Research Project: Advancing Molecular Pest Management, Diagnostics, and Eradication of Fruit Flies and Invasive Species

Location: Tropical Pest Genetics and Molecular Biology Research Unit

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Applying PCR cycle autonormalization to PacBio full-length 16S rRNA library preparations: Impacts on error rates and sequence distributions - (Peer Reviewed Journal)
Mason, C.J., Weaver, M., Kissinger, K.R., Johnson, M.A., Copeland, D.C., Anderson, K.E., Geib, S.M. 2026. Applying PCR cycle autonormalization to PacBio full-length 16S rRNA library preparations: Impacts on error rates and sequence distributions. mSphere. Article e00295-26. https://doi.org/10.1128/msphere.00295-26.

The tortured past of young polymorphic sex chromosomes revealed through multiple de novo genome assemblies of the mountain pine beetle - (Pre-print Publication)
Lagunas-Robles, G., Bentz, B., Verma, M., Vandygriff, J., Hansen, M., Simmonds, T.J., Corpuz, R.L., Kauwe, A.N., Geib, S.M., Bracewell, R. 2026. The tortured past of young polymorphic sex chromosomes revealed through multiple de novo genome assemblies of the mountain pine beetle. bioRxiv. https://doi.org/10.64898/2026.01.27.702068.

Chromosome-level genome assembly of the Erythrina Gall Wasp, Quadrastichus erythrinae (Hymenoptera: Eulophidae) - (Pre-print Publication)
Zhang, Y.M., Merondun, J., Corpuz, R.L., Kauwe, A.N., Geib, S.M., Sim, S.B. 2026. Chromosome-level genome assembly of the Erythrina Gall Wasp, Quadrastichus erythrinae (Hymenoptera: Eulophidae). bioRxiv. https://doi.org/10.64898/2026.01.23.701414.

Cryptic insect microbiome compositions unveiled with full-length 16s sequencing - (Pre-print Publication)
Mason, C.J., Hansen, T.E., Newell, N.E., Geib, S.M. 2026. Cryptic insect microbiome compositions unveiled with full-length 16s sequencing . bioRxiv. https://doi.org/10.64898/2026.01.22.701149.

Applying PCR cycle autonormalization to improve PacBio full-length 16S-rRNA amplicon sequencing - (Pre-print Publication)
Mason, C.J., Weaver, M., Kissinger, K.R., Johnson, M.A., Copeland, D.C., Anderson, K.E., Geib, S.M. 2026. Applying PCR cycle autonormalization to improve PacBio full-length 16S-rRNA amplicon sequencing. bioRxiv. https://doi.org/10.64898/2026.01.13.699363.

Evidence from a specialist parasitic insect supports range expansion and domestication of sunchoke in the Eastern Agricultural Complex - (Peer Reviewed Journal)
Hippee, A.C., Geib, S.M., Renquist, W., Sim, S.B., Weinrich, C.L., Mueller, N.G., Kitchen, A., Forbes, A.A. 2026. Evidence from a specialist parasitic insect supports range expansion and domestication of sunchoke in the Eastern Agricultural Complex. Proceedings of the National Academy of Sciences (PNAS). 293. https://doi.org/10.1098/rspb.2025.3044.

CiFi: Accurate long-read chromatin conformation capture sequencing with low-input requirements - (Peer Reviewed Journal)
Mcginty, S.P., Gulhan, K., Sim, S.B., Corpuz, R.L., Quail, M., Lawniczak, M., Geib, S.M., Korlach, J., Dennis, M.Y. 2025. CiFi: Accurate long-read chromatin conformation capture sequencing with low-input requirements. Nature Methods. 14(8). https://doi.org/10.1038/s41467-025-66918-y.

Symbiont gene expression predicts insect host’s response to high temperatures - (Peer Reviewed Journal)
Stillson, P.T., Sim, S.B., Corpuz, R.L., Ravenscraft, A. 2025. Symbiont gene expression predicts insect host’s response to high temperatures. Molecular Ecology. 34(22). Article e70154. https://doi.org/10.1111/mec.70154.

Genome report: Chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae) - (Peer Reviewed Journal)
Hansen, T.E., Corpuz, R.L., Simmonds, T.J., Aldebron, C., Mason, C.J., Geib, S.M., Sim, S.B. 2025. Genome report: Chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae). Evolution. 16(1). Article jkaf235. https://doi.org/10.1093/g3journal/jkaf235.

Host preferences of Acalolepta aesthetica in Hawai'i - (Peer Reviewed Journal)
Sofaer, H.R., Miles, B.J., Zarders, J.A., Dunkle, E.J., Corpuz, R.L., Sim, S.B., Peck, R.W. 2025. Host preferences of Acalolepta aesthetica in Hawai'i. Agricultural and Forest Entomology. 28(2):149-159. https://doi.org/10.1111/afe.70015.

