @article{lonsdale_marshall_fu_wiegmann_2010, title={Phylogenetic analysis of the druid flies (Diptera: Schizophora: Clusiidae) based on morphological and molecular data}, volume={41}, ISSN={["1876-312X"]}, DOI={10.1163/187631210x500628}, abstractNote={Abstract In this paper, the Clusiidae (Diptera: Schizophora) is analyzed phylogenetically using morphological and molecular data sets, and then redefined on the basis of derived morphological characters. The biology and distribution of the Clusiidae are also reviewed, a key is provided to the World genera, the status of the genus Craspedochaeta Czerny is reevaluated and the type of Heterochroa pictipennis Wulp is discussed. Molecular data sets include genomic DNA sequences from the mitochondrial genes COI (cytochrome oxidase subunit I) and COII (cytochrome oxidase subunit II), the large ribosomal nuclear subunit 28S, and the nuclear protein-coding carbomoylphosphate synthase (CPS) domain of CAD (or “rudimentary”). Genes were analyzed separately, in combination with each other, and in combination with a morphological data set. Although individual molecular data sets often provided conflicting phylogenetic signals, the topologies of the cladograms produced from each data set alone or in combination were largely similar. Most genus-level relationships and several basal divergences were unresolved, but Apiochaeta was very strongly and consistently supported as Sobarocephalinae, not Clusiinae. The Clusiinae and Sobarocephalinae are subsequently redefined using an adjusted morphological tree — retaining Apiochaeta in the Sobarocephalinae — that is only slightly longer (8.4%, or seven steps) than the most parsimonious tree. Our results illustrate the benefits of multiple independent data sets for phylogenetic reconstruction in order to verify and refine existing classifications.}, number={3}, journal={INSECT SYSTEMATICS & EVOLUTION}, author={Lonsdale, Owen and Marshall, Stephen A. and Fu, Jinzhong and Wiegmann, Brian}, year={2010}, pages={231–274} }
 @article{petersen_bertone_wiegmann_courtney_2010, title={Phylogenetic synthesis of morphological and molecular data reveals new insights into the higher-level classification of Tipuloidea (Diptera)}, volume={35}, ISSN={["0307-6970"]}, DOI={10.1111/j.1365-3113.2010.00524.x}, abstractNote={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.}, number={3}, journal={SYSTEMATIC ENTOMOLOGY}, author={Petersen, Matthew J. and Bertone, Matthew A. and Wiegmann, Brian M. and Courtney, Gregory W.}, year={2010}, month={Jul}, pages={526–545} }
 @article{reidenbach_cook_bertone_harbach_wiegmann_besansky_2009, title={Phylogenetic analysis and temporal diversification of mosquitoes (Diptera: Culicidae) based on nuclear genes and morphology}, volume={9}, ISSN={["1471-2148"]}, DOI={10.1186/1471-2148-9-298}, abstractNote={Abstract Background Phylogenetic analyses provide a framework for examining the evolution of morphological and molecular diversity, interpreting patterns in biogeography, and achieving a stable classification. The generic and suprageneric relationships within mosquitoes (Diptera: Culicidae) are poorly resolved, making these subjects difficult to address. Results We carried out maximum parsimony and maximum likelihood, including Bayesian, analyses on a data set consisting of six nuclear genes and 80 morphological characters to assess their ability to resolve relationships among 25 genera. We also estimated divergence times based on sequence data and fossil calibration points, using Bayesian relaxed clock methods. Strong support was recovered for the basal position and monophyly of the subfamily Anophelinae and the tribes Aedini and Sabethini of subfamily Culicinae. Divergence times for major culicid lineages date to the early Cretaceous. Conclusions Deeper relationships within the family remain poorly resolved, suggesting the need for additional taxonomic sampling. Our results support the notion of rapid radiations early in the diversification of mosquitoes.}, journal={BMC EVOLUTIONARY BIOLOGY}, author={Reidenbach, Kyanne R. and Cook, Shelley and Bertone, Matthew A. and Harbach, Ralph E. and Wiegmann, Brian M. and Besansky, Nora J.}, year={2009}, month={Dec} }
 @article{barr_wiegmann_2009, title={Phylogenetic relationships of Ceratitis fruit flies inferred from nuclear CAD and tango/ARNT gene fragments: Testing monophyly of the subgenera Ceratitis (Ceratitis) and C. (Pterandrus)}, volume={53}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2009.07.008}, abstractNote={Systematic studies of Ceratitis (Tephritidae) fruit flies using molecular (i.e., COI, ND6, and period genes) and morphological (plus host-use characters) data have recently challenged the monophyly of the subgenera Ceratitis (Ceratitis) and Ceratitis (Pterandrus). In this paper, we report on the phylogenetic utility of three single-copy nuclear gene regions (two non-overlapping fragments of the carbamoylphosphate synthetase, CPS, locus of CAD, and a fragment of tango) within these taxa and investigate evolutionary relationships based on a concatenated ca. 3.4kb data set that includes the six protein encoding gene regions. Results indicate that the CAD and tango genes provide useful phylogenetic signal within the taxa and are compatible with the previously studied genes. The two subgenera, as currently classified, are not monophyletic. Our molecular phylogenetic analyses support a revised classification in which (1) the subgenus C. (Pterandrus) comprises two lineages called A and B, (2) the C. (Pterandrus) B species should be included in C. (Ceratitis), and (3) the newly defined subgenera C. (Pterandrus) (=Pterandrus section A) and C. (Ceratitis) [=C. (Ceratitis)+C. (Pterandrus) section B] are reciprocally monophyletic.}, number={2}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Barr, Norman B. and Wiegmann, Brian M.}, year={2009}, month={Nov}, pages={412–424} }
 @article{wiegmann_trautwein_kim_cassel_bertone_winterton_yeates_2009, title={Single-copy nuclear genes resolve the phylogeny of the holometabolous insects}, volume={7}, ISSN={["1741-7007"]}, DOI={10.1186/1741-7007-7-34}, abstractNote={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 single-copy nuclear protein coding genes used to reconstruct phylogenetic relationships and estimate evolutionary divergence times for all holometabolan orders. Our results strongly support Hymenoptera as the earliest branching holometabolan lineage, the monophyly of the extant orders, including the fleas, and traditionally recognized groupings of Neuropteroidea and Mecopterida. Most significantly, we find strong support for a close relationship between Coleoptera (beetles) and Strepsiptera, a previously proposed, but analytically controversial relationship. Exploratory analyses reveal that this relationship cannot be explained by long-branch attraction or other systematic biases. Bayesian divergence times analysis, with reference to specific fossil constraints, places the origin of Holometabola in the Carboniferous (355 Ma), a date significantly older than previous paleontological and morphological phylogenetic reconstructions. The origin and diversification of most extant insect orders began in the Triassic, but flourished in the Jurassic, with multiple adaptive radiations producing the astounding diversity of insect species for which these groups are so well known. These findings provide the most complete evolutionary framework for future comparative studies on holometabolous model organisms and contribute strong evidence for the resolution of the 'Strepsiptera problem', a long-standing and hotly debated issue in insect phylogenetics.}, journal={BMC BIOLOGY}, author={Wiegmann, Brian M. and Trautwein, Michelle D. and Kim, Jung-Wook and Cassel, Brian K. and Bertone, Matthew A. and Winterton, Shaun L. and Yeates, David K.}, year={2009}, month={Jun} }
