Dr Gert-Jan Jeunen, Our staff, Department of Marine Science

Contact details

Office 310 Castle Street, room 153
Email gert-jan.jeunen@otago.ac.nz

Academic qualifications

BSc Hasselt University (Belgium)
MSc Ghent University (Belgium); Université de Pierre et Marie Curie (UPMC; France); Universidad de Oviedo (Spain)
PhD Otago University

Research interests

Environmental DNA metabarcoding
Historical and ancient DNA

Postgraduate students

Joseph Muldoon, MSc: Investigating the effects of historical spatial distributions of fish in the Indo-Pacific through eDNA obtained from museum-stored sponges
Ella Dewar, MSc: Genomic and transcriptomic analysis of New Zealand's freshwater Porifera
Taylor Allan, MSc: Uncovering nitrogen cycling processes in estuaries through eDNA metabarcoding
Jonika Edgecombe, PhD: Early detection of marine NIS through a novel molecular toolbox
Michelle Liddy, PhD: Marine sponges as natural eDNA accumulators
Ryan Easton, PhD: Investigating the impact of barriers on New Zealand's freshwater fish through electrofishing and eDNA analysis
Benjamin Duran-Vinet, PhD: CRISPR-Cas-based biomonitoring for marine environments

Publications

Bennington, S. M., Bourke, S. D., Wilkinson, S. P., Englebert, N., Bond, D. M., Jeunen, G.-J., Dawson, S., Slooten, E., Dillingham, P. W., Rayment, W. J., & Alexander, A. (2024). New insights into the population structure of Hector's dolphin (Cephalorhynchus hectori) revealed using environmental DNA. Environmental DNA, 6, e70024. doi: 10.1002/edn3.70024 Journal - Research Article

Jeunen, G.-J., Mills, S., Lamare, M., Duffy, G. A., Knapp, M., Stanton, J.-A. L., … Treece, J., Ferreira, S., Durán-Vinet, B., Zavodna, M., & Gemmell, N. J. (2024). Unlocking Antarctic molecular time-capsules: Recovering historical environmental DNA from museum-preserved sponges. Molecular Ecology Resources. Advance online publication. doi: 10.1111/1755-0998.14001 Journal - Research Article

Jeunen, G.-J., Mills, S., Mariani, S., Treece, J., Ferreira, S., Stanton, J.-A. L., Durán-Vinet, B., Duffy, G. A., Gemmell, N. J., & Lamare, M. (2024). Streamlining large-scale oceanic biomonitoring using passive eDNA samplers integrated into vessel's continuous pump underway seawater systems. Science of the Total Environment, 946, 174354. doi: 10.1016/j.scitotenv.2024.174354 Journal - Research Article

Seymour, M., Guibert, I., Jeunen, G.-J., Hellström, M., Leray, M., Elbrect, V., … Moffitt, J., … Zhao, M. (2024). The First International eDNA Workshop in Hong Kong: A beginner's guide for the next-generation eDNA researcher. Environmental DNA, 6, e552. doi: 10.1002/edn3.552 Journal - Research Other

Jeunen, G.-J., Lamare, M., Devine, J., Mariani, S., Mills, S., Treece, J., Ferreira, S., & Gemmell, N. J. (2024). Characterizing Antarctic fish assemblages using eDNA obtained from marine sponge bycatch specimens. Reviews in Fish Biology & Fisheries, 34, 221-238. doi: 10.1007/s11160-023-09805-3 Journal - Research Article

2024

Journal - Research Article

Journal - Research Other

2023

Journal - Research Article

Urban, L., Miller, A. K., Eason, D., Vercoe, D., Shaffer, M., Wilkinson, S. P., Jeunen, G.-J., Gemmell, N. J., & Digby, A. (2023). Non-invasive real-time genomic monitoring of the critically endangered kākāpō. eLIFE, 12, RP84553. doi: 10.7554/eLife.84553

Jeunen, G.-J., Lamare, M., Cummings, V., Treece, J., Ferreira, S., Massuger, J., … Gemmell, N. (2023). Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys. Environmental DNA. Advance online publication. doi: 10.1002/edn3.500

Olmedo-Rojas, P., Jeunen, G.-J., Lamare, M., Turnbull, J., Terauds, A., Gemmell, N., & Fraser, C. I. (2023). Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: A case study in Antarctica. Antarctic Science, 35(1), 15-30. doi: 10.1017/S0954102022000384

Adams, C. I. M., Jeunen, G.-J., Cross, H., Taylor, H. R., Bagnaro, A., Currie, K., Hepburn, C., Gemmell, N. J., … Knapp, M. (2023). Environmental DNA metabarcoding describes biodiversity across marine gradients. ICES Journal of Marine Science, fsad017. Advance online publication. doi: 10.1093/icesjms/fsad017

