@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{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{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} }