 @misc{lambkin_trueman_yeates_holston_webb_hauser_metz_hill_skevington_yang_et al._2009, title={Supertrees and the Tree of Life: generating a metaphylogeny for a diverse invertebrate family (Insecta : Diptera : Therevidae) using constraint trees and the parsimony ratchet to overcome low taxon overlap}, volume={23}, ISSN={["1447-2600"]}, DOI={10.1071/is08035}, abstractNote={The dipteran family Therevidae (stiletto flies) is cosmopolitan and has been the focus of many taxonomic and phylogenetic studies over the last 25 years. Despite this work, questions remain concerning the relationships between subfamilies, genera and generic groups and membership of those groups. We use the supertree method to produce an inclusive phylogeny for the family Therevidae from 24 phylogenetic studies using matrix representation with parsimony (MRP) analysis. The supertree method, one of the most common approaches to calculating globally inclusive phylogenies from smaller more exclusive analyses, produced the therevid metaphylogeny despite only 34% of the terminal taxa being found in more than one source tree. We describe a method for handling low taxon overlap in supertree analyses, in combination with the parsimony ratchet and constraint tree techniques. The supertree presented here is an overarching phylogenetic hypothesis of the Therevidae, incorporating extensive sampling of major lineages and summarising past phylogenetic work on the family. The inclusive metaphylogeny for 362 therevid taxa robustly retrieves the subfamilies Agapophytinae, Phycinae, Therevinae and Xestomyzinae, and the tribes Cyclotelini and Therevini. The Phycinae and Xestomyzinae form a clade, sister to the remaining Therevidae. The Australasian and South American Taenogera Kröber genus-group is monophyletic and sister to a clade of Therevinae and the Australian endemic Agapophytinae. The Therevinae consists of the Anabarhynchus Macquart genus-group of Australian, South American, New Caledonian and New Zealand taxa as sister to the non-Australasian ‘higher Therevinae’, which contains the tribes Cyclotelini and Therevini. The Therevini includes the Hoplosathe Lyneborg & Zaitzev, Litolinga Irwin & Lyneborg, Baryphora Loew, Pandivirilia Irwin & Lyneborg and Thereva Latreille generic-groups. MRP supertree methods can be used to produce inclusive metaphylogenies in situations where source trees have poor data overlap and low taxon overlap, and are therefore valuable in species-rich groups such as arthropods. These methods may be necessary for constructing the ‘Tree of Life’, representing phylogenetic relationships among the millions of known species. However, our analyses show that in situations of source tree conflict, MRP supertree analyses present only the majority signal. We also show that conflict between source trees can be hidden in MRP supertrees, thus our results emphasise the need to evaluate the resulting clades with reference to the source trees.}, number={2}, journal={INVERTEBRATE SYSTEMATICS}, author={Lambkin, Christine L. and Trueman, John W. H. and Yeates, David K. and Holston, Kevin C. and Webb, Donald W. and Hauser, Martin and Metz, Mark A. and Hill, Hilary N. and Skevington, Jeffrey H. and Yang, Longlong and et al.}, year={2009}, pages={171–191} }
 @misc{zhang_xiang_thomas_wiegmann_frohlich_soltis_2008, title={Molecular evolution of PISTILLATA-like genes in the dogwood genus Cornus (Cornaceae)}, volume={47}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2007.12.022}, abstractNote={The MADS-box gene family encodes critical regulators determining floral organ development. Understanding evolutionary patterns and processes of MADS-box genes is an important step toward unraveling the molecular basis of floral morphological evolution. In this study, we investigated the evolution of PI-like genes of the MADS-box family in the dogwood genus Cornus (Cornaceae). Cornus is a eudicot lineage in the asterids clade, and is intriguing in evolving petaloid bract morphology in two major lineages within the genus. The gene genealogy reconstructed using genomic DNA and cDNA sequences suggests multiple PI-like gene duplication events in Cornus. An ancient duplication event resulted in two ancient paralogs, CorPI-A and CorPI-B, which have highly diverged intron regions. Duplication of CorPI-A further resulted in two paralogs in one subgroup of Cornus, the BW group that does not produce modified bracts. Most species analyzed were found to contain more than one copy of the PI-like gene with most copies derived recently within species. Estimation and comparison of dN/dS ratios revealed relaxed selection in the PI-like gene in Cornus in comparison with the gene in the closely related outgroups Alangium and Davidia, and in other flowering plants. Selection also differed among major gene copies, CorPI-A and CorPI-B, and among different morphological subgroups of Cornus. Variation in selection pressures may indicate functional changes in PI-like genes after gene duplication and among different lineages. Strong positive selection at three amino acid sites of CorPI was also detected from a region critical for dimerization activity. Total substitution rates of the CorPI gene also differ among lineages of Cornus, showing a trend similar to that found in dN/dS ratios. We also found that the CorPI-A copy contains informative phylogenetic information when compared across species of Cornus.}, number={1}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Zhang, Wenheng and Xiang, Qiu-Yun and Thomas, David T. and Wiegmann, Brian M. and Frohlich, Michael W. and Soltis, Douglas E.}, year={2008}, month={Apr}, pages={175–195} }
 @article{bertone_courtney_wiegmann_2008, title={Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes}, volume={33}, ISSN={["1365-3113"]}, DOI={10.1111/j.1365-3113.2008.00437.x}, abstractNote={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 ¼ Thaumaleidae þ Simuliidae), Tipulomorpha (Tipulidae sensu lato þ Trichoceridae) and Bibionomorpha sensu lato. We find support for a limited Psychodomorpha (Blephariceridae, Tanyderidae and Psycho- didae) 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.}, number={4}, journal={SYSTEMATIC ENTOMOLOGY}, author={Bertone, Matthew A. and Courtney, Gregory W. and Wiegmann, Brian M.}, year={2008}, month={Oct}, pages={668–687} }
 @article{kutty_pape_pont_wiegmann_meier_2008, title={The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes}, volume={49}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2008.08.012}, abstractNote={Approximately 5% of the known species-level diversity of Diptera belongs to the Muscoidea with its approximately 7000 described species. Despite including some of the most abundant and well known flies, the phylogenetic relationships within this superfamily are poorly understood. Previous attempts at reconstructing the relationships based on morphology and relatively small molecular data sets were only moderately successful. Here, we use molecular data for 127 exemplar species of the Muscoidea, two species from the Hippoboscoidea, ten species representing the Oestroidea and seven outgroup species from four acalyptrate superfamilies. Four mitochondrial genes 12S, 16S, COI, and Cytb, and four nuclear genes 18S, 28S, Ef1a, and CAD are used to reconstruct the relationships within the Muscoidea. The length-variable genes were aligned using a guide tree that was based on the protein-encoding genes and the indel-free sections of the ribosomal genes. We found that, based on topological considerations, this guide tree was a significant improvement over the default guide trees generated by ClustalX. The data matrix was analyzed using maximum parsimony (MP) and maximum likelihood (ML) and yielded very similar tree topologies. The Calyptratae are monophyletic and the Hippoboscoidea are the sister group to the remaining calyptrates (MP). The Muscoidea are paraphyletic with a monophyletic Oestroidea nested within the Muscoidea as sister group to Anthomyiidae+Scathophagidae. The monophyly of three of the four recognized families in the Muscoidea is confirmed: the Fanniidae, Muscidae, and Scathophagidae. However, the Anthomyiidae are possibly paraphyletic. Within the Oestroidea, the Sarcophagidae and Tachinidae are sister groups and the Calliphoridae are paraphyletic.}, number={2}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Kutty, Sujatha Narayanan and Pape, Thomas and Pont, Adrian and Wiegmann, Brian M. and Meier, Rudolf}, year={2008}, month={Nov}, pages={639–652} }
 @article{fan_xiang_remington_purugganan_wiegmann_2007, title={Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae)}, volume={130}, ISSN={0016-6707, 1573-6857}, url={http://link.springer.com/10.1007/s10709-006-0016-3}, DOI={10.1007/s10709-006-0016-3}, number={1}, journal={Genetica}, author={Fan, Chuanzhu and Xiang, Qiu-Yun (Jenny) and Remington, David L. and Purugganan, Michael D. and Wiegmann, Brian M.}, year={2007}, month={Apr}, pages={19–34} }