To a loss of independence: genomic insights into a pest fruit fly-bacterial mutualism - (Pre-print Publication)
Hansen, T.E., Corpuz, R.L., Simmonds, T.J., Aldebron, C., Geib, S.M., Mason, C.J., Sim, S.B. 2025. To a loss of independence: genomic insights into a pest fruit fly-bacterial mutualism. bioRxiv. https://doi.org/10.1101/2025.08.03.667778.

Genome report: Chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae) - (Pre-print Publication)
Hansen, T.E., Corpuz, R.L., Simmonds, T.J., Aldebron, C., Mason, C.J., Geib, S.M., Sim, S.B. 2025. Genome report: Chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae) . bioRxiv. https://doi.org/10.1101/2025.07.30.665224.

Genomic analysis of Vanessa tameamea, the threatened Hawaiian endemic butterfly, reveals population genetic structure relevant to conservative efforts - (Peer Reviewed Journal)
Arnold, H.E., Dupuis, J.R., Rubinoff, D., Haines, W.P., Geib, S.M., Sim, S.B. 2525. Genomic analysis of Vanessa tameamea, the threatened Hawaiian endemic butterfly, reveals population genetic structure relevant to conservative efforts. Molecular Ecology. 26:1097-1111. https://doi.org/10.1007/s10592-025-01718-x.

Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing - (Peer Reviewed Journal)
Mason, C.J., Nelson, R.C., Weaver, M., Simmonds, T.J., Geib, S.M., Shikano, I. 2025. Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing. Microbiology Spectrum. 13(6). Article e02881-24. https://doi.org/10.1128/spectrum.02881-24.

CCS-consensuser: A haplotype-aware consensus generator for PacBio amplicon sequences - (Peer Reviewed Journal)
Congrains, C., Bremer, F., Dupuis, J.R., Barr, N.B., Garzón-Orduña, I.J., Rubinoff, D., Doorenweerd, C., San Jose, M., Morris, K., Kauwe, A., Geib, S. 2025. CCS-consensuser: A haplotype-aware consensus generator for PacBio amplicon sequences. Molecular Ecology Resources. Article e14113. https://doi.org/10.1111/1755-0998.14113.

CiFi: Accurate long-read chromatin conformation capture sequencing with low-input requirements - (Pre-print Publication)
Mcginty, S.P., Gulhan, K., Sim, S.B., Corpuz, R.L., Quail, M.A., Lawniczak, M.K., Geib, S.M., Korlach, J., Dennis, M.Y. 2025. CiFi: Accurate long-read chromatin conformation capture sequencing with low-input requirements. bioRxiv. Article 635566. https://doi.org/10.1101/2025.01.31.635566.

Functional genomics implicates ebony in the black pupae phenotype of tephritid fruit flies - (Peer Reviewed Journal)
Paulo, D.F., Nguyen, T.N.M., Ward, C.M., Corpuz, R.L., Kauwe, A.N., Rendon, P., Ruano, R.E.Y., Cardoso, A.A.S., Gouvi, G., Fung, E., Crisp, P., Okada, A., Choo, A., Stauffer, C., Bourtzis, K., Sim, S.B., Baxter, S.W., Geib, S.M. 2025. Functional genomics implicates ebony in the black pupae phenotype of tephritid fruit flies. Communications Biology. 8. Article 60. https://doi.org/10.1038/s42003-025-07489-y.

Effects of baculovirus-killed cadavers on plant defenses and insect behavior - (Peer Reviewed Journal)
Jones, A.G., Shikano, I., Mason, C.J., Peiffer, M., Felton, G.W., Hoover, K. 2025. Effects of baculovirus-killed cadavers on plant defenses and insect behavior. Arthropod-Plant Interactions. 19. Article 22. https://doi.org/10.1007/s11829-024-10129-7.

Genomic analysis of Vanessa tameamea, the threatened Hawaiian endemic butterfly, reveals population genetic structure relevant to conservative efforts - (Pre-print Publication)
Arnold, H.E., Dupuis, J.R., Rubinoff, D., Haines, W., Sim, S.B., Geib, S.M. 2024. Genomic analysis of Vanessa tameamea, the threatened Hawaiian endemic butterfly, reveals population genetic structure relevant to conservative efforts. bioRxiv. 1. https://doi.org/10.22541/au.173470779.97962199/v1.

Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee - (Peer Reviewed Journal)
Jones, B.M., Webb, A.E., Geib, S.M., Sim, S.B., Schweizer, R.M., Branstetter, M.G., Evans, J.D., Kocher, S.D. 2024. Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee. Molecular Biology and Evolution. 41(11). Article msae229. https://doi.org/10.1093/molbev/msae229.

Utilizing full-length 16S rRNA sequencing to assess the impact of diet formulation and age on targeted gut microbiome colonization in laboratory and mass-reared Mediterranean fruit flies - (Pre-print Publication)
Mason, C.J., Nelson, R.C., Weaver, M., Simmonds, T.J., Geib, S.M., Shikano, I. 2025. Utilizing full-length 16S rRNA sequencing to assess the impact of diet formulation and age on targeted gut microbiome colonization in laboratory and mass-reared Mediterranean fruit flies. bioRxiv. 2024.12.27.630527. https://doi.org/10.1101/2024.12.27.630527.

Chromosome-scale genome of the polyphagous pest Anastrepha ludens (Diptera: Tephritidae) provides insights on sex chromosome evolution in Anastrepha - (Peer Reviewed Journal)
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.

Adult dietary experience influences mortality of the pest melon fly, Zeugodacus cucurbitae (Diptera: Tephritidae), to an ingested toxin - (Peer Reviewed Journal)
Mason, C.J., Grummer, A., Bosch, M., Shikano, I. 2024. Adult dietary experience influences mortality of the pest melon fly, Zeugodacus cucurbitae (Diptera: Tephritidae), to an ingested toxin. Physiological Entomology. 50(1):77-87. https://doi.org/10.1111/phen.12468.

Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee - (Pre-print Publication)
Jones, B.M., Webb, A.E., Geib, S.M., Sim, S.B., Schweizer, R.M., Branstetter, M.G., Evans, J.D., Kocher, S.D. 2024. Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee. bioRxiv. https://doi.org/10.1101/2024.08.15.608154.

Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow - (Peer Reviewed Journal)
Glover, A.N., Sousa, V.C., Ridenbaugh, R.D., Sim, S.B., Geib, S.M., Linnen, C.R. 2024. Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow. Molecular Ecology. 33(18). Article e17509. https://doi.org/10.1111/mec.17509.

Host range of a parasitoid wasp is linked to host susceptibility to its mutualistic viral symbiont - (Peer Reviewed Journal)
Coffman, K.A., Kauwe, A.N., Gillette, N.E., Burke, G.R., Geib, S.M. 2024. Host range of a parasitoid wasp is linked to host susceptibility to its mutualistic viral symbiont. Molecular Ecology. Article e17485. https://doi.org/10.1111/mec.17485.

Evaluating impacts of radiation-induced sterilization on the performance and gut microbiome of mass-reared Mediterranean fruit fly (Ceratitis capitata) in Hawai’i - (Peer Reviewed Journal)
Mason, C.J. 2024. Evaluating impacts of radiation-induced sterilization on the performance and gut microbiome of mass-reared Mediterranean fruit fly (Ceratitis capitata) in Hawai’i. Journal of Economic Entomology. Article toae173. https://doi.org/10.1093/jee/toae173.

Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies - (Peer Reviewed Journal)
Herrig, D.K., Ridenbaugh, R.D., Vertacnik, K.L., Everson, K.M., Sim, S.B., Geib, S.M., Weisrock, D.W., Linnen, C.R. 2024. Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies. Systematic Biology. 73(5):839-860. https://doi.org/10.1093/sysbio/syae036.

Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies - (Peer Reviewed Journal)
Doorenweerd, C., San Jose, M., Leblanc, L., Barr, N., Geib, S.M., Chung, A.Y., Dupuis, J.R., Ekayanti, A., Fiegalan, E., Hemachandra, K.S., Aftab Hossain, M., Huang, C., Hsu, Y., Morris, K.E., Mustapeng, A.A., Niogret, J., Hong Pham, T., Thi Nguyen, N., Sirisena, U.G., Todd, T., Rubinoff, D. 2024. Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies. Molecular Ecology Resources. 24(6). Article e13987. https://doi.org/10.1111/1755-0998.13987.

The genetic basis of the black pupae phenotype in tephritid fruit flies - (Pre-print Publication)
Paulo, D.F., Nguyen, T.N., Ward, C.M., Corpuz, R.L., Kauwe, A.N., Rendon, P., Ruano, R.E., Cardoso, A.A., Gouvi, G., Fung, E., Okada, A., Choo, A., Crisp, P., Stauffer, C., Bourtzis, K., Sim, S.B., Baxter, S.W., Geib, S.M. 2024. The genetic basis of the black pupae phenotype in tephritid fruit flies . bioRxiv. Article 597636. https://doi.org/10.1101/2024.06.07.597636.

