Emily Anne Hartop

About

I am a biodiversity scientist specializing in the study of dark taxa. My work focuses on employing integrative taxonomic techniques to explore hyperdiverse, yet poorly understood, groups that form a major component of our planet's biodiversity. Through this, I aim to deepen our understanding of their diversity and ecological roles. As a specialist in the fly genus Megaselia (Diptera: Phoridae), I use this group as a model taxon to pioneer new strategies for studying some of the world's most challenging and underexplored organisms.

I am originally from California, where I got my B.S. in Entomology from the University of California Riverside. I later worked on the BioSCAN project at the Natural History Museum of Los Angeles, where I got hooked on the hyperdiverse fly family Phoridae, also known as scuttle flies.

In 2017, I was awarded a Swedish Taxonomy Initiative grant to work on scuttle fly material from the Swedish Malaise Trap Project at Station Linné on the island of Öland. This work became part of my PhD thesis in the Ronquist Lab at Stockholm University. My thesis tackled questions about the diversity of scuttle flies, but also developed integrative methodologies to handle "dark taxa", groups that are hyperdiverse and abundant but poorly known due to the complexity of their study.

My work on dark taxa continued and expanded when I took a position with the Center for Integrative Biodiversity Discovery at the Museum für Naturkunde in Berlin from 2021-2024. There, our team employed molecular techniques in combination with robotics and machine learning to accelerate biodiversity science.

In 2024 I joined NTNU as an Onsager Fellow with the goal of leading a team of innovators who are similarly interested in exploring the richest and most abundant taxa on earth with integrative, multidisciplinary perspectives.

Publications

Resolving biology’s dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon

We use megabarcoding to assess a model dark taxon, investigating species diversity, variation across time and space, and the environmental drivers. We demonstrate how dark taxon research can provide critical insights in the era of climate change.

Opportunity in our Ignorance: Urban Biodiversity Study Reveals 30 New Species and One New Nearctic Record for Megaselia (Diptera: Phoridae) in Los Angeles (California, USA).

Description of thirty new species of scuttle flies from Los Angeles using a table-based description system.

The Swedish Malaise Trap Project: A 15 Year Retrospective on a Countrywide Insect Inventory.

Everything you'd want to know about one of the most ambitious insect inventories of all time.

Towards Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa.

Systematic and integrative approach to discovering and delimiting species in hyperdiverse groups.

Meier, R., Hartop, E., Pylatiuk, C., Srivathsan, A. (2024) Towards holistic insect monitoring: species discovery, description, identification, and traits for all insects. Phil. Trans. R. Soc. B. 10.1098/rstb.2023-0120

Lewthwaite, J.M.M., Baiotto, T.M., Brown, B.V., Cheung, Y.Y., Baker, A.J., Lehnen, C., McGlynn, T.P., Shirey, V., Gonzalez, L., Hartop, E., Kerr, P.H., Wood, E., Guzman, L.M. (2024) Drivers of arthropod biodiversity in an urban ecosystem. Sci Rep 14, 390. https://doi.org/10.1038/s41598-023-50675-3

Wührl, L., Rettenberger, L., Meier, R., Hartop, E., Graf, J., Pylatiuk, C. (2024) Entomoscope: An Open-Source Photomicroscope for Biodiversity Discovery. IEEE Access 12, 11785-11794. DOI: 10.1109/ACCESS.2024.3355272.

Vasilita, C., Feng, V., Hansen, A.K., Hartop, E., Srivathsan, A., Meier, R. (2024) Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples. Molecular Ecology Resources, 24(3), e13922. https://doi.org/10.1111/1755-0998.13922

Iwaszkiewicz-Eggebrecht, E., Łukasik, P., Buczek, M., Deng, J., Hartop, E., Havnås, H, Prus-Frankowska, M., Ugarph, C., Viteri, P., Andersson, A., Roslin, T., Tack, A., Ronquist, F., Miraldo, A. (2023) FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples. PloS one, 18(7): e0286272. https://doi.org/10.1371/journal.pone.0286272

Hartop, E., Srivathsan, A., Ronquist, F., Meier, R. (2022) Towards Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa. Systematic Biology, syac033. https://doi.org/10.1093/sysbio/syac033