 @article{schuehli_carvalho_wiegmann_2007, title={Molecular phylogenetics of the Muscidae (Diptera : Calyptratae): new ideas in a congruence context}, volume={21}, ISSN={["1447-2600"]}, DOI={10.1071/IS06026}, abstractNote={Hypotheses about the evolution of Muscidae have long been the subject of continuous re-evaluation and reinterpretation. Current understandings of the relationships among these flies are based mainly on a single set of characters and are therefore questionable. Our understanding of muscid phylogeny thus needs greater support and further corroboration from additional suites of characters. In the current study, we analysed phylogenetic relationships among 24 species of muscid flies (18 genera and six subfamilies) using 2989 characters derived from sequences of mitochondrial (COI and COII) and nuclear genes (CAD and EF-1α). Data from each gene partition were analysed both in combined and separate phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference. Support was found for the monophyly of the Muscidae in all analyses and for a sister-group relationship between Coenosiini and Phaoniinae. The latter group was placed in a clade with sampled species of Reinwardtiini and Cyrtoneurininae. The genera Ophyra and Hydrotaea were placed in the Muscinae and a sister-group relationship for Musca and Stomoxys was supported. Sampled species of Polietina form a monophyletic lineage, while Morellia was found to be paraphyletic. Combined analysis of gene partitions improved support and resolution for resulting topologies despite significant incongruence between data partitions found through application of the Incongruence Length Difference test.}, number={3}, journal={INVERTEBRATE SYSTEMATICS}, author={Schuehli, Guilherme Schnell e and Carvalho, Claudio Jose Barros and Wiegmann, Brian M.}, year={2007}, pages={263–278} }
 @article{holston_irwin_wiegmann_2007, title={Monophyly and phylogenetic relationships of Thereva and therevine genus-groups (Insecta : Diptera : Therevidae) based on EF-1 alpha, 28S rDNA and mitochondrial 16S rDNA sequences}, volume={21}, ISSN={["1447-2600"]}, DOI={10.1071/IS06005}, abstractNote={Phylogenetic analyses using 28S rDNA, elongation factor (EF)-1α, and mt 16S rDNA sequences were performed to test the monophyly of Thereva Latreille. Two of the three Afrotropical Thereva species groups lack the genitalia characters that unambiguously diagnose Thereva in the Holarctic Region, but phylogenetic relationships among Thereva species groups and therevine genera are poorly understood. Using an extensive taxonomic sample (39 of the 62 therevine genera) and Thereva, sensu lato (15 spp.), simultaneous analyses of all three gene partitions recovered Nearctic and Palaearctic Thereva species in a well supported clade that includes the Afrotropical seminitida-group but excludes the Afrotropical analis- and turneri-groups. Stronger phylogenetic signal from the EF-1α partition, measured by the skewness statistic and proportion of total parsimony informative characters, dominated conflicting signal from the 16S partition and weaker, but more congruent, signal from 28S. Reducing the taxonomic sample in analyses of Therevinae reduced homoplasy, increased phylogenetic structure and partitioned Bremer support values and reduced incongruence with 28S for the 16S partition. Although molecular analyses yielded partial recovery of informal therevine genus-groups, morphological diagnoses of higher-level groups are poorly supported with the exception of Cyclotelini. The ‘Holarctic radiation’ refers to a diverse clade of genera closely related to Pandivirilia Irwin & Lyneborg and Acrosathe Irwin & Lyneborg widely distributed throughout the Holarctic Region that is the sister-group to Thereva, sensu stricto. Results from these analyses underscore the importance of male and female genitalia characters in recognising monophyletic groups and regional endemism in therevine diversification.}, number={3}, journal={INVERTEBRATE SYSTEMATICS}, author={Holston, Kevin C. and Irwin, Michael E. and Wiegmann, Brian M.}, year={2007}, pages={279–296} }
 @article{scheffer_winkler_wiegmann_2007, title={Phylogenetic relationships within the leaf-mining flies (Diptera : Agromyzidae) inferred from sequence data from multiple genes}, volume={42}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2006.12.018}, abstractNote={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.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Scheffer, Sonja J. and Winkler, Isaac S. and Wiegmann, Brian M.}, year={2007}, month={Mar}, pages={756–775} }
 @misc{winterton_wiegmann_schlinger_2007, title={Phylogeny and Bayesian divergence time estimations of small-headed flies (Diptera : Acroceridae) using multiple molecular markers}, volume={43}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2006.08.015}, abstractNote={The first formal analysis of phylogenetic relationships among small-headed flies (Acroceridae) is presented based on DNA sequence data from two ribosomal (16S and 28S) and two protein-encoding genes: carbomoylphosphate synthase (CPS) domain of CAD (i.e., rudimentary locus) and cytochrome oxidase I (COI). DNA sequences from 40 species in 22 genera of Acroceridae (representing all three subfamilies) were compared with outgroup exemplars from Nemestrinidae, Stratiomyidae, Tabanidae, and Xylophagidae. Parsimony and Bayesian simultaneous analyses of the full data set recover a well-resolved and strongly supported hypothesis of phylogenetic relationships for major lineages within the family. Molecular evidence supports the monophyly of traditionally recognised subfamilies Philopotinae and Panopinae, but Acrocerinae are polyphyletic. Panopinae, sometimes considered “primitive” based on morphology and host-use, are always placed in a more derived position in the current study. Furthermore, these data support emerging morphological evidence that the type genus Acrocera Meigen, and its sister genus Sphaerops, are atypical acrocerids, comprising a sister lineage to all other Acroceridae. Based on the phylogeny generated in the simultaneous analysis, historical divergence times were estimated using Bayesian methodology constrained with fossil data. These estimates indicate Acroceridae likely evolved during the late Triassic but did not diversify greatly until the Cretaceous.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Winterton, Shaun L. and Wiegmann, Brian M. and Schlinger, Evert I.}, year={2007}, month={Jun}, pages={808–832} }
 @misc{yeates_wiegmann_courtney_meier_lambkin_pape_2007, title={Phylogeny and systematics of Diptera: Two decades of progress and prospects}, number={1668}, journal={Zootaxa}, author={Yeates, D. K. and Wiegmann, B. M. and Courtney, G. W. and Meier, R. and Lambkin, C. and Pape, T.}, year={2007}, pages={565–590} }
 @article{moulton_wiegmann_2007, title={The phylogenetic relationships of flies in the superfamily Empidoidea (Insecta : Diptera)}, volume={43}, ISSN={["1055-7903"]}, DOI={10.1016/j.ympev.2007.02.029}, abstractNote={We conducted a molecular phylogenetic study of the Empidoidea, a diverse group of 10,000 species of true flies, with two major goals: to reconstruct a taxonomically complete and robustly supported phylogeny for the group and to use this information to assess several competing classifications for the clade. We amassed 3900+ nucleotides of coding data from the carbamoylphosphate synthase domain of the rudimentary locus (CAD) and 1200+ nucleotides from the large nuclear ribosomal subunit (28S) from 72 and 71 species, respectively, representing several orthorrhaphan and cyclorrhaphan families and all previously recognized empidoidean subfamilies. Independent and combined phylogenetic analyses of these data were conducted using parsimony, maximum likelihood, and Bayesian criteria. The combined matrix included 61 taxa for which both CAD and 28S sequences were obtained. Analyses of CAD first and second codon positions alone and when concatenated with 28S sequences yielded trees with similar and largely stable topologies. Analyses of 28S data alone supported many clades although resolution is limited by low sequence divergence. The following major empidoid clades were recovered with convincing support in a majority of analyses: Atelestidae, Empidoidea exclusive of Atelestidae, Hybotidae sensu lato, Dolichopodidae + Microphorinae (including Parathallassius), and Empididae sensu lato (including Brachystomatinae, Ceratomerinae, Clinocerinae, Empidinae, Hemerodromiinae, Oreogetoninae, and Trichopezinae). The branching arrangement among these four major clades was Atelestidae, Hybotidae, Dolichopodidae/Microphorinae, Empididae. Previously recognized subclades recovered with robust support included Hybotinae, Brachystomatinae, Tachydromiinae, Clinocerinae (in part), Hemerodromiinae, Empidinae, and Empidiini.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Moulton, John K. and Wiegmann, Brian M.}, year={2007}, month={Jun}, pages={701–713} }
