Location: Tropical Crop and Commodity Protection Research
2025 Annual Report
Objectives
Objective 1: Enhance or develop new technologies for the biological control of tephritids and other tropical pests by developing new methods for testing for host specificity, improved mass rearing techniques, enhanced understanding of the fundamental biology of parasitism and insect pathology, and the integration of biological control agent ecology into management techniques.
Sub-objective 1A: Investigate cues driving host specificity in braconid parasitoids of fruit flies in order to improve the safety and acceptability of biological control programs using these wasps.
Sub-objective 1B: Explore the genomic basis for host preference and the role of associated viruses in host suitability of tephritid parasitoids.
Objective 2: Develop new methods for invasive pest control including reduced-risk insecticides, new practices for insecticide resistance management, and new components and programs for IPM for tephritids and other tropical plant pests of quarantine significance for Hawaii and the U.S. mainland to promote the unimpeded movement of fruit and vegetable exports.
Sub-objective 2A: Investigate the molecular, physiological, or behavioral basis of evolving resistance to chemical and biological control of tephritids and other tropical pests.
Sub-objective 2B: Validate the effectiveness of coffee berry borer pest control techniques in the context of a comprehensive IPM system to enable economically viable control.
Sub-objective 2C: Develop baseline biological assessments, survey, monitoring, and control tools based on behavioral interventions and other methods for established and emerging insect pests of tropical agriculture (e.g. the Queensland longhorn beetle, Acalolepta aesthetica and the little fire ant, Wasmannia auropunctata).
Approach
Hypothesis 1A: Visual cues, particularly color and shape, are drivers of host specificity in parasitoids used in classical and augmentative biological control programs against tephritid pests (Psyttalia, Fopius, and Dichasmomorpha).
Hypothesis 1B: Across braconid parasitoid species which parasitize tephritids, novel mechanisms for overcoming hosts defenses have developed, which play a role in a species host specificity and host range.
Research Goal 2A: Determine the extent to which wild melon fly have become resistant to insecticides and devise strategies for insecticide rotation and resistance monitoring. Prescribe a standardized test for resistance for use by collaborators at other research centers in geographic locations where flies are established.
Research Goal 2B: To determine the optimal combination of control measures for CBB management in Hawaii, add new techniques, and deliver a "smart agriculture" app.
Research Goal 2C: Develop trapping systems and genetic assays for new invasive species that attack tropical crops and commodities.
Progress Report
This research project focused on improving detection, control, and eradication of fruit fly pests and other tropical pest species, as well as general protection of tropical and sub-tropical crops. This is the final report for the project 2040-22430-027-000D, “Development of New and Improved Surveillance, Detection, Control, and Management Technologies for Fruit Flies and Invasive Pests of Tropical and Sub-tropical Crops”, which will be succeeded by a new project titled “Improving Biosecurity and Agroecosystem Resilience Through Innovative Detection, Eradication, and IPM Solutions for Tropical Pests and Diseases”.
For Sub-objective 1A, data on visual cues (shape and color) that might be related to oviposition behavior in braconid wasps were collected for five species by ARS scientists in Hilo, Hawaii, and Montpellier, France: Psyttalia lounsburyi, Psyttalia ponerophaga, Diachasmimorpha longicaudata, Psyttalia fletcheri, and Fopius arisanus. Laboratory assays showed mixed or minor effects, and planned field cage experiments were cancelled due to pandemic-related travel restrictions and delays, and subsequent termination of colonies in France due to completion of an unrelated project. Additional research on braconid parasitoids by ARS researchers in Hilo, Hawaii, included a two-year survey of olive fly on Hawaii and Maui islands. As a result of this work, ARS researchers identified two previously introduced fruit fly parasitoids targeting olive flies in the state. This discovery provides a valuable starting place for developing an augmentative control program for this pest in Hawaii and opens the possible eventual release of one of the species in other olive growing regions of the world as its ability to parasitize olive fly was previously unknown.