Munk, P., Brinch, B., Møller, F. D., Petersen, T. N., Hendriksen, R. S., Seyfarth, A. M., … Global Sewage Surveillance Consortium, including Jeunen, G.-J., Gemmell, N., Chambers, S. T., … Aarestrup, F. M. (2023). Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nature Communications, 14(1), 7251. doi: 10.1038/s41467-022-34312-7

Jeunen, G.-J., Cane, J. S., Ferreira, S., Strano, F., von Ammon, U., Cross, H., Day, R., … Ellis, K., Urban, L., Pearson, N., Olmedo-Rojas, P., Kardailsky, A., Gemmell, N. J., & Lamare, M. (2023). Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring. Molecular Ecology Resources, 23, 771-786. doi: 10.1111/1755-0998.13754

Jeunen, G.-J., Dowle, E., Edgecombe, J., von Ammon, U., Gemmell, N. J., & Cross, H. (2023). CRABS: A software program to generate curated reference databases for metabarcoding sequencing data. Molecular Ecology Resources, 23, 725-738. doi: 10.1111/1755-0998.13741

Adams, C. I. M., Hepburn, C., Jeunen, G.-J., Cross, H., Taylor, H. R., Gemmell, N. J., … Knapp, M. (2023). Environmental DNA reflects common haplotypic variation. Environmental DNA, 5, 906-919. doi: 10.1002/edn3.352

Journal - Research Other

Durán-Vinet, B., Araya-Castro, K., Zaiko, A., Pochon, X., Wood, S. A., Stanton, J.-A. L., Jeunen, G.-J., … Kardailsky, A., … Gemmell, N. J. (2023). CRISPR-Cas-based biomonitoring for marine environments: Toward CRISPR RNA design optimization via deep learning. CRISPR Journal, 6(4), 316-324. doi: 10.1089/crispr.2023.0019

Conference Contribution - Published proceedings: Abstract

Durán-Vinet, B., Jeunen, G.-J., Stanton, J.-A. L., Zaiko, A., Pochon, X., & Gemmell, N. (2023). CORSAIR-Dx: A CRISPR-Cas13a-based approach for environmental DNA biomonitoring of invasive species from water. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Kardailsky, A., Dowle, E., Matthaei, C., Gemmell, N., & Jeunen, G.-J. (2023). Biomonitoring of freshwater streams using bulk eDNA and CRISPR-Cas enrichment. Proceedings of the 1st Australian & New Zealand Environmental DNA (eDNA) Conference: Innovation & Application. Retrieved from https://ednaconference.com.au

van Os, M., Cross, H., Kardailsky, O., Jeunen, G.-J., Collins, C., McDonald, K., Kinaston, R., Vlok, M., Walter, R., Cook, G., Aung, H. L., Matisoo-Smith, L., Buckley, H., & Knapp, M. (2023). The conundrum of related taxa: Detection and authentication of pathogen DNA in bioarchaeological samples from the Pacific. Proceedings of the 1st Australian & New Zealand Environmental DNA (eDNA) Conference: Innovation & Application. Retrieved from https://ednaconference.com.au

Jeunen, G.-J., Cane, J., Lamare, M., & Gemmell, N. (2023). Biodiversity monitoring through environmental DNA obtained from filter-feeding organisms. Proceedings of the 1st Australian & New Zealand Environmental DNA (eDNA) Conference: Innovation & Application. Retrieved from https://ednaconference.com.au

Edgecombe, J., Keeler-May, G., Zaiko, A., Pochon, X., Stanton, J.-A. L., Treece, J., Rand, C., Jeunen, G.-J., Hepburn, C., & Gemmell, N. (2023). A targeted eDNA approach to detect and quantify Undaria pinnatifida. Proceedings of the 1st Australian & New Zealand Environmental DNA (eDNA) Conference: Innovation & Application. Retrieved from https://ednaconference.com.au

Moffitt, J., Jeunen, G.-J., Ferreira, S., Gemmell, N., Fraser, C., Barnes, D., … Lamare, M. (2023). A snapshot into future warming: In situ warming drives big changes in Benthic communities. Proceedings of the 1st Australian & New Zealand Environmental DNA (eDNA) Conference: Innovation & Application. Retrieved from https://ednaconference.com.au

Adams, C., Hepburn, C., Cross, H., Taylor, H., Gemmell, N., Bunce, M., Jeunen, G.-J., & Knapp, M. (2023). Environmental DNA reflects common genetic variation. Proceedings of the 1st Australian & New Zealand Environmental DNA (eDNA) Conference: Innovation & Application. Retrieved from https://ednaconference.com.au

