Hebert’s research team at the Centre for Biodiversity Genomics tackles major challenges in monitoring biodiversity and identifying species through innovative DNA-based technologies and digital platforms. This includes developing BOLD (Barcode of Life Data System, version 5) and mBRAVE, along with advanced techniques for reading genetic codes in single species (DNA barcoding) and multiple species simultaneously (metabarcoding).
Researchers and decision-makers face significant hurdles in monitoring biodiversity and identifying species, which affects conservation, agricultural management, and ecosystem research. Traditional monitoring methods are slow, expensive, and require extensive expertise in species identification. The DNA barcode reference library, essential for modern large-scale species identification, remains incomplete, containing only a fraction of known animal and plant species. While DNA-based methods like metabarcoding (reading genetic codes for multiple species simultaneously) and environmental DNA analysis (detecting species from DNA left in their environment) have revolutionized species detection, their implementation faces practical challenges: balancing sensitivity with cost, managing contamination risks, standardizing procedures across different environments, and processing an overwhelming volume of genetic data that doubles every nine months. In agriculture, Ontario farmers spend $400 million annually on pesticides without precise data on pest presence and timing, highlighting the need for more efficient, standardized, and cost-effective monitoring systems.
Dr. Paul Hebert leads a large research team that focuses on developing and applying DNA-based identification systems to advance biodiversity genomics and its real-world applications. Hebert’s Food from Thought project supported key improvements in high-speed DNA sequencing methods and metabarcoding protocols for agricultural monitoring. A major outcome was developing two globally used systems for storing, managing, and classifying DNA data: BOLD version 5 and mBRAVE, a cloud-based platform designed for handling large amounts of DNA sequence data in biodiversity research. The Centre for Biodiversity Genomics, headed by Hebert, has led the adoption of DNA barcoding for species discovery and identification, with recent technological advances enabling significant cost reductions. A key goal was to lower the cost of DNA barcoding fresh specimens to less than $1 per sample to enable rapid and cost-effective expansion of the reference library of DNA barcodes. The research also included developing protocols for agricultural monitoring, using specialized insect traps across Ontario to establish a real-time pest detection system.
Image of Cimbicidae documented by the Centre for Biodiversity Genomics.
Hebert’s team advanced biodiversity informatics through three key platforms: BOLD (Barcode of Life Data System), the BIN (Barcode Index Number) system for organizing species information, and mBRAVE (Multiplex Barcode Research and Visualization Environment). BOLD Version 5 introduces three major improvements: a customizable database system, the ability to analyze DNA from old museum specimens, and automated species classification. The new database allows researchers to create personalized organization systems while maintaining compatibility with broader biodiversity databases. mBRAVE complements BOLD by handling large-scale DNA sequencing data, providing standardized analysis methods, scalable storage, and user-friendly tools for processing complex genetic information.
Hebert and the Centre for Biodiversity Genomics’ ongoing work continues to revolutionize biodiversity monitoring through advances in DNA analysis and high-speed sequencing. The team’s innovations, particularly the BOLD and mBRAVE platforms, enable faster and more accurate species identification while dramatically reducing costs from over $2 to potentially less than $0.10 per sample. In agriculture, new metabarcoding protocols and real-time pest monitoring system will help farmers make data-driven decisions about pest control. The technology also allows scientists to analyze degraded DNA from museum specimens, reconstructing historical ecosystems and assessing long-term environmental changes. While challenges remain in standardization and large-scale implementation, these tools are helping transform biodiversity science into a more accessible and practical field for researchers, conservationists, and policymakers.