For Sub-objective 1B, genomic resources were developed for a broad range of economically important tephritid parasitoids. These resources have been curated and are being released to the National Center for Biotechnology Information (NCBI) genome sequence and assembly archive. In concert with molecular work, morphological characterization of virus containing structures (ovaries, venom gland, calyx) for each species were recorded, and DNA plus RNA sequences were generated to characterize the host wasp and associated viruses. Some of the wasps had consistently associated, free-living viruses associated with specific structures of the wasp (e.g. entomopoxvirus replicating in venom glands of Diachasmimorpha longicaudata), or endogenous viruses in the host genome (e.g. endogenous nudivirus in Fopius arisanus). In other cases, there was no distinct association with viruses and no evidence of replication in specific structures. This is a demonstration of the repeated and diverse associations that these wasps make with viruses, enabling them to be successful as parasitoids. Of most interest is the discovery by ARS researchers in Hilo, Hawaii, of several unique strains (sub-species) of D. longicaudata in local agroecosystems in Hawaii. This adds to a body of information describing a deep association of this species with an entomopoxvirus, showing that the virus can impact the success of the wasp and the host range of the parasitoid. One strain of D. longicaudata has a unique ovary and calyx phenotype that appears to be lacking the expected entomopoxvirus particles but instead showed a weak association with a filamentous virus species. This information is very helpful for researchers to understand the host specificity of these biological control agents, which affects their ability to be used in practice. The system appears to be mediated by viral associations.
In support of Sub-objective 2A, ARS researchers in Hilo, Hawaii, completed experiments to characterize the molecular and physiological basis for evolving resistance to Spinosad in the melon fly, Zeugodacus cucurbitae. To achieve this, researchers performed selection experiments and genomic analyses on wild-caught individuals which were observed to be resistant to Spinosad in the field. Both the genome and transcriptome were sequenced and analyzed for field-resistant flies, field-resistant flies selected for increased resistance, and Spinosad-susceptible flies were all analyzed. High-effect SNPs and genes under selection were identified in field-resistant flies and further selected for increased resistance. Contrary to previous studies in Tephritidae and other insect taxa, no evidence supporting the hypothesis that Spinosad resistance was caused by a splice variant for a nicotinoid acetyl-choline receptor (NaChR) gene was found.
For Sub-objective 2B research goal A, data on cultural, physical, chemical and biological controls for coffee berry borer (CBB, Hypothenemus hampei) were collected and analyzed by ARS researchers in Hilo, Hawaii. 1) Cultural controls: Poorly managed farms were shown to have significantly higher CBB loads relative to feral and abandoned sites and should be targeted for landscape-level IPM. Examination of post-harvest CBB reservoirs showed that dried berries left on the ground were a significant source of CBB and should be targeted for removal. Frequent and efficient harvesting was found to be more effective and cost-efficient in controlling CBB than calendar sprays of pesticides, resulting in a 48% net increase in profits. Lastly, field studies demonstrated that block-stumping was the most effective and cost-efficient method of pruning to control CBB and resulted in significantly higher yields relative to traditional pruning methods, 2) Physical control: Experiments demonstrated the use of exclusion netting as a sustainable physical control for CBB and showed that this novel approach can reduce infestation without negatively impacting yield or coffee quality, 3) Chemical control: Research on CBB flight patterns showed that pesticide sprays should target low to mid-level branches and aim to be conducted in the early afternoon when CBB are flying and most vulnerable. A location-optimized pesticide spray schedule was developed for CBB in Hawaii and showed that the number of sprays could be reduced by 33-75% in comparison to the existing IPM recommendations, 4) Biological control: In 2024, mass-rearing of a parasitoid wasp (Phymastichus coffea) that attacks adult CBB was initiated by ARS personnel in Hilo, Hawaii. Field releases for P. coffea began in Summer 2025 to investigate the optimal timing and number of releases, impact on CBB populations at various locations, and compatibility with Beauveria bassiana sprays.