 @article{petersen_meier_kutty_wiegmann_2007, title={The phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers}, volume={45}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2007.04.023}, abstractNote={Hippoboscoidea is a superfamily of Diptera that contains the Glossinidae or tsetse flies, the Hippoboscidae or louse flies, and two families of bat flies, the Streblidae and the Nycteribiidae. We reconstruct the phylogenetic relationships within Hippoboscoidea using maximum parsimony and Bayesian methods based on nucleotide sequences from fragments of four genes: nuclear 28S ribosomal DNA and the CPSase domain of CAD, and mitochondrial 16S rDNA and cytochrome oxidase I. We recover monophyly for most of the presently recognized groups within Hippoboscoidea including the superfamily as a whole, the Hippoboscidae, the Nycteribiidae, the bat flies, and the Pupipara (=Hippoboscidae+Nycteribiidae+Streblidae), as well as several subfamilies within the constituent families. Streblidae appear to be paraphyletic. Our phylogenetic hypothesis is well supported and decisive in that most competing topological hypotheses for the Hippoboscoidea require significantly longer trees. We confirm a single shift from a free-living fly to a blood-feeding ectoparasite of vertebrates and demonstrate that at least two host shifts from mammals to birds have occurred. Wings have been repeatedly lost, but never regained. The hippoboscoid ancestor also evolved adenotrophic viviparity and our cladogram is consistent with a gradual reduction in the motility of the deposited final instar larvae from active burrowing in the soil to true pupiparity where adult females glue the puparium within the confines of bat roosts.}, number={1}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Petersen, Frederik Torp and Meier, Rudolf and Kutty, Suiatha Narayanan and Wiegmann, Brian M.}, year={2007}, month={Oct}, pages={111–122} }
 @article{yeates_irwin_wiegmann_2006, title={Evocoidae (Diptera : Asiloidea), a new family name for Ocoidae, based on Evocoa, a replacement name for the Chilean genus Ocoa Yeates, Irwin, and Wiegmann 2003 (vol 31, pg 373, 2006)}, volume={31}, ISSN={["0307-6970"]}, DOI={10.1111/j.1365-3113.2006.00332.x}, number={2}, journal={SYSTEMATIC ENTOMOLOGY}, author={Yeates, DK and Irwin, ME and Wiegmann, BM}, year={2006}, month={Apr}, pages={373–373} }
 @article{laamanen_meier_miller_hille_wiegmann_2005, title={Phylogenetic analysis of Themira (Sepsidae : Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study}, volume={21}, ISSN={["1096-0031"]}, DOI={10.1111/j.1096-0031.2005.00066.x}, abstractNote={In this study we use sensitivity analysis sensuWheeler (1995) for a matrix entirely composed of DNA sequences. We propose that not only congruence but also phylogenetic structure, as measured by character resampling, should be used to choose among competing weighting regimes. An extensive analysis of a five-gene data set for Themira (Sepsidae: Diptera) reveals that even with different ways of partitioning the data, measures of topological congruence, character incongruence, and phylogenetic structure favor similar weighting regimes involving the down-weighting of transitions. We furthermore use sensitivity analysis for obtaining empirical evidence that allows us to select weights for third positions, deciding between treating indels as fifth character states or missing values, and choosing between manual and computational alignments. For our data, sensitivity analysis favors manual alignment over a Clustal-generated numerical alignment, the treatment of indels as fifth character states over considering them missing values, and equal weights for all positions in protein-encoding genes over the down-weighting of third positions. Among the topological congruence measures compared, symmetric tree distance performed best. Partitioned Bremer Support analysis reveals that COI contributes the largest amount of support for our phylogenetic tree for Themira.



© The Willi Hennig Society 2005.}, number={3}, journal={CLADISTICS}, author={Laamanen, TR and Meier, R and Miller, MA and Hille, A and Wiegmann, BM}, year={2005}, month={Jun}, pages={258–271} }
 @article{moulton_wiegmann_2004, title={Evolution and phylogenetic utility of CAD (rudimentary) among Mesozoic-aged Eremoneuran Diptera (Insecta)}, volume={31}, ISSN={["1095-9513"]}, DOI={10.1016/S1055-7903(03)00284-7}, abstractNote={We sequenced nearly the entire carbomoylphosphate synthase (CPS) domain of CAD, or rudimentary, (ca. 4 kb) from 29 species of flies representing all major clades within Eremoneura, or higher flies, and several orthorrhaphous brachyceran outgroups. We compared these sequences with orthologs from Anopheles gambiae and Drosophila melanogaster to assess structure, compositional bias, and phylogenetic utility. CAD is large (6.6+ kb), complex (comprised of three major and myriad minor functional domains) and relatively free of introns, extreme nucleotide bias (except third codon positions), and large hypervariable regions. The CPS domain possesses moderate levels of nonsynonymous divergence among taxa of intermediate evolutionary age and conveys considerable phylogenetic signal. Phylogenetic analysis of CPS sequences under varying methods and assumptions resulted in well-resolved, strongly supported trees concordant with many traditional ideas about higher dipteran phylogeny and with prior inferences from 28S rDNA. The most robustly supported major eremoneuran clades were Cyclorrhapha, Platypezoidea, Eumuscomorpha, Empidoidea, Atelestidae, Empidoidea exclusive of Atelestidae, Hybotidae s.l., Microphoridae+Dolichopodidae, and Empididae s. str. Because CAD is ubiquitous, apparently single copy (at least within holometabolous insects), readily obtained from several insect orders using primers described herein, and exhibits considerable phylogenetic utility, it should have wide applicability in insect molecular systematics.}, number={1}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Moulton, JK and Wiegmann, BM}, year={2004}, month={Apr}, pages={363–378} }
 @article{fan_purugganan_thomas_wiegmann_xiang_2004, title={Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae)}, volume={33}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2004.08.002}, abstractNote={Anthocyanin is a major pigment in vegetative and floral organs of most plants and plays an important role in plant evolution. The anthocyanin regulatory genes are responsible for regulating transcription of genes in the anthocyanin synthetic pathway. To assess evolutionary significance of sequence variation and evaluate the phylogenetic utility of an anthocyanin regulatory gene, we compared nucleotide sequences of the myc-like anthocyanin regulatory gene in the genus of dogwoods (Cornus: Cornaceae). Phylogenetic analyses demonstrate that the myc-like anthocyanin regulatory gene has potential as an informative phylogenetic marker at different taxonomic levels, depending on the data set considered (DNA or protein sequences) and regions applied (exons or introns). Pairwise nonsynonymous and synonymous substitution rate tests and codon-based substitution models were applied to characterize variation and to identify sites under diversifying selection. Mosaic evolution and heterogeneous rates among different domains and sites were detected.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Fan, CZ and Purugganan, MD and Thomas, DT and Wiegmann, BM and Xiang, QY}, year={2004}, month={Dec}, pages={580–594} }
