Emily Anne Hartop

About

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, a model dark taxon.

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.

Research

I am a biodiversity scientist and entomologist. My research focuses on Dark Taxa: species-rich but poorly known groups that comprise the majority of Earth’s biodiversity. I combine taxonomy, DNA barcoding, morphometrics, and ecological modelling to develop scalable workflows for discovering species, linking historical collections to molecular data, and analysing community structure in hyperdiverse systems. I am a specialist on scuttle flies (Diptera: Phoridae), a model dark taxon.

I serve as co-lead of the Scientific Research working group of CETAF (Consortium of European Taxonomic Facilities), where I promote integrative, collections-driven approaches to biodiversity science and advocate for the inclusion of Dark Taxa in European research and policy frameworks.

I am a partner in the recently funded Horizon Europe projects BGE+ and TETTRIX, where I will be contributing expertise in integrative taxonomy, molecular workflows, and the mobilisation of natural history collections. In these projects, I will work to strengthen research infrastructures, develop best practices for biodiversity data generation and interoperability, and ensure that underrepresented taxa are fully integrated into large-scale European biodiversity initiatives.

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.

2026

Williamson, David; Hartop, Emily Anne; Speed, James. (2026) Learning from Digital Collections: Digitisation and Machine Learning for Large-Scale Museum Studies. Biodiversity Information Science and Standards (BISS)
Academic article

2025

Hartop, Emily Anne. (2025) Dark Taxa are a THING.
Other presentation
H., Nowak, Karol; Hartop, Emily Anne; Monika, Prus-Frankowska,; Mateusz, Buczek,; R., Kolasa, Michał; Tomas, Roslin,. (2025) What lurks in the dark? An innovative framework for studying diverse wild insect microbiota. Microbiome
Academic article
Ekrem, Torbjørn; Hartop, Emily Anne; Aspaas, Aina Mærk. (2025) Finn arten med DNA-strekkoding.
Museum exhibition

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
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
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
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
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

Journal publications

Williamson, David; Hartop, Emily Anne; Speed, James. (2026) Learning from Digital Collections: Digitisation and Machine Learning for Large-Scale Museum Studies. Biodiversity Information Science and Standards (BISS)
Academic article
H., Nowak, Karol; Hartop, Emily Anne; Monika, Prus-Frankowska,; Mateusz, Buczek,; R., Kolasa, Michał; Tomas, Roslin,. (2025) What lurks in the dark? An innovative framework for studying diverse wild insect microbiota. Microbiome
Academic article
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
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
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
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
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

UTSTILLING

Hartop, Emily Anne. (2025) Dark Taxa are a THING.
Other presentation
Ekrem, Torbjørn; Hartop, Emily Anne; Aspaas, Aina Mærk. (2025) Finn arten med DNA-strekkoding.
Museum exhibition

Teaching

Courses

BI2001 - Biosystematics and biodiversity in space and time

I am the course organizer and a lecturer for Biosystematics and biodiversity in space and time (BI2001) here at NTNU.

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 teach for the Nordic Academy of Biodiversity and Systematic Studies (NABiS) field course “Insects: Inventory and identification” on the island of Öland every year (since 2018).

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

Supervision

I am always open to hearing from those interested in Master's (including NABiS), PhD, or Postdoctoral positions. If you are passionate about biodiversity, systematics, or interdisciplinary research and would like to join my team, please feel free to contact me by email to discuss potential opportunities.

Current Students and Scholars

PhD Supervisor, Lucas Geisler

MSc Supervisor, Thomas Wetteland Woxen

MSc Supervisor, Linnea Sørum

Fulbright Host, Erin Connolly

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
Paula is now Head of Diptera at Zoologische Staatssammlung München.

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
Leshon is currently pursuing his PhD at Humboldt University, Berlin, Germany.

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
Valerio is currently a researcher at the University of Padua, Padua, Italy.

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

Outreach

The search for Earth’s most mysterious creatures is turning up extraordinary results

Vox article about the global hunt for dark taxa.

2025

Academic lecture

Hartop, Emily Anne; Williamson, David R.. (2025) The R.H.L. Disney Phoridae Collection: Evolving a Legacy for the Taxonomic Future. Dipterists Forum Annual Meeting , Cambridge Museum of Zoology 15.11.2025 -
Academic lecture

Hartop, Emily Anne; Williamson, David R.. (2025) Too Many Flies, Too Few Taxonomists: Let Machines Do the Boring Bits. Norsk symposium i biosystematikk , Trondheim 03.11.2025 - 04.11.2025
Poster

Williamson, David R.; Welch, Mark; Connolly, Erin M.; Yiu, Anna; Hartop, Emily Anne. (2025) Museum Collections and the Taxonomic Future of Dark Taxa: Phoridae as a testcase. Dipterists Day , Cambridge 15.11.2025 - 15.11.2025

2024

Lecture

Ekrem, Torbjørn; Hartop, Emily Anne; Prestø, Tommy; Vinje, Christina; Martin, Michael David; Lagos, Jaime Gerardo Morin. (2024) Jul i VIMU magasinet: Reinsdyr, småkryp og julens krydder. Omvisninger i samlingene , Trondheim 10.12.2024 - 11.12.2024
Lecture

Hartop, Emily Anne. (2024) GLOW: Evolving workflows for Dark Taxon Biology. Institute of Biology Seminar 21.11.2024 -
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 05.09.2024 -
Lecture

Hartop, Emily Anne. (2024) Megabarcoding with ONT. Seminar for NIBIO Svanhovd 04.12.2024 -
Academic lecture

Hartop, Emily Anne. (2024) Webinar on DNA-barcoding using nanopores: Bridging theory to real-world implementation. Online Webinar for iBOL EUROPE 06.06.2024 -
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. Omvisning med foredrag i naturhistoriske samlinger , Trondheim 23.10.2024 -
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. Omvisning med foredrag i naturhistoriske samlinger , Trondheim 24.10.2024 -
Lecture

Ekrem, Torbjørn; Hartop, Emily Anne; Aspaas, Aina Mærk. (2024) Finn arten med DNA-strekkoding. Ungdommens forskernatt ved NTNU , Trondheim 27.09.2024 -

Språkvelger

Emily Anne Hartop