Systematics of Flies of Importance in Agroecosystems and the Environment

Goals / Objectives
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.

Project Methods
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 10/01/15 to 09/30/20

Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. 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. Accomplishments 01 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 (coffhi.cphst.org/), 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.

Impacts
(N/A)

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.

Progress 10/01/18 to 09/30/19

Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. Taxonomy and natural history of fruit flies. Accomplishments on the taxonomy of the largest and most economically important group of fruit flies in the American tropics (Anastrepha) included the following: publication of research justifying the inclusion of a group of derived species (previously known as Toxotrypana), including the papaya fruit fly; further development of an electronic identification tool for the more than 350 species of this group; preparation for publication of a large data set of DNA sequences (including more than 1900 COI sequences from 260 species); sequencing by anchored hybrid enrichment of hundreds of loci of 90 species of Anastrepha (to be analyzed for species diagnosis and phylogenetic relationships); and collection of thousands of additional samples for DNA analysis. A revision of the taxonomy of a small group of fruit flies feeding on flowers in the sunflower family was published. Data from additional publications were added to names, host plant, and distribution databases for fruit flies, and the Animal and Plant Health Inspection Service (APHIS)-Center for Plant Health Science and Technology (CPHST) web site serving this information was enhanced. This information is critical to APHIS-Plant Health Quarantine (PPQ) and other regulatory agencies to prevent the spread of pest species into the U.S. Molecular systematic and ecological analysis of plant-feeding flies and their parasitoids. Taxon-specific primers were designed for mitochondrial DNA barcode genes in true fruit flies (Blepharoneura) that breed in relatives of pumpkins, cucumbers and squash, and for Bellopius braconid and other wasp parasitoids attacking the flies. Barcode data were collected with a MinION next-generation DNA sequencer, a device using novel technologies to allow the collection of hundreds of long-read sequence data. Primer design included a number of index sequences to allow for individual identification following extensive multiplexing during polymerase chain reaction (PCR). This technology results in a greater amount of data more quickly and more cheaply than is possible with traditional Sanger sequencing. Novel protocols were designed and tested to allow this equipment to be used in remote or poorly equipped locations. These newly developed methods provide a new and rapid approach to mass identifications of pests and other insects. They will be of great interest to a variety of systematists, ecologists, and evolutionary biologists as well as to APHIS-PPQ and other regulatory agencies working to prevent the spread of pest species into the U.S. Taxonomy of tachinid flies and other higher flies. The scientist responsible for this objective retired and the position is vacant. Scientific identification of agriculturally important flies. In the period from October 1, 2018 to May 22, 2019, 220 submittals (805 specimens) were identified, including 155 "urgent" submittals for USDA- APHIS-PPQ of specimens intercepted on perishable commodities at ports-of- entry. Accomplishments 01 Protecting American agriculture from pest fruit flies. True fruit flies include some of the most important pests of commercial fruits. Of the 5000+ currently known species, more than 100 are agricultural pests, attacking commercial and subsistence crops including citrus, mango, peach, apple, and many others. Many species are invasive and threaten U. S. agriculture, including the papaya fruit fly, which is invasive in Florida. A new publication improved the classification of these flies. The papaya fruit fly and six closely related species were previously classified in a separate genus, Toxotrypana, but our recent investigation of their evolutionary relationships showed that they are actually derived species of Anastrepha, the largest and most economically important genus in the American tropics and subtropics. A new publication formally transferred these species, and a petition to the International Commission of Zoological Nomenclature was submitted to validate this action. Normally, the older name (in this case, Toxotrypana) would be adopted for all species, but due to the much greater economic significance of other species of Anastrepha, such action would cause great confusion in scientific communication regarding these flies. This new information already is being used by USDA-APHIS and other regulatory agencies and is being incorporated into an online identification system for these flies.