Brown, B., Hartop, E., Wong, M. (2022) Sixteen in one: white-belted Megaselia Rondani (Diptera: Phoridae) from the New World challenge species concepts. Insect systematics and diversity, 6(3), 1-17. https://doi.org/10.1093/isd/ixac008

Meier, R., Blaimer, B., Buenaventura, E., Hartop, E., von Rintelen, T., Srivathsan, A., Yeo, D. (2021) A re-analysis of the data in Sharkey et al.’s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science. Cladistics, 38(2), 264-275. https://doi.org/10.1111/cla.12489

Srivathsan, A., Lee, L., Katoh, K., Hartop, E., Narayanan Kutty, S., Wong, J., Yeo, D., Meier, R. (2021) ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biology 19, 217. https://doi.org/10.1186/s12915-021-01141-x

Hartop, E., Häggqvist, S., Ulefors, S.O, Ronquist, F. (2020) Scuttling Towards Monophyly: Phylogeny of the mega-diverse genus Megaselia (Diptera: Phoridae). Systematic Entomology, 46(1), 71-82. https://doi.org/10.1111/syen.12448

Karlsson, D., Hartop, E., Forshage, M., Jaschhof, M., & Ronquist, F. (2020). The Swedish Malaise Trap Project: A 15 Year Retrospective on a Countrywide Insect Inventory. Biodiversity data journal, 8, e47255. https://doi.org/10.3897/BDJ.8.e47255

Srivathsan, A., Hartop, E., Puniamoorthy, J., Lee, W.T., Narayanan Kutty, S., Kurina, O., Meier, R. (2019) Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing. BioMed Central Biology 17, 96. https://doi.org/10.1186/s12915-019-0706-9

McGlynn T.P, Meineke E.K., Bahlai E.A., Li E., Hartop E.A., Brown B.V. (2019) Temperature accounts for the biodiversity of a hyperdiverse group of insects in urban Los Angeles. Proceedings of the Royal Society B, 286: 20191818. DOI: 10.1098/rspb.2019-1818.

Brown B., Wong M., Hartop E. (2019) A new white-spotted Megaselia Rondani (Diptera: Phoridae) from Western North America. Biodiversity Data Journal 7: e34310.

Hartop, E.A., Gonzalez, L.A., Brown, B.V. (2018) Backyard Biodiversity: Unravelling life histories of the new fly species discovered by the BioSCAN Project proves harder than first assumed. Journal of Negative Results 12, 1-8.

Hartop, E.A., Long, E., Bornstein, C., Gonzalez, L.A., Brown, B.V. (2018) Urban Nature Gardens at the Natural History Museum of Los Angeles County attract “wildlife spectacle” of insect pollinators. In: Hartop, E.A. and Brown, B.V. (Eds.), Beyond Pests: Biodiversity in the Urban Environment, International Congress of Entomology, 25-30 September 2016, Orlando, Florida, USA. Zoosymposia 12, 29-50.

Brown, B.V., Hartop, E. A. (2017) Mystery mushroom malingerers: Megaselia marquezi Hartop et al. 2015 (Diptera: Phoridae). Biodiversity Data Journal 5: e15052. DOI: 10.3897/BDJ.5.e15052

Brown, B.V., Hash, J., Hartop, E., Porras, W., Amorim, D. (2017) Baby Killers: Documentation and Evolution of Scuttle Fly (Diptera: Phoridae) Parasitism of Ant (Hymenoptera: Formicidae) Brood. Biodiversity Data Journal 5: e11277. DOI: 10.3897/BDJ.5.e11277

Brown, B.V., Hartop, E.A. (2016) Big data from tiny flies: patterns revealed from over 42,000 phorid flies (Insecta: Diptera: Phoridae) collected over one year in Los Angeles, California, USA. Urban Ecosystems 20(3), 521-534. DOI:10.1007/s11252-016-0612-7

Hartop, E. A., Brown, B. V., Disney, R. H. L. (2016) Flies from L.A., The Sequel: A further twelve new species of Megaselia (Diptera: Phoridae) from the BioSCAN Project in Los Angeles (California, USA). Biodiversity Data Journal 4: e7756.