For Sub-objective 2B research goal B, a mobile application called Best Beans was developed to assist coffee growers in monitoring pests and diseases. This app provides growers with two ways to monitor pests on their farms (trees or traps), provides heatmaps for targeted control, issues management alerts and recommendations, and allows detailed record keeping. The app currently has 125 user accounts and has been shared with growers at multiple extension webinars and on-site demos.
In support of Sub-objective 2C, a rapid response effort was initiated to detect and monitor coffee leaf rust (CLR, Hemileia vastatrix), a devastating disease of coffee first detected in Hawaii in 2020. A monitoring protocol was developed and can detect infection levels as low as 0.2%; detection at levels <5% is critical to disease control. Four years of surveys across Hawaii Island have provided insights into infection patterns, spore dispersal, and disease development under natural conditions. Field trials demonstrated the efficacy and duration of protection of six commercial fungicides; the translaminar fungicide and copper fungicides were able to reduce infection below 5% and were the most cost-effective to apply.
In further support of Sub-objective 2C, ARS researchers in Hilo, Hawaii, have completed five experiments over the course of this project plan to characterize the genetics, phenology, behavior, distribution, and genomics of the Queensland longhorned beetle, Acalolepta aesthetica. Analysis of the CO1 sequence of A. aesthetica and common Cerambycidae on Hawaii island, and closely related Lamiinae revealed no variation within the A. aesthetica sequenced and sequences diagnostic of A. aesthetica. Species specific primers were designed around this diagnostic region of CO1 and used to detect the provenance of frass samples. Characterization of its larval phenology showed histogram bins of larval head capsule widths representing five larval instars which is consistent with other beetles in the sub-family Lamiinae. Behavior analysis in a wind-tunnel and field setting using harmonic radar revealed punctuated nocturnal activity and limited migration. Finally, a data collection web-application was deployed by ARS scientists using ArcGIS to collect publicly sourced beetle sighting data. These data were collected over the five years of this project plan and summarized in distribution across Hawaii island over time and a brief season of heightened activity throughout the year; they have now been analyzed and a manuscript reporting the findings is in preparation.
Accomplishments
Review Publications
Willden, S.A., Nyrop, J., Sanderson, J., Wentworth, K., Stockton, D.G., Loeb, G.M. 2024. Rearing impacts on dispersal and biocontrol performance: A case study on Phytoseiulus persimilis. Journal of Applied Ecology. 61(12):3092-3103. https://doi.org/10.1111/1365-2664.14798.
Gomez-Zapata, P.A., Johnson, M.A., Bonacci, T., Aime, M.C. 2024. Phylogeny, biogeography, and host range of gall midges (Diptera: Cecidomyiidae) feeding on spores of rust fungi (Basidiomycota: Pucciniales). Journal of Insect Science. 24(4). Article 18. https://doi.org/10.1093/jisesa/ieae077.
Tietjen, M., Stahlke, A.R., Luecke, D.M., Saelao, P., Sim, S.B., Geib, S.M., Scheffler, B.E., Childers, A.K., Kneubehl, A.R., Teel, P.D., Lopez, J.E. 2025. Genome Report: Whole-genome assembly of the relapsing fever tick Ornithodoros turicata Dugès (Acari: Argasidae). G3: Genes, genomics, genetics. https://doi.org/10.1093/g3journal/jkaf103.
Cohen, Z.P., Perkin, L.C., Raszick, T.J., Sim, S.B., Geib, S.M., Childers, A.K., Sword, G.A., Suh, C. P.-C. 2025. Pangenomics links boll weevil divergence with ancient Mesoamerican cotton cultivation. Molecular Ecology. Article e14054. https://doi.org/10.1111/1755-0998.14054.
Congrains, C., Sim, S.B., Paulo, D.F., Corpuz, R.L., Kauwe, A.N., Simmonds, T.J., Simpson, S.A., Scheffler, B.E., Geib, S.M. 2024. Chromosome-scale genome of the polyphagous pest Anastrepha ludens (Diptera: Tephritidae) provides insights on sex chromosome evolution in Anastrepha. G3: Genes, genomics, genetics. 14(12). Article jkae239. https://doi.org/10.1093/g3journal/jkae239.