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Braukmann, T. W. A., Ivanova, N. v., Prosser, S. W. J., Elbrecht, V., Steinke, D., Ratnasingham, S., de Waard, J. R., Sones, J. E., Zakharov, E. v., & Hebert, P. D. N. (2019). Metabarcoding a diverse arthropod mock community. Molecular Ecology Resources, 19(3), 711–727. https://doi.org/10.1111/1755-0998.13008
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Chimeno, C., Hausmann, A., Schmidt, S., Raupach, M. J., Doczkal, D., Baranov, V., Hübner, J., Höcherl, A., Albrecht, R., Jaschhof, M., Haszprunar, G., & Hebert, P. D. N. (2022). Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany. Insects, 13(1). https://doi.org/10.3390/insects13010082
Čkrkić, J., Petrović, A., Kocić, K., Ye, Z., Vollhardt, I. M. G., Hebert, P. D. N., Traugott, M., & Tomanović, Ž. (2019). Hidden in plain sight: phylogeography of an overlooked parasitoid species Trioxys sunnysidensis Fulbright & Pike (Hymenoptera: Braconidae: Aphidiinae). Agricultural and Forest Entomology, 21(3), 299–308. https://doi.org/10.1111/afe.12332
Copilaș-Ciocianu, D., Palatov, D., Rewicz, T., Sands, A. F., Arbačiauskas, K., Hebert, P. D. N., Grabowski, M., & Marin, I. (2023). A widespread Ponto-Caspian invader with a mistaken identity: integrative taxonomy elucidates the confusing taxonomy of Trichogammarus trichiatus (= Echinogammarus) (Crustacea: Amphipoda). Zoological Journal of the Linnean Society, 198, 821–846. https://doi.org/10.5883/DS-DCTRICH
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Cordone, G., Lozada, M., Vilacoba, E., Thalinger, B., Bigatti, G., Lijtmaer, D. A., Steinke, D., & Galván, D. E. (2022). Metabarcoding, direct stomach observation and stable isotope analysis reveal a highly diverse diet for the invasive green crab in Atlantic Patagonia. Biological Invasions, 24(2), 505–526. https://doi.org/10.1007/s10530-021-02659-5
Correa-Carmona, Y., Rougerie, R., Arnal, P., Ballesteros-Mejia, L., Beck, J., Dolédec, S., Ho, C., Kitching, I. J., Lavelle, P., le Clec’h, S., Lopez-Vaamonde, C., Martins, M. B., Murienne, J., Oszwald, J., Ratnasingham, S., & Decaëns, T. (2022). Functional and taxonomic responses of tropical moth communities to deforestation. Insect Conservation and Diversity, 15(2), 236–247. https://doi.org/10.1111/icad.12549
Cristescu, M. E., & Hebert, P. D. N. (2018). Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation. Annu. Rev. Ecol. Evol. Syst, 49, 209–239. https://doi.org/10.1146/annurev-ecolsys-110617
Cruaud, A., Delvare, G., Nidelet, S., Sauné, L., Ratnasingham, S., Chartois, M., Blaimer, B. B., Gates, M., Brady, S. G., Faure, S., van Noort, S., Rossi, J. P., & Rasplus, J. Y. (2021). Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics, 37(1), 1–35. https://doi.org/10.1111/cla.12416
Dahruddin, H., Sholihah, A., Sukmono, T., Sauri, S., Nurhaman, U., Wowor, D., Steinke, D., & Hubert, N. (2021). Revisiting the diversity of barbonymus (Cypriniformes, cyprinidae) in sundaland using dna-based species delimitation methods. Diversity, 13(7). https://doi.org/10.3390/d13070283
D’Ercole, J., Dapporto, L., Schmidt, B. C., Dincă, V., Talavera, G., Vila, R., & Hebert, P. D. N. (2022). Patterns of DNA barcode diversity in butterfl y species (Lepidoptera) introduced to the Nearctic. European Journal of Entomology, 119, 379–387. https://doi.org/10.14411/eje.2022.039
D’Ercole, J., Prosser, S. W. J., & Hebert, P. D. N. (2021). A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera) – Patterns of nucleotide misincorporation. PeerJ, 9. https://doi.org/10.7717/peerj.10420
Dincă, V., Bálint, Z., Vodă, R., Dapporto, L., Hebert, P. D. N., & Vila, R. (2018). Use of genetic, climatic, and microbiological data to inform reintroduction of a regionally extinct butterfly. Conservation Biology, 32(4), 828–837. https://doi.org/10.1111/cobi.13111
D’Souza, M. L., & Hebert, P. D. N. (2018). Stable baselines of temporal turnover underlie high beta diversity in tropical arthropod communities. Molecular Ecology, 27(10), 2447–2460. https://doi.org/10.1111/mec.14693
D’Souza, M. L., van der Bank, M., Shongwe, Z., Rattray, R. D., Stewart, R., van Rooyen, J., Govender, D., & Hebert, P. D. N. (2021). Biodiversity baselines: Tracking insects in Kruger National Park with DNA barcodes. Biological Conservation, 256. https://doi.org/10.1016/j.biocon.2021.109034