2022

Journal - Research Article

Jeunen, G.-J., von Ammon, U., Cross, H., Ferreira, S., Lamare, M., Day, R., Treece, J., … Gemmell, N. J., & Stanton, J.-A. L. (2022). Moving environmental DNA (eDNA) technologies from benchtop to the field using passive sampling and PDQeX extraction. Environmental DNA, 4, 1420-1433. doi: 10.1002/edn3.356

Jeunen, G.-J., Lipinskaya, T., Gajduchenko, H., Golovenchik, V., Moroz, M., Rizevsky, V., … Gemmell, N. J. (2022). Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. Metabarcoding & Metagenomics, 6, 171-186. doi: 10.3897/mbmg.6.e68575

Conference Contribution - Published proceedings: Abstract

Edgecombe, J., Zaiko, A., Pochon, X., Stanton, J.-A. L., Jeunen, G.-J., & Gemmell, N. (2022). Point-of-need molecular detection techniques and engagement in citizen-based surveillance. In A. Finigan, R. Richards & P. Vakaoti (Eds.), Proceedings of the Pacific Postgraduate Symposium: Pacific Voices XIX. (pp. 11). Dunedin, New Zealand: Pacific Islands Centre, University of Otago. Retrieved from http://hdl.handle.net/10523/16237

Conference Contribution - Poster Presentation (not in published proceedings)

Kardailsky, A., Jeunen, G. J., Matthaei, C. D., Gemmell, N., & Dowel, E. (2022, August-September). Improving abundance estimates in metabarcoding analyses through CRISPR-Cas enrichment. Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Jeunen, G.-J., von Ammon, U., Cross, H., Ferreira, S., Lamare, M., Day, R., Treece, J., … Gemmell, N. J., & Stanton, J.-A. L. (2022, August-September). Moving environmental DNA (eDNA) technologies from benchtop to the field using passive sampling and PDQeX extraction. Verbal presentation at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Jeunen, G.-J., Cane, J., Lamare, M., & Gemmell, N. J. (2022, August-September). Squeezing out ecological insights from contemporary and historic sponge borne eDNA. Verbal presentation at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

2021

Journal - Research Article

Bowers, H. A., Pochon, X., von Ammon, U., Gemmell, N., Stanton, J.-A. L., Jeunen, G. J., … Zaiko, A. (2021). Towards the optimization of eDNA/eRNA sampling technologies for marine biosecurity surveillance. Water, 13(8), 1113. doi: 10.3390/w13081113

Conference Contribution - Published proceedings: Abstract

Luu, S., Matisoo-Smith, E., Summerhayes, G. R., Cross, H., & Jeunen, G.-J. (2021). Diving into the bone scrapheap: Ancient DNA metabarcoding of holocene zooarchaeological remains in the Papua New Guinea highlands. Proceedings of the Australasian Research Cluster for Archaeological Science (ARCAS) Virtual Conference: From Micro to Macro: Exploring the Big Picture in Archaeology. Retrieved from http://arcas.org.au

Olmedo-Rojas, P., Jeunen, G.-J., McGaughran, A., Terauds, A., Lamare, M., Gemmell, N., & Fraser, C. (2021). Environmental drivers of diversity in Antarctic terrestrial plants and animals: Using genomic approaches to discover broad-scale patterns. Proceedings of the New Zealand Antarctic Science Conference: Connecting through change. (pp. 134-135). Retrieved from https://www.antarcticanz.govt.nz/nzasc21

2020

Journal - Research Article

Nieuwenhuijse, D. F., Oude Munnink, B. B., Phan, M. V. T., the Global Sewage Surveillance project consortium, including Jeunen, G.-J., Munk, P., … Koopmans, M. P. G. (2020). Setting a baseline for global urban virome surveillance in sewage. Scientific Reports, 10, 13748. doi: 10.1038/s41598-020-69869-0

Ferreira, S., Ashby, R., Jeunen, G.-J., Rutherford, K., Collins, C., Todd, E. V., & Gemmell, N. J. (2020). DNA from mollusc shell: A valuable and underutilised substrate for genetic analyses. PeerJ, 8, e9420. doi: 10.7717/peerj.9420

Jeunen, G.-J., Lamare, M. D., Knapp, M., Spencer, H. G., Taylor, H. R., Stat, M., … Gemmell, N. J. (2020). Water stratification in the marine biome restricts vertical environmental DNA (eDNA) signal dispersal. Environmental DNA, 2(1), 99-111. doi: 10.1002/edn3.49

Conference Contribution - Published proceedings: Abstract

Olmedo-Rojas, P., Jeunen, G.-J., McGaughran, A., Terauds, A., Lamare, M., & Gemmell, N. (2020). Environmental drivers of diversity in Antarctic terrestrial plants and animals: Using genomic approaches to discover broad-scale patterns. Proceedings of the XXXVI Scientific Committee on Antarctic Research (SCAR) 9th Open Science Conference: Antarctic Science: Global Connections. 398. Retrieved from https://www.scar2020.org