Impacts
(N/A)

Publications

Scheffer, S.J., Lonsdale, O. 2018. A survey of Agromyzidae (Diptera) reared from leafmines on Long Island, New York; host associations, distribution data, and the description and host association of a new species. Zootaxa. 4450(1):77-90.
Savaris, M., Norrbom, A.L., Marinoni, L., Lampert, S. 2019. Revision of the genus Euarestoides Benjamin (Diptera: Tephritidae). Zootaxa. 4551:299- 329.
Norrbom, A.L., Barr, N., Kerr, P.H., Mengual, X. 2018. Case 3772 ⿿ Anastrepha Schiner, 1868 (Insecta, Diptera, TEPHRITIDAE): Proposed precedence over Toxotrypana Gerstaecker, 1860. The Bulletin of Zoological Nomenclature. 75:165-169.
Norrbom, A.L., Barr, N., Kerr, P.H., Mengual, X., Nolazcon Alvarado, N., Rodriquez, E.J., Steck, G.J., Sutton, B.D., Uramoto, K., Zucchi, R.A. 2018. Synonymy of toxotrypana gerstaecker with anastrepha schiner (Diptera: Tephritidae). Proceedings of the Entomological Society of Washington. 12:834-841.

Progress 10/01/17 to 09/30/18

Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. Taxonomy and natural history of fruit flies. Accomplishments on the taxonomy of the largest and most economically important group of fruit flies (Anastrepha) in the American tropics included publication of new molecular markers to distinguish multiple pest species, publication of new distribution and taxonomic data for 60 species (including first records of 33 species from Colombia), description of the immature stages of three species, further development of an electronic identification tool for the more than 300 species of this group, and collection of thousands of additional samples for DNA analysis. Two studies of the fly biodiversity in Costa Rica were published. A checklist of the largest and most economically important group of fruit flies in Africa, Asia and Australia was published. Data from additional publications were added to names and host plant databases for fruit flies, and progress was made to serve this information on an APHIS-CPHST web site. 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 analysis of pest leaf-mining, galling, and fruit flies, and their parasitoids. Additional primers necessary for DNA sequencing were designed for both mitochondrial and nuclear genes in a variety of plant-feeding groups of flies and their associated parasitoids. These specialized primers have been designed for leaf-mining flies (Liriomyza, Phytomyza) that are pests of fruit and vegetables, fruit flies (Blepharoneura) that breed in relatives of pumpkins, cucumbers and squash, and for braconid and other wasp parasitoids attacking these groups. Molecular analysis of the evolutionary radiation of fruit flies (Blepharoneura) was published. Data collection continued on genetic variation and distribution of globally invasive leaf-mining pests (Liriomyza) of vegetable crops in order to better understand species limits, ecological interactions, and host ranges of the plant pests and their parasitoids. This information is critical to effective management of pest populations as well as to APHIS- PPQ and other regulatory agencies working to prevent the spread of pest species into the U.S. Taxonomy of tachinid flies and other higher flies. The scientist responsible for this objective retired and the position is vacant. Scientific identification of agriculturally important flies. In the period from October 1, 2017 to June 13, 2018, 2,012 submittals (7,690 specimens) were identified, including 405 "urgent" submittals for USDA- APHIS-PPQ of specimens intercepted on perishable commodities at ports-of- entry. Accomplishments 01 Protecting American agriculture from pest fruit flies. True fruit flies include some of the most important pests of commercial fruits. Of the 5000+ currently known species, more than 100 are agricultural pests, attacking commercial and subsistence crops including citrus, mango, peach, apple, and many others. Many species are invasive and threaten U. S. agriculture. Current identification capabilities are based mainly on adult morphology, sometimes of only one sex, and the larvae, the stage most commonly intercepted at ports of entry, are difficult if not impossible to identify. Scientists from USDA-ARS Beltsville, Maryland, USDA-APHIS-CPHST, Department of Agriculture from California and Florida, several universities, and international collaborators are working to develop new diagnostic tools to more rapidly and reliably identify all life stages of fruit flies, by studying the morphology and DNA of the adults and larvae demonstrated the utility and limits of DNA barcodes (a particular DNA region commonly used for identification) as a diagnostic tool. Four major pest species can be identified using DNA barcodes, but other pests cannot be distinguished. This new information already is being used by USDA to identify specimens captured in detection programs and at ports of entry and is extremely valuable to regulatory agencies such as APHIS-PPQ in limiting the spread of fruit fly pests.