 @article{savage_wheeler_wiegmann_2004, title={Phylogenetic analysis of the genus Thricops Rondani (Diptera : Muscidae) based on molecular and morphological characters}, volume={29}, ISSN={["1365-3113"]}, DOI={10.1111/j.0307-6970.2004.00252.x}, abstractNote={Abstract. The muscid genus Thricops Rondani comprises forty-four species and two subspecies restricted to the northern hemisphere. A species-level phylogenetic analysis of Thricops was conducted using forty-four morphological characters, 426 bp of the nuclear gene white and 523 bp spanning the 5′ end of the cytochrome c oxidase subunit I (COI), the tRNA leucine gene (L2 region) and the 3′ end of the cytochrome c oxidase subunit II (COII). Thirty-nine species and two subspecies of Thricops were included in the analysis. Two species of Azelia Robineau-Desvoidy and one species of Hydrotaea Robineau-Desvoidy were used as outgroups. Morphological characters were coded for all included species, the mitochondrial gene fragment (COI + II) was sequenced for a subset of seventeen species of Thricops and three outgroup species, and white for twelve of those seventeen Thricops species and two outgroup species. Six separate maximum parsimony analyses were performed on three taxon sets of different sizes (n = 14, n = 20, n = 44). Results from the partition homogeneity test indicated no significant incongruence between data partitions, and four combined maximum parsimony analyses were conducted (DNA + morphology for n = 14; COI + II + morphology for n = 20; DNA + morphology for n = 20; DNA + morphology for n = 44). The relative contribution of each data partition to individual nodes was assessed using partitioned Bremer support. Strict consensus trees resulting from the unweighted analyses of each dataset are presented. Combination of datasets increased resolution for the small taxon set (n = 14), but not for the larger ones (n = 20, n = 44), most probably due to increasing amounts of missing data in the larger taxon sets. Results from both individual and combined analyses of the smaller taxon sets (n = 14, n = 20) provided support for the monophyly of Thricops and a complete division of the genus into two monophyletic subgroups. The strict consensus cladograms resulting from the analysis of the morphological data alone and the combined data for the large taxa set (n = 44) both supported the monophyly of the genus, but placed the species Thricops foveolatus (Zetterstedt) and Thricops bukowskii (Ringdahl) at the base of the ingroup, in a polytomy with a relatively well-resolved branch comprising all remaining species of the genus. The basal position of these two species, included in the morphological taxon set but absent in the others, illustrates the potential pitfalls of taxon sampling and missing data in phylogenetic analyses. The synonymy of Alloeostylus with Thricops as proposed by previous authors was supported by our results. Relative contributions of different data partitions is discussed, with the mitochondrial sequence generally providing finer resolution and better branch support than white.}, number={3}, journal={SYSTEMATIC ENTOMOLOGY}, author={Savage, J and Wheeler, TA and Wiegmann, BM}, year={2004}, month={Jul}, pages={395–414} }
 @article{schuehli_de carvalho_wiegmann_2004, title={Regarding the taxonomic status of Ophyra Robineau-Desvoidy (Diptera: Muscidae): A molecular approach}, number={712}, journal={Zootaxa}, author={Schuehli, G. S. E. and De Carvalho, C. J. B. and Wiegmann, B. M.}, year={2004}, pages={12-} }
 @article{cryan_wiegmann_deitz_dietrich_whiting_2004, title={Treehopper trees: phylogeny of Membracidae (Hemiptera : Cicadomorpha : Membracoidea) based on molecules and morphology}, volume={29}, ISSN={["1365-3113"]}, DOI={10.1111/j.0307-6970.2004.00260.x}, abstractNote={Abstract. Recent independent phylogenetic analyses of membracid relationships based on molecular and morphological data have identified monophyletic lineages within the family. However, the results of these studies have not fully resolved treehopper phylogeny, and relationships among some higher membracid lineages remain in doubt. Portions of three datasets (958 aligned nucleotides from elongation factor-1α, 2363 aligned nucleotides from 28S ribosomal DNA, and eighty-three morphological features of adults and nymphs) introduced in recent studies were reanalysed separately and in combination with two new molecular datasets (321 aligned nucleotides from wingless and 1829 aligned nucleotides from 18S ribosomal DNA). The results of the combined data analyses, contrary to previous analyses of morphological data alone, grouped membracids into two well-supported lineages, one comprising Stegaspidinae and Centrotinae, the other comprising Membracinae, Darninae and Smiliinae. The analyses recovered Centrotinae, Membracinae and Darninae as monophyletic groups, but Stegaspidinae was paraphyletic with respect to Centrotinae, and Smiliinae was polyphyletic with Micrutalini placed as a sister group to the clade comprising Membracinae, Darninae and Smiliinae. These results are consistent with the following hypotheses, proposed previously based on an analysis of morphological data: (1) the posterior pronotal process was derived and lost multiple times during the evolution of Membracidae; (2) Membracidae originated in the New World and reached the Old World subsequently via dispersal; (3) maternal care evolved independently multiple times and may or may not have been preceded by the acquisition of ant mutualism.}, number={4}, journal={SYSTEMATIC ENTOMOLOGY}, author={Cryan, JR and Wiegmann, BM and Deitz, LL and Dietrich, CH and Whiting, MF}, year={2004}, month={Oct}, pages={441–454} }
 @article{yeates_irwin_wiegmann_2003, title={Ocoidae, a new family of asiloid flies (Diptera : Brachycera : Asiloidea), based on Ocoa chilensis gen. and sp.n. from Chile, South America}, volume={28}, ISSN={["1365-3113"]}, DOI={10.1046/j.1365-3113.2003.00224.x}, abstractNote={Abstract. The monotypic new family Ocoidae is described to accommodate Ocoa gen.n., small, elongate, delicate, asiloid flies known from west-central Chile, South America. Both sexes of adult O. chilensis sp.n. are described and illustrated; immature stages are unknown. Diagnostic morphological features of adults include the antennal postpedicel comprising a single, undivided structure consisting of a bulbous base and a long, threadlike terminal element; vein M3 lacking, anal vein complete; acropod heterodactylus; spurs lacking on all tibiae; and anterior surface of hind coxa with strong, knoblike, bulbous projection; and abdominal tergite 2 lacking sensory patches of hairs. The epandrium of the male terminalia is divided along the midline into two sicklelike sections; gonostyli articulate in a horizontal plane. The female terminalia has well-developed acanthophorite spines; posterior margin of hypoproct with several ventrally projecting, elongate, needlelike setae; two large, poorly sclerotized spermathecae; and a spermathecal sac that is smaller than each spermatheca. The relationships of this enigmatic family are discussed in relation to recent findings on the phylogeny and classification of the Asiloidea. Ocoidae are similar to Therevidae and close relatives Scenopinidae and Apsilocephalidae, comprising the therevoid group of families; however, they lack defining synapomorphies of those families. Morphological evidence supports a sister-group relationship between Ocoidae and Scenopinidae. Molecular evidence from 28S rDNA provides further support for the monophyly of the therevoid group of families, and suggests that Ocoidae belongs within this clade, in agreement with the morphological data. The nucleotide data place Ocoidae as sister to the Scenopinidae + Therevidae, but the morphology-based hypothesis of relationships (Ocoidae + Scenopinidae) is only two additional steps (0.2%) on the optimal trees from the molecular data.}, number={4}, journal={SYSTEMATIC ENTOMOLOGY}, author={Yeates, DK and Irwin, ME and Wiegmann, BM}, year={2003}, month={Oct}, pages={417–431} }
 @article{wiegmann_yeates_thorne_kishino_2003, title={Time flies, a new molecular time-scale for brachyceran fly evolution without a clock}, volume={52}, number={6}, journal={Systematic Biology}, author={Wiegmann, B. M. and Yeates, D. K. and Thorne, J. L. and Kishino, H.}, year={2003}, pages={745–756} }
 @article{meier_wiegmann_2002, title={A phylogenetic analysis of Coelopidae (Diptera) based on morphological and DNA sequence data}, volume={25}, ISSN={["1095-9513"]}, DOI={10.1016/S1055-7903(02)00276-2}, abstractNote={The phylogenetic relationships of 22 species of Coelopidae are reconstructed based on a data matrix consisting of morphological and DNA sequence characters (16S rDNA, EF-1alpha). Optimal gap and transversion costs are determined via a sensitivity analysis and both equal weighting and a transversion cost of 2 are found to perform best based on taxonomic congruence, character incongruence, and tree support. The preferred phylogenetic hypothesis is fully resolved and well-supported by jackknife, bootstrap, and Bremer support values, but it is in conflict with the cladogram based on morphological characters alone. Most notably, the Coelopidae and the genus Coelopa are not monophyletic. However, partitioned Bremer Support and an analysis of node stability under different gap and transversion costs reveal that the critical clades rendering these taxa non-monophyletic are poorly supported. Furthermore, the monophyly of Coelopidae and Coelopa is not rejected in analyses using 16S rDNA that was manually aligned. The resolution of the tree based on this reduced data sets is, however, lower than for the tree based on the full data sets. Partitioned Bremer support values reveal that 16S rDNA characters provide the largest amount of tree support, but the support values are heavily dependent on analysis conditions. Problems with direct comparison of branch support values for trees derived using fixed alignments with those obtained under optimization alignment are discussed. Biogeographic history and available behavioral and genetic data are also discussed in light of this first cladogram for Coelopidae based on a quantitative phylogenetic analysis.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Meier, R and Wiegmann, BM}, year={2002}, month={Dec}, pages={393–407} }
