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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Systematic Entomology Laboratory » Research » Research Project #430068

Research Project: Systematics of Flies of Importance in Agroecosystems and the Environment

Location: Systematic Entomology Laboratory

2020 Annual Report

ARS is interested in performing research to increase and enhance understanding of the systematics of flies (Diptera) important to agriculture and the environment, especially fruit flies, leaf-mining flies, tachinid flies. We will develop new identification tools (descriptions, diagnoses, molecular markers, illustrations, keys and computer identification systems), determine the correct names of species and higher taxa, and elucidate the relationships (phylogeny) and classification of select groups of these flies, which include invasive crop pests, parasitoids of plant pests, and potential biological control agents for weeds. The objectives of our project are: 1) Investigate the taxonomy and natural history of fruit flies; analyze species concepts, develop diagnoses, descriptions, illustrations and identification tools, biosystematic databases, determine host plants, and analyze phylogenetic relationships; 2) Conduct molecular systematic and ecological analysis of pest leaf-mining, galling, and fruit flies, and their parasitoids, including sequencing of DNA of previously unstudied species, development of diagnostic tools, discovery of possible cryptic species and host races, and analysis of phylogenetic relationships; 3) Investigate taxonomy of tachinid flies and other higher flies; analyze species concepts, develop diagnoses, descriptions, illustrations and identification keys, and analyze phylogenetic relationships; and 4) Provide scientific identifications of plant-feeding and other agriculturally important flies.

ARS will undertake research to generate morphological and molecular characters (DNA sequences) that will be used to test species concepts and hypotheses of relationship among agriculturally important flies and parasitoid wasps that attack them. These data also will be used to develop new diagnostic tools (descriptions, illustrations, keys) to permit more rapid and accurate identification of these flies and wasps. Databases containing scientific names, distributions, taxonomic literature, and host plant and specimen data pertaining to fruit flies will be expanded and disseminated to the user community. These and other taxonomic tools will be made accessible to the public via publications, the internet, and other electronic media. Timely and accurate identifications of flies will be provided, including those intercepted at ports-of-entry by APHIS-PPQ or submitted by a wide range of scientists and regulatory agencies, and portions of the National Collection in the National Museum of Natural History, a vital tool for research and identification, will be maintained and expanded.