Impacts
(N/A)

Publications

Borkent, A., Brown, B.V., Adler, P.H., Desouza Amorim, D., Barber, K., Bickel, D., Boucher, S., Brooks, S.E., Burger, J., Capellari, R.S., Costa, D.N., Cumming, J.M., Curler, G., Dick, C.W., Epler, J.H., Fisher, E., Gaimari, S.D., Gelhaus, J., Grimaldi, D.A., Hash, J., Hippa, H., Ib��ez- Bernal, S., Jaschhof, M., Kameneva, E.P., Kvifte, G.M., Lonsdale, O., Marshall, S.A., Mathis, W., Michelsen, V., Naglis, S., Norrbom, A.L., Pape, T., Pereira-Colavite, A., Pollet, M., Runyon, J.B., Savage, J., Silva, V. C., Sinclair, B.J., Swann, J., Vilkamaa, P., Whitworth, T., Woodley, N., Zavortink, T.J., Zumbado, M.A. 2018. Remarkable fly (Diptera) diversity in a patch of Costa Rican cloud forest: Why inventory is a vital science. Zootaxa. 4402:53-90.
Gagne, R.J., Ley-Lopez, J.M., Hanson, P.E. 2018. First new world record of a gall midge from palms: a new species of Contarinia (Diptera: Cecidomyiidae) from Geonoma cuneata in Costa Rica. Proceedings of the Entomological Society of Washington. 120(1):51-61.
Brown, B.V., Borkent, A., Alder, P.H., Amorim, D., Barber, K., Bickel, D., Boucher, S., Brooks, S.E., Burger, J., Burington, Z.L., Capellari, R.S., Costa, D.R., Cumming, J.M., Curler, G., Dick, C.W., Epler, J.H., Fisher, E. , Gaimari, S.D., Gelhaus, J., Grimaldi, D.A., Hash, J., Hauser, M., Hippa, H., Ibanez-Bernal, S., Jaschhof, M., Kameneva, E.P., Hash, J., Hauser, M., Kerr, P.H., Kormeyev, V., Korytkowski, C.A., Kung, G., Kvifte Mikalsen, G., Lonsdale, O., Marshall, S.A., Mathis, W., Michelsen, V., Naglis, S., Norrbom, A.L., Paiero, S., Pape, T., Pereira-Colavite, A., Pollet, M., Rochefort, S., Rung, A., Runyon, J.B., Savage, J., Silva, V.C., Sinclair, B.J., Skevington, J.H., Stireman, J.O., Swann, J., Vilkamaa, P., Wheeler, T., Whitworth, T., Wong, M., Wood, D., Woodley, N., Yau, T., Zavortink, T. J., Zumbado, M.A. 2018. First comprehensive inventory of a tropical site for a megadiverse group of insects, the true flies (Diptera). Communications Biology. 2018(1):1-21.
Doorenweerd, C., Leblanc, L., Norrbom, A.L., San Jose, M., Rubinoff, D. 2018. A global checklist of the 933 fruit fly species in the tribe Dacini (Diptera: Tephritidae). ZooKeys. 730:17-54.
Gagne, R.J. 2018. Key to adults of North American genera of the subfamily Cecidomyiinae (Diptera: Cecidomyiidae). Zootaxa. 4392(3):401-457.
Barr, N., Ruiz-Arce, R., Farris, R., Silva, J.G., Lima, K., Dutra, V., Ronchi-Teles, B., Kerr, P.H., Norrbom, A.L., Nolazco, A.N., Thomas, D.B. 2017. Identifying seven Anastrepha (Diptera; Tephritidae) species using DNA barcodes. Journal of Economic Entomology. 111:405-421.
Dutra, V., Ronchi-Teles, B., Steck, G.L., Rodriguez, E.J., Norrbom, A.L., Sutton, B.D., Silva, J.G. 2018. Description of third instar larvae of Anastrepha curitis, Anastrepha pickeli and Anastrepha pulchra (Diptera: Tephritidae). Annals of the Entomological Society of America. 120:9-24.
Rodriguez Clavijo, P.A., Norrbom, A.L., Arevalo, E., Balseiro, T.F., Diaz, P., Paula, A., Montes, J., Benitez, M., Cruz, M., Rodriguez, E.J., Steck, G.J., Sutton, B.D., Quisberth, E., Lagrava Sanchez, J.J., Colque, F. 2018. New records of Anastrepha (Diptera: Tephritidae) primarily from Colombia. Zootaxa. 4390(1):1-63.
Winkler, I., Scheffer, S.J., Lewis, M.L., Ottens, K.J., Rasmussen, A.P., Gomes-Costa, G.A., Huerto Santillan, L.M., Condon, M.A., Forbes, A.A. 2018. Anatomy of an adaptive radiation: Blepharoneura fruit flies. BMC Evolutionary Biology. 18:30-33.
Martinez-Alva, J.O., Sema, F., Norrbom, A.L. 2017. New records of Rhagoletis (Diptera: Tephritidae) in Colombia, with discussion on the morphological variations of some species. Zootaxa. 4273:549-558.