 @article{wiegmann_regier_mitter_2002, title={Combined molecular and morphological evidence on the phylogeny of the earliest lepidopteran lineages}, volume={31}, ISSN={["1463-6409"]}, DOI={10.1046/j.0300-3256.2001.00091.x}, abstractNote={Agreement among recent morphological and molecular phylogenetic analyses has strengthened estimates of the relationships among the earliest lineages of the holometabolan order Lepidoptera. For a few major groups, evidence for monophyly and basal relationships remains relatively weak or contradictory — chiefly within the clades of basal Glossata and Heteroneura. Here we assess the support for these controversial areas of lepidopteran classification through molecular systematic investigation of 18S rDNA sequence variation. Parsimony and maximum likelihood analyses are presented for 1379 alignable sites of 18S. These data are then combined with 61 morphological features scored for major lineages of basal Glossata and Heteroneura. Our 18S rDNA data support recent hypotheses for the placement of Micropterigidae and Agathiphagidae as the basal-most lineages of Lepidoptera, and support the monophyly of the groups Neolepidoptera and Exoporia. 18S data alone are shown to be insufficient for resolving the monophyly and relationships of the Glossata, and for specifying relationships above the Neolepidoptera. Combination of the 18S data with published morphological ground-plan scorings improves overall support for the morphology-based hypothesis for basal glossatans, but phylogenetic resolution among published alternatives for the basal Heteroneura remains a major question for lepidopteran systematics.}, number={1}, journal={ZOOLOGICA SCRIPTA}, author={Wiegmann, BM and Regier, JC and Mitter, C}, year={2002}, month={Feb}, pages={67–81} }
 @article{mukha_wiegmann_schal_2002, title={Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta)}, volume={32}, ISSN={["1879-0240"]}, DOI={10.1016/S0965-1748(01)00164-3}, abstractNote={The organization, structure, and nucleotide variability of the ribosomal repeat unit was compared among families, genera, and species of cockroaches (Insecta:Blattodea). Sequence comparisons and molecular phylogenetic analyses were used to describe rDNA repeat unit variation at differing taxonomic levels. A reverse similar 1200 bp fragment of the 28S rDNA sequence was assessed for its potential utility in reconstructing higher-level phylogenetic relationships in cockroaches. Parsimony and maximum likelihood analyses of these data strongly support the expected pattern of relationships among cockroach groups. The examined 5' end of the 28S rDNA is shown to be an informative marker for larger studies of cockroach phylogeny. Comparative analysis of the nucleotide sequences of the rDNA internal transcribed spacers (ITS1 and ITS2) among closely related species of Blattella and Periplaneta reveals that ITS sequences can vary widely in primary sequence, length, and folding pattern. Secondary structure estimates for the ITS region of Blattella species indicate that variation in this spacer region can also influence the folding pattern of the 5.8S subunit. These results support the idea that ITS sequences play an important role in the stability and function of the rRNA cluster.}, number={9}, journal={INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY}, author={Mukha, D and Wiegmann, BM and Schal, C}, year={2002}, month={Sep}, pages={951–960} }
 @article{collins_wiegmann_2002, title={Phylogenetic relationships and placement of the Empidoidea (Diptera : Brachycera) based on 28S rDNA and EF-1 alpha sequence}, volume={33}, ISSN={["1876-312X"]}, DOI={10.1163/187631202X00226}, abstractNote={Abstract The phylogenetic relationships within the Eremoneura (Empidoidea + Cyclorrhapha) have been controversial. The monophyly of the Empidoidea, as well as the position and rank of higher-level empidoid clades remains unresolved despite numerous analyses using morphological data. In addition, the origin of the Cyclorrhapha and their relationship to the Empidoidea continues to be debated. We present the results of a molecular phylogenetic analysis using nucleotide sequences collected from 28S ribosomal DNA (rDNA) and elongation factor-1α (EF-1α) genes. All currently recognized empidoid families and subfamilies, many lower cyclorrhaphan families (including Opetiidae), and several asiloid outgroups are represented in this study. Unweighted and weighted parsimony, as well as maximum likelihood analyses were applied to individual data partitions and a combined data set. Our results support the monophyly of both Empidoidea and Cyclorrhapha (including Opetia), as well as their sister-group relationship. Within Empidoidea we find support for the following: 1) Chvála's (1983) proposal to divide Empidoidea into five families; 2) Atelestidae as the basal empidoid lineage; and 3) monophyly of Microphoridae + Dolichopodidae.}, number={4}, journal={INSECT SYSTEMATICS & EVOLUTION}, author={Collins, KP and Wiegmann, BM}, year={2002}, pages={421–444} }
 @article{collins_wiegmann_2002, title={Phylogenetic relationships of the lower Cyclorrhapha (Diptera : Brachycera) based on 28S rDNA sequences}, volume={33}, ISSN={["1876-312X"]}, DOI={10.1163/187631202X00235}, abstractNote={Abstract Cyclorrhaphan Diptera are an extremely successful clade of ecologically and phylogenenetically important flies. Despite their significance the relationships among lower cyclorrhaphans ('Aschiza') remain controversial in spite of several morphologically based phylogenetic analyses. We sequenced a 2.7-kb fragment of 28S rDNA for taxa representing all lower cyclorrhaphan families (except Ironomyiidae), four schizophoran families, and seven empidoid out-group taxa. Phylogenetic analysis of these data strongly supports a monophyletic Cyclorrhapha (including the enigmatic taxon Opetia nigra) that is divided into two clades - a well-supported Eumuscomorpha (Syrphidae + Pipunculidae + Schizophora), and a weakly-supported Platypezoidea (all non-Eumuscomorpha). Consequently, the former grouping known as Aschiza, which included syrphids and pipunculids, is not a valid monophyletic clade. Within Platypezoidea, most of our analyses place Lonchopteridae as sister group to Opetiidae, and strongly support the monophyly of Sciadoceridae + Phoridae. Among the Eumuscomorpha we do not recover the monophyly of Syrphoidea (Syrphidae + Pipunculidae). Instead, all analyses place Pipunculidae as the sister group to Schizophora. This novel finding has never been proposed based on morphological data and will require more data (both molecular and morphological) and taxa to confirm.}, number={4}, journal={INSECT SYSTEMATICS & EVOLUTION}, author={Collins, KP and Wiegmann, BM}, year={2002}, pages={445–456} }
 @article{winterton_yang_wiegmann_yeates_2001, title={Phylogenetic revision of Agapophytinae subf.n. (Diptera : Therevidae) based on molecular and morphological evidence}, volume={26}, ISSN={["0307-6970"]}, DOI={10.1046/j.1365-3113.2001.00142.x}, abstractNote={Agapophytinae subf.n. is a highly diverse lineage of Australasian Therevidae, comprising eight described and two new genera: Agapophytus Guérin-Méneville, Acupalpa Kröber, Acraspisa Kröber, Belonalys Kröber, Bonjeania Irwin & Lyneborg, Parapsilocephala Kröber, Acatopygia Kröber, Laxotela Winterton & Irwin, Pipinnipons gen.n. and Patanothrix gen.n. A genus-level cladistic analysis of the subfamily was undertaken using sixty-eight adult morphological characters and c. 1000 base pairs of the elongation factor-1α (EF-1α) protein coding gene. The morphological data partition produced three most parsimonious cladograms, whereas the molecular data partition gave a single most parsimonious cladogram, which did not match any of the cladograms found in the morphological analysis. The level of congruence between the data partitions was determined using the partition homogeneity test (HTF) and Wilcoxon signed ranks test. Despite being significantly incongruent in at least one of the incongruence tests, the partitions were combined in a