Molik, D.C., Stahlke, A., Sharma, S.P., Corpuz, R.L., Kauwe, A.N., Schrader, J.E., Mason, C.J., Sim, S.B., Geib, S.M. 2024. otb: an Automated HiC/HiFi Pipeline Assembles the Prosapia bicincta Genome. Genes, Genomes, and Genomics. 14(7). https://doi.org/10.1093/g3journal/jkae129.
Johnson, M.A., Maeda, C.T., Pulakkatu-Thodi, I. 2024. Vertical and temporal flight patterns of coffee berry borer (Coleoptera: Curculionidae) in Hawaii. Environmental Entomology. 53(4):640–647. https://doi.org/10.1093/ee/nvae051.
Wilson, S.M., Thorne, M.S., Johnson, M.A., Peck, D.C., Wright, M.G. 2024. Prosapia bicincta (Hemiptera: Cercopidae) abundance, host plant associations, and impacts on groundcover in Hawai'i Island rangelands. Environmental Entomology. 53(5):870-880. https://doi.org/10.1093/ee/nvae062.
Aristizabal, L.F., Maeda, C.T., Matsumoto Brower, T.K., Johnson, M.A. 2025. Fungicide efficacy and duration of protection against coffee leaf rust (Hemileia vastatrix) on commercial coffee farms in Hawaii. Crop Protection. 196. Article 107269. https://doi.org/10.1016/j.cropro.2025.107269.
Welty Peachey, A.M., Moses, E.R., Johnson, A.J., Lehman, M.G., Yoder, J.M., De Faveri, S.G., Cheesman, J., Manoukis, N., Siderhurst, M.S. 2024. Wind effects on individual male and female Bactrocera jarvisi (Diptera: Tephritidae) tracked using harmonic radar. Environmental Entomology. 54(1):1-14. https://doi.org/10.1093/ee/nvae108.
Moses, E.R., Lehman, M.G., Johnson, A.J., Welty Peachey, A.M., Yoder, J.M., De Faveri, S.G., Cheesman, J., Manoukis, N., Siderhurst, M.S. 2025. Tracking individual Bactrocera tryoni: Wind effects and natural movement. Entomologia Experimentalis et Applicata. 173(8):854-868. https://doi.org/10.1111/eea.13578.
Hurst, A., O'Brien, A., Miller, N.D., Welty Peachey, A.M., Yoder, J.M., De Faveri, S.G., Cheesman, J., Manoukis, N., Siderhurst, M.S. 2024. Tracking and modeling the movement of Queensland fruit flies, Bactrocera tryoni, using harmonic radar in papaya fields. Scientific Reports. 14. Article 17521. https://doi.org/10.1038/s41598-024-67372-4.
Lee, H., Carvalho, L.A., Manoukis, N. 2025. Enhanced survival of mass-reared Mediterranean fruit flies via regular diurnal temperature oscillations. Journal of Economic Entomology. 118(2):655-661. https://doi.org/10.1093/jee/toaf026.
Clement, R.A., Lee, H., Manoukis, N.C., Pacheco, Y.M., Ross, F., Sisterson, M.S., Owen, C.L. 2025. Addressing biological invasions in agriculture with big data in an informatics age. Agriculture. 15(11):1157. https://doi.org/10.3390/agriculture15111157.
Caton, B.P., Fang, H., Hain, E., Kandel, N., Nelson, R.C., Pallipparambil, G.R., Manoukis, N. 2025. Evaluating a novel core-and-perimeter delimiting trapping survey design for insects. I. Field experiment. Journal of Economic Entomology. Article toaf095. https://doi.org/10.1093/jee/toaf095.
Caton, B.P., Manoukis, N.C., Pallipparambil, G.R., Nelson, R., Hain, E., Fang, H. 2025. Evaluating a novel core-and-perimeter delimiting trapping survey design for insects. II. Simulations and case studies. Journal of Economic Entomology. 118(3):1235-1250. https://doi.org/10.1093/jee/toaf090.