Progress 10/01/16 to 09/30/17

Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. Taxonomy and natural history of fruit flies. Accomplishments on the taxonomy of Anastrepha, the largest and most economically important group of fruit flies in the American tropics, included: publication of new molecular markers to distinguish the Caribbean fruit fly, publication of new distribution, host plant, and taxonomic data for two species in Brazil, further development of an electronic identification tool for the nearly 300 species of this group, and collection of additional samples for DNA analysis. A molecular analysis of the evolutionary relationships within Anastrepha, based on 6 DNA regions and 159 species, was published. Additional new information was published for species in another group of fruit flies that includes pests of apple, cherries, blueberries, tomato and eggplant, and a host plant list for the apple maggot fly was developed in collaboration with APHIS. Data from additional publications were added to names and host plant databases for fruit flies, and progress was made to serve this information on an APHIS-CPHST web site. 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 analysis of pest leaf-mining, galling, and fruit flies, and their parasitoids. Primers necessary for DNA sequencing were designed for both mitochondrial and nuclear genes in a variety of plant-feeding groups of flies and their associated parasitoids. Specifically, these specialized primers have been designed for leaf- mining flies (Liriomyza, Phytomyza) that are pests of fruit and vegetables, fruit flies (Blepharoneura) that breed in pumpkins and relatives (Cucurbitaceae), and for braconid and other wasp parasitoids attacking these groups. Molecular analysis of ecological associations and host-specificity in parasitoids attacking holly leaf-mining flies was completed. Data collection is continuing on leaf-mining pests and related groups in order to better understand species limits, ecological interactions, and host ranges of the plant pests and their parasitoids. This information is critical to effective management of pest populations as well as to APHIS-PPQ and other regulatory agencies working to prevent the spread of pest species into the U.S. Taxonomy of tachinid flies and other higher flies. The scientist responsible for this objective retired and the position is vacant. Scientific identification of agriculturally important flies. In the period from October 1, 2016 to June 16, 2017, 842 submittals were identified, including 509 "urgent" submittals for USDA-APHIS-PPQ of specimens intercepted on perishable commodities at ports-of-entry. Accomplishments 01 Protecting American agriculture from pest fruit flies. True fruit flies include some of the most important pests of commercial fruits. Of the 5000+ currently known species, more than 100 are agricultural pests, attacking commercial and subsistence crops including citrus, mango, peach, apple, and many others. Many species are invasive and threaten U. S. agriculture. Current identification capabilities are based mainly on adult morphology, sometimes of only one sex, and the larvae, the stage most commonly intercepted at ports of entry, are difficult if not impossible to identify. Scientists from USDA-ARS, USDA-APHIS-CPHST, Departments of Agriculture from California and Florida, several universities, and international collaborators are working to develop new diagnostic tools to more rapidly and reliably identify all life stages of fruit flies, by studying the morphology and DNA of the adults and larvae. A new study of evolutionary relationships within the largest group of fruit flies in the Americas, including pests like the Mexican, West Indian, South American and Caribbean fruit flies, provides a framework for ongoing diagnostic studies and significantly builds the data library of DNA sequences critical to reliable identification of the pest. It also shows that a small morphologically derived group that includes the papaya fruit fly should be included within this group. This new information already is being used by USDA to identify specimens captured in detection programs and at ports of entry and is extremely valuable to regulatory agencies such as APHIS- PPQ in limiting the spread of fruit fly pests.