Eaton, W. D., McGee, K. M., Donnelly, R., Lemenze, A., Karas, O., & Hajibabaei, M. (2019). Differences in the soil microbial community and carbon-use efficiency following development of Vochysia guatemalensis tree plantations in unproductive pastures in Costa Rica. Restoration Ecology, 27(6), 1263–1273. https://doi.org/10.1111/rec.12978
Elbrecht, V., Hebert, P. D. N., & Steinke, D. (2018). Slippage of degenerate primers can cause variation in amplicon length. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-29364-z
Elbrecht, V., & Steinke, D. (2019). Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring. Freshwater Biology, 64(2), 380–387. https://doi.org/10.1111/fwb.13220
Estrada-Franco, J. G., Fernández-Santos, N. A., Adebiyi, A. A., López-López, M. de J., Aguilar-Durán, J. A., Hernández-Triana, L. M., Prosser, S. W. J., Hebert, P. D. N., Fooks, A. R., Hamer, G. L., Xue, L., Rodríguez-Pérez, M. A., & Kittayapong, P. (2020). Vertebrate-aedes aegypti and Culex quinquefasciatus (diptera)-arbovirus transmission networks: Non-human feeding revealed by meta-barcoding and nextgeneration sequencing. PLoS Neglected Tropical Diseases, 14(12), 1–22. https://doi.org/10.1371/journal.pntd.0008867
Farrell, M. J., Govender, D., Hajibabaei, M., van der Bank, M., & Davies, T. J. (2019). Bacterial diversity in the waterholes of the Kruger National Park: An eDNA metabarcoding approach. Genome, 62(3), 229–242. https://doi.org/10.1139/gen-2018-0064
Floren, A., von Rintelen, T., Hebert, P. D. N., de Araujo, B. C., Schmidt, S., Balke, M., Narakusumo, R. P., Peggie, D., Ubaidillah, R., von Rintelen, K., & Müller, T. (2020). Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-73519-w
Gadawski, P., Rossaro, B., Giłka, W., Rewicz, T., Magoga, G., Hebert, P., Montagna, M., & Grabowski, M. (2021). DNA barcode library revealed unknown diversity of chironomid midges in Montenegro. ARPHA Conference Abstracts, 4. https://doi.org/10.3897/aca.4.e65497
Gauthier, M., Konecny-Dupré, L., Nguyen, A., Elbrecht, V., Datry, T., Douady, C., & Lefébure, T. (2020). Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. Molecular Ecology Resources, 20(1), 79–96. https://doi.org/10.1111/1755-0998.13088
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Gleason, J. E., Elbrecht, V., Braukmann, T. W. A., Hanner, R. H., & Cottenie, K. (2021). Assessment of stream macroinvertebrate communities with eDNA is not congruent with tissue-based metabarcoding. Molecular Ecology, 30(13), 3239–3251. https://doi.org/10.1111/mec.15597
González, M. A., Goiri, F., Prosser, S. W. J., Cevidanes, A., Hernández-Triana, L. M., Barandika, J. F., Hebert, P. D. N., & García-Pérez, A. L. (2022). Culicoides species community composition and feeding preferences in two aquatic ecosystems in northern Spain. Parasites and Vectors, 15(1). https://doi.org/10.1186/s13071-022-05297-5
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Hleap, J. S., Littlefair, J. E., Steinke, D., Hebert, P. D. N., & Cristescu, M. E. (2021). Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes. Molecular Ecology Resources, 21(7), 2190–2203. https://doi.org/10.1111/1755-0998.13407
Hu, G. L., Hua, Y., Hebert, P. D. N., & Hua, B. Z. (2019). Evolutionary history of the scorpionfly Dicerapanorpa magna (Mecoptera, Panorpidae). Zoologica Scripta, 48(1), 93–105. https://doi.org/10.1111/zsc.12326
Hu, G.-L., Gao, K., Wang, J.-S., Hebert, P. D. N., & Hua, B.-Z. (2019). Molecular phylogeny and species delimitation of the genus Dicerapanorpa (Mecoptera: Panorpidae). In Zoological Journal of the Linnean Society (Vol. 187). http://zoobank.org/
Hubert, N., Pepey, E., Mortillaro, J. M., Steinke, D., Andria-Mananjara, D. E., & de Verdal, H. (2021). Mitochondrial genetic diversity among farmed stocks of Oreochromis spp. (perciformes, cichlidae) in Madagascar. Diversity, 13(7). https://doi.org/10.3390/d13070281
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Huemer, P., Wieser, C., Stark, W., Hebert, P. D. N., & Wiesmair, B. (2019). DNA barcode library of megadiverse Austrian Noctuoidea (Lepidoptera) – A nearly perfect match of Linnean taxonomy. Biodiversity Data Journal, 7. https://doi.org/10.3897/BDJ.7.e37734
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Kocić, K., Petrović, A., Čkrkić, J., Kavallieratos, N. G., Rakhshani, E., Arnó, J., Aparicio, Y., Hebert, P. D. N., & Tomanović, Ž. (2020). Resolving the taxonomic status of potential biocontrol agents belonging to the neglected genus lipolexis förster (hymenoptera, braconidae, aphidiinae) with descriptions of six new species. Insects, 11(10), 1–30. https://doi.org/10.3390/insects11100667
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