simultaneous analysis. The combined data yielded a single cladogram that was better supported than that of the individual partitions analysed separately. The relative contributions of the data partitions to support for individual nodes on the combined cladogram were investigated using Partitioned Bremer Support. The level of support for many nodes on the combined cladogram was non-additive and often greater than the sum of support for the respective nodes on individual partitions. This synergistic interaction between incongruent data partitions indicates a common phylogenetic signal in both partitions. It also suggests that criteria for partition combination based solely on incongruence may be misleading. The phylogenetic relationships of the genera are discussed using the combined data. A key to genera of Agapophytinae is presented, with genera diagnosed and figured. Two new genera are described: Patanothrix with a new species (Pat. skevingtoni) and Pat. wilsoni (Mann) transferred from Parapsilocephala, and Pipinnipons with a new species (Pip. kroeberi). Pipinnipons fascipennis (Kröber) is transferred from Squamopygia Kröber and Pip. imitans (Mann) is transferred from Agapophytus. Agapophytus bicolor (Kröber) is transferred from Parapsilocephala. Agapophytus varipennis Mann is synonymised with Aga. queenslandi Kröber and Aga. flavicornis Mann is synonymised with Aga. pallidicornis (Kröber).}, number={2}, journal={SYSTEMATIC ENTOMOLOGY}, author={Winterton, SL and Yang, LL and Wiegmann, BM and Yeates, DK}, year={2001}, month={Apr}, pages={173–211} }
 @article{mukha_sidorenko_lazebnaya_wiegmann_schal_2000, title={Analysis of intraspecies polymorphism in the ribosomal DNA cluster of the cockroach Blattella germanica}, volume={9}, ISSN={["0962-1075"]}, DOI={10.1046/j.1365-2583.2000.00175.x}, abstractNote={HindIII restriction digests of the rDNA repeat unit of the German cockroach, Blattella germanica, reveal significant intraspecies sequence polymorphism. This variability is probably caused by structural differences within the nontranscribed spacer regions (NTS) of the ribosomal repeat unit. HindIII rDNA fragment polymorphisms in three cockroach strains show that individuals from different populations may have different HindIII rDNA patterns, whereas individuals within populations exhibit relatively similar rDNA patterns. We suggest that HindIII restriction fragment polymorphisms within cockroach ribosomal DNA will be a valuable tool for measuring population-level parameters within and between natural cockroach populations.}, number={2}, journal={INSECT MOLECULAR BIOLOGY}, author={Mukha, DV and Sidorenko, AP and Lazebnaya, IV and Wiegmann, BM and Schal, C}, year={2000}, month={Apr}, pages={217–222} }
 @article{clements_wiegmann_sorenson_smith_neese_roe_2000, title={Genetic variation in the Myzus persicae complex (Homoptera : Aphididae): Evidence for a single species}, volume={93}, ISSN={["1938-2901"]}, DOI={10.1603/0013-8746(2000)093[0031:GVITMP]2.0.CO;2}, abstractNote={Journal Article Genetic Variation in the Myzus persicae Complex (Homoptera: Aphididae): Evidence for a Single Species Get access Kieran M Clements, Kieran M Clements Department of Entomology, North Carolina State University, Raleigh, NC 27695–7647 Search for other works by this author on: Oxford Academic Google Scholar Brian M Wiegmann, Brian M Wiegmann Department of Entomology, North Carolina State University, Raleigh, NC 27695–7647 Search for other works by this author on: Oxford Academic Google Scholar Clyde E Sorenson, Clyde E Sorenson Department of Entomology, North Carolina State University, Raleigh, NC 27695–7647 Search for other works by this author on: Oxford Academic Google Scholar Clyde F Smith, Clyde F Smith Department of Entomology, North Carolina State University, Raleigh, NC 27695–7647 Search for other works by this author on: Oxford Academic Google Scholar Paul A Neese, Paul A Neese Department of Entomology, North Carolina State University, Raleigh, NC 27695–7647 Search for other works by this author on: Oxford Academic Google Scholar R Michael Roe R Michael Roe Department of Entomology, North Carolina State University, Raleigh, NC 27695–7647. To whom correspondence should be addressed: Dearstyne Entomology Building, Box 7647, W. Ligon Street Extension, North Carolina State University, Raleigh, NC 27695-7647. Fax: 919-515-4325, michael_roe@ncsu.edu Search for other works by this author on: Oxford Academic Google Scholar Annals of the Entomological Society of America, Volume 93, Issue 1, 1 January 2000, Pages 31–46, https://doi.org/10.1603/0013-8746(2000)093[0031:GVITMP]2.0.CO;2 Published: 01 January 2000 Article history Accepted: 06 July 1999 Published: 01 January 2000}, number={1}, journal={ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA}, author={Clements, KM and Wiegmann, BM and Sorenson, CE and Smith, CF and Neese, PA and Roe, RM}, year={2000}, month={Jan}, pages={31–46} }
 @article{clements_sorenson_wiegmann_neese_roe_2000, title={Genetic, biochemical, and behavioral uniformity among populations of Myzus nicotianae and Myzus persicae}, volume={95}, ISSN={["1570-7458"]}, DOI={10.1046/j.1570-7458.2000.00666.x}, abstractNote={Prior to designation as distinct species, an appellation presently in question, the tobacco aphid, Myzus nicotianae Blackman (Homoptera: Aphididae), was classified as a tobacco-feeding form of the green peach aphid, Myzus persicae (Sulzer). In this study, RAPD polymorphisms distinguished members of the Myzus persicae complex (M. persicae and M. nicotianae) from three outgroup Myzus species (M. cerasi (F.), M. hemerocallis Takahashi, and M. varians Davidson). Polymorphisms within the complex did not separate populations on the basis of host association (tobacco versus other host plants) or geographic origin (collections from the United States, Europe, and Japan). Similarly, while GC-MS analysis of cuticular hydrocarbon profiles revealed both developmental and inter-populational differences within the M. persicae complex, it did not separate populations of tobacco feeding aphids from those collected off non-tobacco hosts. Finally, with the exception of their responses to a choice between lettuce and collards, the host preference behavior of a green peach aphid population, a red tobacco aphid population, and a green tobacco aphid population was indistinguishable in host preference experiments. These results add to a growing body of evidence suggesting M. nicotianae and M. persicae are conspecific.}, number={3}, journal={ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA}, author={Clements, KM and Sorenson, CE and Wiegmann, BM and Neese, PA and Roe, RM}, year={2000}, month={Jun}, pages={269–281} }
 @article{yang_wiegmann_yeates_irwin_2000, title={Higher-level phylogeny of the Therevidae (Diptera : Insecta) based on 28S ribosomal and elongation factor-1 alpha gene sequences}, volume={15}, ISSN={["1095-9513"]}, DOI={10.1006/mpev.1999.0771}, abstractNote={Therevidae (stilleto flies) are a little-known family of asiloid brachyceran Diptera (Insecta). Separate and combined phylogenetic analyses of 1200 bases of the 28S ribosomal DNA and 1100 bases of elongation factor-1alpha were used to infer phylogenetic relationships within the family. The position of the enigmatic taxon Apsilocephala Kröber is evaluated in light of the molecular evidence. In all analyses, molecular data strongly support the monophyly of Therevidae, excluding Apsilocephala, and the division of Therevidae into two main clades corresponding to a previous classification of the family into the subfamilies Phycinae and Therevinae. Despite strong support for some relationships within these groups, relationships at the base of the two main clades are weakly supported. Short branch lengths for Australasian clades at the base of the Therevinae may represent a rapid radiation of therevids in Australia.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Yang, LL and Wiegmann, BM and Yeates, DK and Irwin, ME}, year={2000}, month={Jun}, pages={440–451} }