Impacts
(N/A)

Publications

Adaime, R., Jesus-Barros, C.R., Uramoto, K., Norrbom, A.L., Zucchi, R.A. 2016. First record of Anastrepha zacharyi Norrbom (Diptera, Tephritidae) in Brazil, and notes on its host plant and parasitoid. Proceedings of the Entomological Society of Washington. 118:636-640.
Barr, N., Ruiz-Arce, R., Obregon, O., Shatters, R.G., Norrbom, A.L., Nolazco, A., Thomas, D.B. 2017. Diagnostic characters within ITS2 DNA support molecular identification of Anastrepha suspensa. Florida Entomologist. 100:182-185.
Hebert, J.B., Scheffer, S.J., Hawthorne, D.J. 2016. Evidence for ecological speciation via a host shift in the holly leafminer, Phytomyza glabricola (Diptera: Agromyzidae). Molecular Ecology. 6:6565-6577.
Ottens, K., Winkler, I.S., Lewis, M.L., Scheffer, S.J., Gomes-Costa, G.A., De V. Barbosa, M.R., Condon, M.A., Forbes, A.A. 2017. Genetic differentiation associated with host plants and geography among six widespread lineages of South American Blepharoneura fruit flies (Tephritidae). Journal of Evolutionary Biology. 30:696-710.
Schutze, M.K., Virgilio, M., Norrbom, A.L., Clarke, A.R. 2017. Integrative taxonomy: Where we are now, with a focus on the resolution of three tropical fruit fly species complexes. Annual Review Of Entomology. 62:147- 64.
Weintraub, P.G., Scheffer, S.J., Visser, D., Valladares, G., Soares, C.A., Shepard, B.M., Rauf, A., Murphy, S.T., Mujica, N., Mac Vean, C., Kroschel, J., Kishinevsky, M., Joshi, R.C., Johansen, N.S., Hallette, R., Civelek, H. S., Chen, B. 2017. The invasive Liriomyza huidobrensis (Diptera: Agromyzidae): Understanding its pest status and management globally. Journal of Insect Science. 28:1-27.
Uramoto, K., Norrbom, A.L., Zucchi, R.A. 2016. Redescription, lectotype designation and new records of Anastrepha luederwaldti Lima (Diptera, Tephritidae). Zootaxa. 4168:341-346.
Mengual, X., Kerr, P., Norrbom, A.L., Barr, N., Lewis, M.L., Stapelfeldt, A., Scheffer, S.J., Woods, P., Islam, M.S., Korytkowski, C.A., Uramoto, K., Rodriguez, E.J., Sutton, B.D., Nolazco, N., Steck, G.J., Gaimari, S. 2017. Phylogenetic relationships of the tribe Toxotrypanini (Diptera: Tephritidae) based on molecular characters. Molecular Phylogenetics and Evolution. 113:84-112.