Hartop, E. A., Wong, M. A., Eiseman, C. S. (2016) Material from the BioSCAN project in Los Angeles (Calfornia: USA) yields another new species and leads to clarity for two confused type series of Megaselia Rondani (Diptera: Phoridae). Proceedings of the Entomological Society of Washington 118(1): 93-100.

Hartop, E. A., Brown, B. V. (2015) Natural Blondes: New Species of Brilliantly Yellow Colored and Morphologically Distinct Megaselia (Diptera: Phoridae) from Central America. Studia Dipterologica 21(2): 257–265.

Hartop, E. A., Brown, B. V. (2015) Seeing spots: Another distinct spotted wing species of Megaselia Rondani (Diptera: Phoridae) from Costa Rican cloud forests. Studia Dipterologica 21(2): 181–185

Eiseman, C. S., Hartop, E. A. (2015) A New Species of Megaselia Rondani (Diptera: Phoridae) Reared from a Macrodiplosis Kieffer (Diptera: Cecidomyiidae) Gall on Black Oak. Proceedings of the Entomological Society of Washington 117(4):463-466.

Hartop, E. A., Brown, B. V., Disney, R. H. L. (2015) Opportunity in our Ignorance: Urban Biodiversity Study Reveals 30 New Species and One New Nearctic Record for Megaselia (Diptera: Phoridae) in Los Angeles (California, USA). Zootaxa 3941(4), 451-484.

Hartop, E. A., Brown, B. V. (2014) The tip of the iceberg: a distinctive new spotted-wing Megaselia species (Diptera: Phoridae) from a tropical cloud forest survey and a new, streamlined method for Megaselia descriptions. Biodiversity Data Journal, 2, e4093.

Brown, B. V., Hartop, E. A. (2014) Recognition of Megaselia arizonensis (Malloch, 1912) (Diptera: Phoridae), a Common North American Fly. Contributions in Science 522, 45-49.

Mottern, J. L., Heraty, J. M., Hartop, E. A. (2011) Cales (Hymenoptera: Chalcidoidea): morphology of an enigmatic taxon with a review of species. Systematic Entomology 36, 267–284.

2024

Li, Xuankun; Hash, John M.; Hartop, Emily Anne; Yang, Ding; Smith, Paul T.; Brown, Brian V.. (2024) A molecular phylogeny of scuttle flies (Diptera: Phoridae) unveils extensive concordance but intriguing divergences from morphological results. Systematic Entomology
Academic article
Riccardi, Paula Raile; Hartop, Emily Anne. (2024) Large-scale integrative taxonomy of Swedish grass flies (Diptera, Chloropidae) reveals hitherto unknown complexity of a dark taxon. Zoologica Scripta
Academic article
Meier, Rudolf; Hartop, Emily Anne; Pylatiuk, Christian; Srivathsan, Amrita. (2024) Towards holistic insect monitoring: Species discovery, description, identification and traits for all insects. Philosophical Transactions of the Royal Society of London. Biological Sciences
Academic literature review
Caruso, Valerio; Hartop, Emily Anne; Chimeno, Caroline; Noori, Sajad; Srivathsan, Amrita; Haas, Michael. (2024) An integrative framework for dark taxa biodiversity assessment at scale: A case study using Megaselia (Diptera, Phoridae). Insect Conservation and Diversity
Academic article
Hartop, Emily Anne; Lee, Leshon; Srivathsan, Amrita; Jones, Mirkka; Peña-Aguilera, Pablo; Ovaskainen, Otso Tapio. (2024) Resolving biology’s dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon. BMC Biology
Academic article

Journal publications

Li, Xuankun; Hash, John M.; Hartop, Emily Anne; Yang, Ding; Smith, Paul T.; Brown, Brian V.. (2024) A molecular phylogeny of scuttle flies (Diptera: Phoridae) unveils extensive concordance but intriguing divergences from morphological results. Systematic Entomology
Academic article
Riccardi, Paula Raile; Hartop, Emily Anne. (2024) Large-scale integrative taxonomy of Swedish grass flies (Diptera, Chloropidae) reveals hitherto unknown complexity of a dark taxon. Zoologica Scripta
Academic article
Meier, Rudolf; Hartop, Emily Anne; Pylatiuk, Christian; Srivathsan, Amrita. (2024) Towards holistic insect monitoring: Species discovery, description, identification and traits for all insects. Philosophical Transactions of the Royal Society of London. Biological Sciences
Academic literature review
Caruso, Valerio; Hartop, Emily Anne; Chimeno, Caroline; Noori, Sajad; Srivathsan, Amrita; Haas, Michael. (2024) An integrative framework for dark taxa biodiversity assessment at scale: A case study using Megaselia (Diptera, Phoridae). Insect Conservation and Diversity
Academic article
Hartop, Emily Anne; Lee, Leshon; Srivathsan, Amrita; Jones, Mirkka; Peña-Aguilera, Pablo; Ovaskainen, Otso Tapio. (2024) Resolving biology’s dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon. BMC Biology
Academic article