 @article{scheffer_wiegmann_2000, title={Molecular phylogenetics of the holly leaf miners (Diptera : Agromyzidae : Phytomyza): Species limits, speciation, and dietary specialization}, volume={17}, ISSN={["1095-9513"]}, DOI={10.1006/mpev.2000.0830}, abstractNote={A molecular phylogenetic analysis was conducted to determine relationships and to investigate character evolution in the Phytomyza ilicis group of leafmining flies on hollies (Aquifoliaceae: Ilex). A total of 2207 bp of the mitochondrial cytochrome oxidase I and II genes were sequenced for all known holly leafminers, as well as for several undescribed members of this group. Maximum-parsimony analysis of the sequence data indicates that these leafminers form a monophyletic group with the inclusion of an undescribed leafminer that feeds on the distantly related plant Gelsemium sempevirens (Loganiaceae). Species boundaries of previously known and of undescribed holly leafmining species were confirmed with the molecular data, with one exception. Optimization of variable ecological and morphological characters onto the most parsimonious phylogeny suggests that these traits are evolutionarily labile, requiring multiple instances of convergence and/or reversal to explain their evolutionary history. Speciation in holly leafminers is associated with host shifts and appears to involve colonization of new hosts more often than cospeciation as the hosts diverge. Monophagy is the most common feeding pattern in holly leafminers, and more generalized feeding is inferred to have evolved at least two separate times, possibly as a prelude to speciation.}, number={2}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Scheffer, SJ and Wiegmann, BM}, year={2000}, month={Nov}, pages={244–255} }
 @article{wiegmann_tsaur_webb_yeates_cassel_2000, title={Monophyly and relationships of the Tabanomorpha (Diptera : Brachycera) based on 28S ribosomal gene sequences}, volume={93}, ISSN={["1938-2901"]}, DOI={10.1603/0013-8746(2000)093[1031:MAROTT]2.0.CO;2}, abstractNote={Higher-level relationships among the earliest lineages of brachyceran Diptera remain poorly resolved by comparative morphology. Nucleotide sequence data should be useful in clarifying brachyceran relationships, especially where morphological evidence is either contradictory or controversial. We examined phylogenetic relationships among the family-level taxa of the brachyceran infraorder Tabanomorpha using sequences of a large portion of the 28S ribosomal DNA. Twenty-five species were sequenced, including five outgroup species from the Stratiomyomorpha and Xylophagomorpha. Parsimony and maximum likelihood-based phylogenetic analysis of 2,371 alignable sites yielded identical inferred tree topologies. 28S rDNA supports the monophyly of the Tabanomorpha (Vermileonidae, Rhagionidae, Pelecorhynchidae, Athericidae and Tabanidae). Our results contradict several published hypotheses that associate Vermileonidae with asiloid or eremoneuran taxa remote from the Tabanomorpha. The molecular data also support monophyly for all of the included family-level lineages, and corroborate several recent phylogenetic hypotheses based on comparative morphology.}, number={5}, journal={ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA}, author={Wiegmann, BM and Tsaur, SC and Webb, DW and Yeates, DK and Cassel, BK}, year={2000}, month={Sep}, pages={1031–1038} }
 @misc{wiegmann_mitter_regier_friedlander_wagner_nielsen_2000, title={Nuclear genes resolve Mesozoic-aged divergences in the insect order Lepidoptera}, volume={15}, ISSN={["1095-9513"]}, DOI={10.1006/mpev.1999.0746}, abstractNote={Compared to the number of genes available for study of both younger and older divergences, few genes have yet been identified that can strongly resolve phylogenetic splits of Mesozoic age ( approximately 65-250 mya). Thus, reconstruction of Mesozoic-age phylogenies, exemplified by basal divergences within the major orders of holometabolous insects, is likely to be especially dependent on combining multiple lines of evidence. This study tests the potential of the 18S ribosomal RNA gene for reconstructing Mesozoic-aged divergences within the insect order Lepidoptera and its ability when combined with a second, previously analyzed nuclear gene (phosphoenolpyruvate carboxykinase, PEPCK) to strongly resolve these relationships. 18S sequences were obtained for 21 taxa, representing major clades of Lepidoptera plus outgroups from the other "panorpoid orders. A well-corroborated morphology-based "test phylogeny was used to evaluate the effects of partitioning the 18S gene according to variable versus conserved domains, paired versus unpaired sites in the secondary structure, and transition versus transversion substitutions. Likelihood and unweighted parsimony analyses of the 18S data recover the "test phylogeny" almost completely, with no improvement of agreement or support provided by any form of weighting or partitioning. No conflict in signal between 18S and PEPCK was detected by the partition homogeneity test. Combined parsimony analysis yielded strong bootstrap support for nearly all relationships, much higher than for either gene alone, thereby also providing strong evidence on several hypotheses about the early evolution of lepidopteran-plant interactions. These genes in combination may be widely useful for resolving insect divergences of comparable age.}, number={2}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Wiegmann, BM and Mitter, C and Regier, JC and Friedlander, TP and Wagner, DM and Nielsen, ES}, year={2000}, month={May}, pages={242–259} }
 @article{cryan_wiegmann_deitz_dietrich_2000, title={Phylogeny of the treehoppers (Insecta : Hemiptera : Membracidae): Evidence from two nuclear genes}, volume={17}, ISSN={["1055-7903"]}, DOI={10.1006/mpev.2000.0832}, abstractNote={We present a molecular systematic investigation of relationships among family-group taxa of Membracidae, comprising nearly 3.5 kb of nucleotide sequence data from the nuclear genes elongation factor-1alpha (EF-1alpha: 958 bp) and 28S ribosomal DNA (28S rDNA: 2363 bp); data partitions are analyzed separately and in combination for 79 taxa. Analysis of the combined sequence data provided a better-resolved and more robust hypothesis of membracid phylogeny than did separate analyses of the individual genes. Results support the monophyly of the family Membracidae and indicate the presence of two major lineages (Centrotinae + Stegaspidinae + Centrodontinae and Darninae + Membracinae + Smiliinae). Within Membracidae, molecular data support the following assertions: (1) the previously unplaced genera Antillotolania and Deiroderes form a monophyletic group with Microcentrini; (2) Centrodontini and Nessorhinini are monophyletic clades that arise independently from within the Centrotinae; (3) Centrotinae is paraphyletic with respect to Centrodontinae; (4) the subfamily Membracinae is monophyletic and possibly allied with the darnine tribe Cymbomorphini; (5) the subfamily Darninae is paraphyletic; (6) the subfamily Smiliinae is paraphyletic, with molecular evidence indicating the exclusion of Micrutalini and perhaps Acutalini and Ceresini; and (7) Membracidae arose and diversified in the New World with multiple subsequent colonizations of the Old World. Our phylogenetic results suggest that morphology-based classifications of the Membracidae need to be reevaluated in light of emerging molecular evidence.}, number={2}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Cryan, JR and Wiegmann, BM and Deitz, LL and Dietrich, CH}, year={2000}, month={Nov}, pages={317–334} }
 @article{castrillo_wiegmann_brooks_1999, title={Genetic variation in Beauveria bassiana populations associated with the darkling beetle, Alphitobius diaperinus}, volume={73}, ISSN={["0022-2011"]}, DOI={10.1006/jipa.1998.4835}, abstractNote={A study was conducted to assess genetic variation within and among populations of Beauveria bassiana (Deuteromycotina: Hyphomycetes) associated with the darkling beetle, Alphitobius diaperinus (Coleoptera: Tenebrionidae), using RAPD markers. A hierarchical collection of samples (strains from the same insect specimen, from insects from the same location, and from insects from different locations) was obtained from infected beetles from North Carolina (NC) and West Virginia (WV), USA. Ten primers resolved 81 strains into 80 distinct multiband phenotypes reflecting the substantial amount of variation that was present. Variation present within populations was evident not only in the separation of each strain as a distinct multiband phenotype but also in the separation of strains within a population into separate clusters. Among populations, a group sharing more than 89% similarity was observed among all the strains from Martin Co. and Greene Co., NC and 61% of the strains collected from WV. Some genetic differentiation was present among the other populations but the separation was not distinct with a few strains from some populations showing greater affinity to strains from other collection sites.}, number={3}, journal={JOURNAL OF INVERTEBRATE PATHOLOGY}, author={Castrillo, LA and Wiegmann, BM and Brooks, WM}, year={1999}, month={May}, pages={269–275} }