Progress Report
The current project 8042-22000-292-00D will end September 30, 2020. The new project will build on the goals and accomplishments of the outgoing project and is currently finishing up NP304 OSQR review, with the continuing objectives of protecting U.S. and global agriculture from the damaging effects of plant-feeding flies. Taxonomy and natural history of fruit flies. Research on the taxonomy of Anastrepha, the largest and most economically important group of fruit flies in the American tropics, included description of 28 species previously unknown to science and the immature stages of three species, new distribution and taxonomic data for 60 species (including first records of 33 species from Colombia), incorporation of the group including the papaya fruit fly (previously known as Toxotrypana), further development of an online identification tool for the more than 350 species of this group, and collection of thousands of samples from Brazil, Ecuador, Peru and Suriname for DNA analysis. A molecular analysis of the evolutionary relationships within Anastrepha, based on 6 DNA regions and 159 species, new molecular markers for Caribbean fruit fly and cryptic species in the South American fruit fly complex, and analysis of DNA barcodes for diagnosis of 74 species, were published. More than 1000 new DNA barcodes were newly sequenced and a library of more than 1900 sequences for 260 species was compiled, verified and reanalyzed. Anchored hybrid enrichment was investigated to generate hundreds of loci of DNA data for 90 species. Additional species were described in other groups of fruit flies that includes pests of apple, cherries, blueberries, tomato and eggplant, and new host and distribution data for other species were published. A host plant list for the apple maggot fly was developed in collaboration with APHIS. A small group of fruit flies (including 3 new species) feeding on flowers in the sunflower family was taxonomically revised, and relationships were analyzed for the group including the sunflower stem maggot. Two studies of the fly biodiversity in Costa Rica and a checklist of the largest and most economically important group of fruit flies in Africa, Asia and Australia were published. Names, distribution and host plant databases for fruit flies were expanded to include more than 77,000 total records and a portal on the Animal and Plant Health Inspection Service (APHIS_- Center for Plant Health Science and Technology (CPHST) web site to make these data accessible was designed and implemented. This information is critical to APHIS-PPQ and other regulatory agencies to prevent the spread of pest species into the U.S. Molecular systematic and ecological analyses of Blephanoneura fruit flies. In order to explore the roles of host-associated versus geographical divergence within species, population structure in six Blephanoneura fruit fly species was assessed using nuclear DNA markers. Flies were collected from up to five hosts in as many as seven South American countries. Both geographic and host-associated divergence was present in most species. Phylogenetic analysis of more than 59 species found a greater effect of geography on divergence and speciation than did host plant use. To determine fly-wasp associations reared from host plants, a novel method based on taxon-specific priming for mitochondrial DNA barcode genes was developed. This method allows for simultaneous amplification of both fly and parasitoid DNA of different sizes and has been previously used with Sanger sequencing to obtain specimen identifications in the lab. Application of this method for use under field conditions was explored using a MinION next-generation DNA sequencer. Primer design included index sequences to allow for individual identification following extensive multiplexing during polymerase chain reaction (PCR). Field testing of the methods was carried out at a primitive field station in Ecuador (i.e., a dining room in a rainforest). These protocols potentially provide a new and rapid approach to mass identifications of pests and other insects. They will be useful to a variety of systematists, ecologists, and evolutionary biologists as well as to APHIS-Plant Protection Quarantine (PPQ) and other regulatory agencies working to prevent the spread of pest species into the U.S. Taxonomy and Natural History of Leafmining and Galling Flies. Information on the host-use, resistance status, and global spread of Liriomyza huidobrensis, a highly invasive and damaging leafminer, was compiled. This species has invaded more than 30 countries and is known from 365 host plants in 49 families. Analysis of genetic variation among 380 L. huidobrensis specimens from 14 countries determined the geographic source of the invasive populations and found no evidence for host-associated structure. Species limits, host specificity, and molecular population structure were assessed in 12 Phytomyza leafminers of hollies, including species on ornamental hollies: American holly, dahoon, yaupon, winterberry, possumhaw, and inkberry. Leafminers were reared from several hundred collecting events across 17 U.S. states, resulting in new host and distribution records based on 1527 identified flies. Host plant-associated genetic structure in P. glabricola which feeds on two holly plant species was assessed using mitochondrial and nuclear DNA markers. All molecular markers showed evidence of host-associated divergence, and amplified fragment length polymorphism data suggested the involvement of host-associated natural selection. Host associated genetic structure based on mitochondrial DNA was also found in the holly leafminers P. ilicicola and P. verticillatae. Phylogeny of Fergusonina galling flies was constructed from one mitochondrial and two nuclear genes from 203 specimens and the evolution of host plant associations was investigated in terms of hypotheses of cospeciation, host tracking, and repeated colonization. Patterns of fly diversity were compared with that of their nematode obligate mutualists. These result on leafmining and galling flies will be of interest to pest managers, ecologists, and evolutionary biologists. Taxonomy of tachinid flies and other higher flies [The scientist responsible for this objective retired in 2016 and the position is vacant]. New material of Belvosia (tachinid flies) from Guanacaste received from collaborator Dan Janzen has been added to the research collection, sorted to morphospecies, and DNA barcoded. Historical type material of Belvosia has been examined, primarily from the Smithsonian, British Museum, and Vienna Natural History Museum, and compared with Guanacaste species. Type material of all known species of the soldier fly genus Arcuavena (soldier flies) has been examined and compared with assembled research material. A species of tachinid fly, Strongygaster triangulifera, was identified as a parasitoid of the invasive kudzu bug, Megacopta cribraria, that damages soybeans and other legume crops. It may be studied as a possible biocontrol agent. A new species of Lixophaga (tachinid fly) was described from Colombia that is a parasitoid of the tomato fruit borer, Neoleucinodes elegantalis. It is another potential biocontrol agent. Fly Identifications October 1, 2015 to May 13, 2020, 4,503 submittals (12,804 specimens) were identified, including 1,941 "urgent" submittals for USDA-APHIS-PPQ of specimens intercepted on perishable commodities at ports-of-entry.

1. Fruit fly databases on the USDA compendium of fruit fly host information. ARS scientists cooperated with APHIS-CPHST staff to develop the Fruit Fly Databases on the USDA Compendium of Fruit Fly Host Information site (, which comprise extensive databases on the names, distributions, and host plants of the more than 5000 species of true fruit flies of the world. These databases now include more than 11,900 name, 37,000 host plant, and 28,000 distribution records. Search options were provided to make available the name, distribution and host information, which is critical for quarantine regulations and trade decisions made by APHIS and other regulatory agencies, and to other scientists who study fruit flies.

Review Publications
Steck, G.J., Rodriguez, E.J., Norrbom, A.L., Dutra, V., Ronchi-Teles, B., Silva, J.G. 2019. Review of Anastrepha (Diptera: Tephritidae) immature stage taxonomy. Book Chapter. 57-88.
Liquido, N.J., Mcquate, G.T., Suiter, K.A., Norrbom, A.L., Yee, W.L., Chang, C.L. 2019. Compendium of fruit fly host plant information: The USDA primary reference in establishing fruit fly regulated host plants. Book Chapter. 363-368.
Konstantinov, A.S., Linzmeier, A.M., Morais Ana Carla, C., Palmer, M.W., Scheffer, S.J., Lewis, M.L. 2019. A discovery of the first Nearctic moss-eating flea beetle, Distigmoptera borealis Blake, 1943 (Coleoptera: Chrysomelidae: Galerucinae: Alticini). The Coleopterists Bulletin. 73(3):599-610.