Progress 10/01/15 to 09/30/16

Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. Taxonomy and natural history of fruit flies. Accomplishments on the taxonomy of Anastrepha, the largest and most economically important group of fruit flies in the American tropics, included publication of new molecular markers to distinguish cryptic species in the South American fruit fly complex, the description of 28 species previously unknown to science, further development of an electronic identification tool for the nearly 300 species of this group, and collection of additional samples for DNA analysis. A molecular analysis of the evolutionary relationships within Anastrepha, based on 6 DNA regions and 159 species, was completed. Additional new species were described in a group that includes pests of apple, cherries, blueberries, tomato and eggplant. Data from additional publications were added to names and host plant databases for fruit flies, and progress was made to serve this information on an APHIS-CPHST web site. 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 analysis of pest leaf-mining, galling, and fruit flies, and their parasitoids. Primers necessary for DNA sequencing were designed for both mitochondrial and nuclear genes in a variety of plant-feeding groups of flies and their associated parasitoids. Specifically, these specialized primers have been designed for leafmining flies (Liriomyza, Phytomyza) that are pests of fruit and vegetables, fruit flies (Blepharoneura) that breed in pumpkins and relatives (Cucurbitaceae), and for braconid and other wasp parasitoids attacking these groups. Analysis of genetic variation in global samples of Liriomyza huidobrensis, a highly damaging invasive leafminer, has found that the invasive populations in Europe, Asia, and Africa have their origins in western South America. This information may be critical for designing management and control procedures around the world. Two manuscripts reporting results from this work are currently being prepared. Data collection is continuing on leafmining pests and related groups in order to better understand species limits, ecological interactions, and host ranges of the plant pests and their parasitoids. This information is critical to Animal and Plant Health Inspection Service-Plant Protection Quarantine (APHIS-PPQ) and other regulatory agencies to prevent the spread of pest species into the U.S. Taxonomy of tachinid flies and other higher flies. The scientist responsible for this objective retired and the position is vacant. Scientific identification of agriculturally important flies. In the period from October 1, 2015 to June 10, 2016, 849 submittals (1,729 specimens) were identified, including 523 "urgent" submittals for USDA- APHIS-PPQ of specimens intercepted on perishable commodities at ports-of- entry. Accomplishments 01 Developed new tools for unambiguous determination of pest fruit flies. New data were published that significantly improve identification capabilities for the largest and most economically important group of fruit flies in the Neotropics. New molecular markers were discovered to distinguish cryptic species in the South American fruit fly complex, which includes the most important pest fruit flies in Latin America. Twenty-eight species previously unknown to science, including species that attack guava and annonas, were named, described, and illustrated, and these species and additional character data were included in further development of an electronic identification tool for the nearly 300 species of this group. A molecular analysis of the evolutionary relationships within Anastrepha was completed. This work will be useful to scientists and regulatory agencies involved in management and control of pest fruit flies.

Impacts
(N/A)

Publications

Norrbom, A.L., Rodriguez, E.J., Steck, G.J., Sutton, B.D., Nolazco Alvarado 2015. New species and host plants of Anastrepha (Diptera: Tephritidae) primarily from Peru and Bolivia. Zootaxa. 4041:1-94.
Norrbom, A.L., Savaris, M., Marinoni, L. 2016. New species of Rhagoletotrypeta (Diptera: Tephritidae) from the Dominican Republic and southern Brazil and Paraguay. Zootaxa. 4088:547-554.
Rodriguez, P., Rodriguez, E.J., Norrbom, A.L., Arevalo, E. 2016. A new species and new records of Cryptodacus (Diptera: Tephritidae) from Colombia, Bolivia and Peru. Zootaxa. 4111(3):276-290.
Sutton, B.D., Steck, G.J., Norrbom, A.L., Rodriguez, E.J., Srivastava, P., Nolazco, A., Colque, F., Yabar, L.E., Lagrava, S., Quisberth, E., Arevalo, E., Rodriguez, C., Alvarez-Baca, J.K., Guevara, Z.T., Ponce, P. 2016. Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region. ZooKeys. 540:175-191.
Chamorro, M.L., Persson, J., Torres, S., Keularts, J., Scheffer, S.J. 2016. Molecular and morphological tools to distinguish Scyphophorus acupunctatus Gyllenhal, 1838: a new weevil pest of the endangered Eggers Agave from St Croix, US Virgin Islands. Proceedings of the Entomological Society of Washington. 118(2):218-243.
Chen, X.L., Norrbom, A.L., Friedberg, A., Chesters, D., Sajedul Islam, M., Zhu, C.D. 2015. A systematic study of Ichneumonosoma Meijere, Pelmatops Enderlein, Pseudopelmatops Shiraki and Soita Walker (Diptera: Tephritidae). Zootaxa. 4013:301-347.
Norrbom, A.L., Mcdiarmid, R., Chen, X.L., David, K.J., De Meyer, M., Freidberg, A., Han, H.Y., Hancock, D.L., Steck, G.J., Thompson, F.C., White, I.M., Zucchi, R.A. 2015. Cryptodacus Hendel, 1914 (Insecta: Diptera: TEPHRITIDAE): Proposed conservation by suppression of Cryptodacus Gundlach, 1862 (Reptilia: Serpentes: COLUBRIDAE). The Bulletin of Zoological Nomenclature. 72:204-208.
Papp, L., Norrbom, A.L. 2015. A review of the genus Dudaia Hedicke, 1923 (Diptera, Sphaeroceridae). Zootaxa. 4011:1-65.