Teaching

I am the course organizer and a lecturer for BI2001: Biosystematics and biodiversity in space and time.

I am actively involved in the Forskerskole I Biosystematikk (ForBio) as an instructor for the course on DNA Barcoding and course content organizer/instructor for the course on Oxford Nanopore Sequencing.

I have previously taught for the ForBio course “Biosystematics, ecology and applied science of flies and midges (Insecta: Diptera)”, the Nordic Academy of Biodiversity and Systematic Studies course “Insects: Inventory and identification”, and the joint ForBio/Swedish Taxonomy Initiative course “Entomology hands-on: collecting, sorting, species ID”.

Supervision

I am currently in the process of starting my lab at NTNU and will be looking for interested students and postdocs.

Past Supervision and Mentorship

Supervisor, Paula Riccardi, Postdoctoral Researcher at Museum für Naturkunde, Berlin, Germany
Capes-Humboldt Research Fellowship on “Evolution and phylogenomics of the grass flies (Diptera: Schizophora)”, 2021-2023

Co-supervisor, Leshon Lee, National University of Singapore, Singapore
MS Thesis: “The species diversity of Scuttle flies from the Singaporean islands Sentosa and Pulau Ubin”, defended June 2023

Co-supervisor, Valerio Caruso, Staatliches Museum für Naturkunde, Stuttgart, Germany
PhD Thesis: “An integrative approach to the Phoridae of Germany” (Part of GBOLIII: Dark Taxa), 2020-2023

Co-supervisor, Karol Nowak, Jagiellonian University, Kraków, Poland
MS Thesis: “Identifying patterns in microbiome composition across insect communities”, defended 8 July 2022.

Outreach

2024

Academic lecture

Hartop, Emily Anne. (2024) Webinar on DNA-barcoding using nanopores: Bridging theory to real-world implementation. Online Webinar for iBOL EUROPE 2024-06-06 -
Popular scientific lecture

Ekrem, Torbjørn; Hartop, Emily Anne; Aspaas, Aina Mærk. (2024) Finn arten med DNA-strekkoding. NTNU Vitenskapsmuseet Ungdommens forskernatt ved NTNU , Trondheim 2024-09-27 -
Popular scientific lecture

Ekrem, Torbjørn; Prestø, Tommy; Hassel, Kristian; Hartop, Emily Anne; Bakken, Torkild; Grankvist, Maria Buhaug. (2024) Terrors from Land and Sea - A journey into Nature’s Nightmares. NTNU Vitenskapsmuseet Omvisning med foredrag i naturhistoriske samlinger , Trondheim 2024-10-23 -
Popular scientific lecture

Ekrem, Torbjørn; Prestø, Tommy; Hassel, Kristian; Hartop, Emily Anne; Bakken, Torkild; Grankvist, Maria Buhaug. (2024) Grøss og gru fra hav og land - En reise i naturens mareritt. NTNU Vitenskapsmuseet Omvisning med foredrag i naturhistoriske samlinger , Trondheim 2024-10-24 -
Lecture

Hartop, Emily Anne. (2024) GLOW: Evolving workflows for Dark Taxon Biology. Institute of Biology Seminar 2024-11-21 -
Academic lecture

Hartop, Emily Anne. (2024) A Dark Decade: Progress on the world's most intractable "genus" (Diptera: Megaselia). 9th International Barcode of Life Conference , Belém 2024-09-05 -
Lecture

Hartop, Emily Anne. (2024) Megabarcoding with ONT. Seminar for NIBIO Svanhovd 2024-12-04 -

Språkvelger

Emily Anne Hartop