Impact of larval food source on the stability of the Bactrocera dorsalis microbiome - (Peer Reviewed Journal)
Kempraj, V., Auth, J.E., Cha, D.H., Mason, C.J. 2024. Impact of larval food source on the stability of the Bactrocera dorsalis microbiome. Microbial Ecology. 87. Article 46. https://doi.org/10.1007/s00248-024-02352-9.

Genome report: Chromosome-scale genome assembly of the West Indian fruit fly Anastrepha obliqua (Diptera: Tephritidae) - (Peer Reviewed Journal)
Sim, S.B., Congrains, C., Velasco-Cuervo, S., Corpuz, R.L., Kauwe, A.N., Scheffler, B.E., Geib, S.M. 2024. Genome report: Chromosome-scale genome assembly of the West Indian fruit fly Anastrepha obliqua (Diptera: Tephritidae). G3, Genes/Genomes/Genetics. 14(4). Article jkae024. https://doi.org/10.1093/g3journal/jkae024.

Genome Report: Chromosome-scale Genome Assembly of the West Indian fruit fly Anastrepha obliqua (Diptera: Tephritidae) - (Pre-print Publication)
Sim, S.B., Congrains, C., Velasco-Cuervo, S.M., Corpuz, R.L., Kauwe, A.N., Scheffler, B., Geib, S.M. 2023. Genome Report: Chromosome-scale Genome Assembly of the West Indian fruit fly Anastrepha obliqua (Diptera: Tephritidae). bioRxiv. Article 559041. https://doi.org/10.1101/2023.09.22.559041.

Gut bacterial population and community dynamics following adult emergence in pest tephritid fruit flies - (Peer Reviewed Journal)
Mason, C.J., Auth, J.E., Geib, S.M. 2023. Gut bacterial population and community dynamics following adult emergence in pest tephritid fruit flies. Scientific Reports. 13. Article 13723. https://doi.org/10.1038/s41598-023-40562-2.

Hotter days, stronger immunity? Exploring the impact of rising temperatures on insect gut health and microbial relationships - (Peer Reviewed Journal)
Mason, C.J., Shikano, I. 2023. Hotter days, stronger immunity? Exploring the impact of rising temperatures on insect gut health and microbial relationships. Current Opinion in Insect Science. 59. Article 101096. https://doi.org/10.1016/j.cois.2023.101096.

A chromosome scale assembly of the parasitoid wasp Venturia canescens provides insight into the process of virus domestication - (Peer Reviewed Journal)
Mao, M., Simmonds, T.J., Stouthamer, C.M., Kehoe, T.M., Geib, S.M., Burke, G.R. 2023. A chromosome scale assembly of the parasitoid wasp Venturia canescens provides insight into the process of virus domestication. G3: Genes, genomics, genetics. 13(10). Article jkad137. https://doi.org/10.1093/g3journal/jkad137.

Toward an integrated understanding of the Lepidoptera microbiome - (Peer Reviewed Journal)
Shao, Y., Mason, C.J., Felton, G. 2023. Toward an integrated understanding of the Lepidoptera microbiome. Annual Review of Entomology. 69:117-137. https://doi.org/10.1146/annurev-ento-020723-102548.

Tomato chemical defenses intensify corn earworm (Helicoverpa zea) mortality from opportunistic bacterial pathogens - (Peer Reviewed Journal)
Mason, C.J., Peiffer, M., Hoover, K., Felton, G. 2023. Tomato chemical defenses intensify corn earworm (Helicoverpa zea) mortality from opportunistic bacterial pathogens. Journal of Chemical Ecology. https://doi.org/10.1007/s10886-023-01420-7.

Whole-genome resequencing data support a single introduction of the invasive white pine sawfly, Diprion similis - (Peer Reviewed Journal)
Davis, J.S., Sim, S.B., Geib, S.M., Scheffler, B.E., Linnen, C.R. 2023. Whole-genome resequencing data support a single introduction of the invasive white pine sawfly, Diprion similis. Journal of Heredity. 114(3):246-258. https://doi.org/10.1093/jhered/esad012.

HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources - (Peer Reviewed Journal)
Vernygora, O.V., Congrains, C., Geib, S.M., Dupuis, J.R. 2023. HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources. Molecular Ecology Resources. 23(5):1155-1167. https://doi.org/10.1111/1755-0998.13762.

Whole-genome resequencing data support a single introduction of the invasive white pine sawfly, Diprion similis - (Other)
Davis, J.S., Sim, S.B., Geib, S.M., Linnen, C.R. 2022. Whole-genome resequencing data support a single introduction of the invasive white pine sawfly, Diprion similis. bioRxiv. https://doi.org/10.1101/2022.09.14.507957.