Project : USDA ARS

ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Systematic Entomology Laboratory » Research » Research Project #439501

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

Location: Systematic Entomology Laboratory

2021 Annual Report

Objectives
Objective 1: Investigate the taxonomy and natural history of plant-feeding, agriculturally important flies, especially fruit flies, leaf-mining flies, and gall midges, using morphological and genomic molecular methods to analyze species concepts, discover possible cryptic fly species and host races, develop diagnoses, descriptions, illustrations and identification tools, create biosystematic databases, determine host plants, and analyze phylogenetic relationships. [C1, PS 1A; C2, PS 2B and 2C; C3, PS 3A and 3B; C4 PS 4A and 4B] Objective 2: Curate and expand the U.S. National Diptera Collection to support agricultural research, and for use for morphological and molecular research by U.S. scientists and stakeholders worldwide. [C1, PS 1A; C2, PS 2B; C3, PS 3A and 3B; C4 PS 4A and 4B] Objective 3: Provide scientific identifications of plant-feeding and other agriculturally important flies for APHIS-PPQ and other regulatory agencies. Accurate and rapid identification relies on both development of diagnostic tools through systematic research and collection improvement. [C1, PS 1A; C2, PS 2B; C3, PS 3A and 3B; C4 PS 4A and 4B]

Approach
This project focuses on the systematics of agriculturally important groups of flies, including pest fruit flies and leaf-mining flies. Taxonomic knowledge, including predictive, phylogenetically-based classifications, and diagnostic tools to rapidly and accurately identify these fly species are crucial to exclude and control the pests and effectively use the beneficial agents. Morphology will be investigated using traditional and new character sets to test species concepts and hypotheses of relationships among these flies, and to develop new diagnostic tools. Molecular data from mitochondrial and nuclear genes will be generated for fly identification and phylogenetics. This will include phylogenomics for assessing both deep and shallow evolutionary relationships using the anchored hybridization approach to multigene sequencing. Biosystematic data about flies will be compiled, verified and disseminated to the user community. Databases containing scientific names, distributions, taxonomic literature, and host plant and specimen data pertaining to fruit flies will be expanded and improved. These and other taxonomic tools will be made accessible to the public via publications, the Internet, and other electronic media. The U.S. National Diptera Collection will be curated and expanded to support agricultural research and to allow morphological and molecular research by U.S. and other scientists.

Progress Report
Published research on the systematics of true fruit flies included analyses of the evolutionary relationships within the group, including the sunflower maggot as well as one of the largest groups of fruit flies in Europe, Asia, and North America, the discovery of the first host plant information for a group in South America, and 7 publications on the largest and most economically important group of fruit flies in the American tropics (Anastrepha), including descriptions of 4 previously unknown species from Colombia and Ecuador and the larvae of 2 species, and numerous new distribution records from Bolivia, Brazil, and Paraguay. New research resulted in the description of 17 previously unknown species of Anastrepha from Suriname, French Guiana, and Brazil, and 4 new species from Colombia, and description of the larvae of 9 species; description of a new species and report of new host plant and distribution records for species in the group including the apple maggot and cherry fruit flies; an analysis of the global drivers of fruit fly invasions; further development of an online identification tool for the more than 350 species of Anastrepha, and collection of hundreds of samples from Brazil, Ecuador, Peru and Suriname for DNA analysis. An analysis of 2700 DNA barcoding sequences for 260 species of Anastrepha was completed, and investigation of additional DNA regions for diagnostics and phylogenetic analysis continued. Samples were collected, and some were analyzed via NextGen sequencing methods towards a phylogenetic analysis of the entire family of true flies. Additional names, distribution, and host plant data for fruit flies were compiled to be added to the comprehensive database available via the APHIS-CPHST website; this information is critical to APHIS-PPQ and other regulatory agencies to prevent the spread of pest species into the U.S. Genomic data were collected and analyzed to determine phylogenetic relationships among leaf-mining Agromyzidae, including the native Phytomyza leafminer pests of ornamental and related hollies. The NextGen genomic technology known as anchored hybridization recovered DNA sequence data from as many as >1000 nuclear coding genes from each individual. Phylogenomic analyses of these sequences have allowed the initial assessment of host shifts of the leafminers between holly species, speciation, and the evolution of dietary specialization. Phylogenetic trees from these nuclear genes are being compared to previously published phylogenetic trees constructed entirely from mitochondrial data to test for congruence and the relative support of the data for different portions of the trees. To further explore patterns of host-use in Phytomyza leafminers, the anchored hybridization data collected for phylogenomic analysis is being screened for single nucleotide polymorphisms (SNPs) that can be used to assess population structure and host-plant associated and geographic divergence within species. These SNPs occur both within the targeted nuclear genes but also as part of the “bycatch” of non-targeted sequences that result from the sequencing process. Population-level SNP analyses allow a detailed assessment of the relative importance of host-associated vs. geographic influences on divergence. Additional research on the molecular phylogenetics of Liriomyza huidobrensis, a highly invasive and damaging leafminer, was conducted. This species has invaded more than 30 countries worldwide and is known from 365 host plants in 49 families. Analysis of genetic variation among L. huidobrensis specimens from 14 countries found no evidence of host plant-associated structure. Strong evidence of geographically structured genetic variation within the native range of South America identified and excluded potential source populations within Peru. Diptera Collection. Incoming Diptera specimens from SEL collecting efforts and from other scientists have been safeguarded and processed as far as possible. Scientific identification of agriculturally important flies. In the period from October 1, 2020, to June 3, 2021, 322 submittals (1,082 specimens) were identified, including 100 "urgent" submittals for USDA-APHIS-PPQ of 271 specimens intercepted on perishable commodities at ports-of-entry.

Accomplishments
1. Protecting American agriculture by improving identification tools for pest fruit flies. True fruit flies include some of the most important pests of commercial and subsistence fruit crops, including citrus, mango, peach, apple, and many others. Many species are invasive and threaten U.S. agriculture, including multiple species of Anastrepha, the largest and most economically important genus in the American tropics and subtropics. Current taxonomy is based mainly on the adult female, the immature stages, which actually damage the fruit, and males of many species cannot be reliably identified. In collaboration with Florida Dept. of Agriculture and Consumer Services, Gainesville, University of Florida, Gainesville, North Carolina State University, Raleigh, and APHIS-CPHST, Edinburg, Texas, an ARS scientist at Washington, D.C., generated or verified and analyzed a large library of DNA barcoding sequences (2700 cytochrome oxidase I sequence for 260 species) of Anastrepha, indicating that the majority of species can be distinguished with this information. However, some closely related pest species cannot be diagnosed with COI, indicating where additional investigation is needed. This new information is already being used by USDA-APHIS and other regulatory agencies and is critical to more rapidly and reliably identify all life stages of invasive fruit fly species.

U.S. DEPARTMENT OF AGRICULTURE

Systematic Entomology Laboratory: Beltsville, MD