Working Paper; Discussion Paper; Technical Report

Jeunen, G.-J., Urban, L., Lewis, R., Knapp, M., Lamare, M., Rayment, W., Dawson, S., & Gemmell, N. (2020). Marine environmental DNA (eDNA) for biodiversity assessments: A one-to-one comparison between eDNA and baited remote underwater video (BRUV) surveys. Authorea. doi: 10.22541/au.160278512.26241559/v1

2019

Journal - Research Article

Hendriksen, R. S., Munk, P., Njage, P., van Bunnik, B., McNally, L., Lukjancenko, O., … The Global Sewage Surveillance project consortium, including Jeunen, G.-J., Gemmell, N., … Aarestrup, F. M. (2019). Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nature Communications, 10(1), 1124. doi: 10.1038/s41467-019-08853-3

Adams, C. I. M., Knapp, M., Gemmell, N. J., Jeunen, G.-J., Bunce, M., Lamare, M. D., & Taylor, H. R. (2019). Beyond biodiversity: Can environmental DNA (eDNA) cut it as a population genetics tool? Gene, 10(3), 192. doi: 10.3390/genes10030192

Jeunen, G.-J., Knapp, M., Spencer, H. G., Taylor, H. R., Lamare, M. D., Stat, M., … Gemmell, N. J. (2019). Species‐level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecology & Evolution, 9, 1323-1335. doi: 10.1002/ece3.4843

Oberacker, P., Stepper, P., Bond, D. M., Höhn, S., Focken, J., Meyer, V., … Sugrue, V. J., Jeunen, G.-J., Moser, T., … Hore, T. A., & Jurkowski, T. P. (2019). Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation. PLoS Biology, 17(1), e3000107. doi: 10.1371/journal.pbio.3000107

Jeunen, G.-J., Knapp, M., Spencer, H. G., Lamare, M. D., Taylor, H. R., Stat, M., … Gemmell, N. J. (2019). Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Molecular Ecology Resources, 19, 426-438. doi: 10.1111/1755-0998.12982

Conference Contribution - Published proceedings: Abstract

Lipinskaya, T., Jeunen, G.-J., Gajduchenko, H., Golovenchik, V., Semenchenko, V., & Gemmell, N. (2019). Environmental DNA metabarcoding enables early detection of non-indigenous aquatic invertebrates and fish in Belarussian rivers. Genome, 62(6), (pp. 399-400). doi: 10.1139/gen-2019-0083

Adams, C. I. M., Jeunen, G. J., & Knapp, M. (2019). Can haplotypes be recovered from environmental DNA? Integrative & Comparative Biology, 59(Suppl. 1), (pp. E262). doi: 10.1093/icb/icz004

Conference Contribution - Verbal presentation and other Conference outputs

Alexander, A., Constantine, R., Roe, W., Baker, C. S., Heimeier, D., Hamner, R. M., … Jeunen, G.-J., & Gemmell, N. (2019, August-September). Hologenomics for conservation: A first test of utility using New Zealand's endemic Māui and Hector's dolphins. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Knapp, M., McDonald, S. K., Buckley, H., Kardailsky, O., Aung, H. L., Cross, H., Jeunen, G.-J., Matisoo-Smith, E., Walter, R., & Cook, G. M. (2019, August-September). Origin and evolution of tuberculosis in New Zealand. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2018

Conference Contribution - Published proceedings: Abstract

Adams, C. I. M.-c., Jeunen, G. J., & Knapp, M. (2018). Can environmental DNA reveal mitochondrial diversity? Proceedings of the Society for Conservation Biology 5th Oceania Congress: Conservation in a Changing World. (pp. 85). Retrieved from http://wellington2018.scboceania.org

Conference Contribution - Poster Presentation (not in published proceedings)

Adams, C. I. M., Jeunen, G., & Knapp, M. (2018, August). Detecting population-level marine diversity with environmental DNA methodology. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Awarded Doctoral Degree

Jeunen, G.-J. (2018). Evaluating environmental DNA (eDNA) metabarcoding as a method for monitoring biodiversity in marine ecosystems (PhD). University of Otago, Dunedin, New Zealand. Retrieved from http://hdl.handle.net/10523/8347

2017

Conference Contribution - Published proceedings: Abstract

Jeunen, G.-J., Spencer, H., Lamare, M., Knapp, M., & Gemmell, N. (2017). Environmental DNA monitoring detects habitat-specific species assemblages in the marine ecosystem. Proceedings of the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB). 678. Retrieved from http://gen2017.w.events4you.currinda.com