Martin Kapun

  • Bioinformatics and biostatistics support & training
  • Software development (UNIX, Python, R)
  • Research in populationsgenomics and phylogenetics
  • Data-management und development of hard- und software-based infrastructure
  • Development of open science und open data policies
Martin Kapuns ORCID record:
Phone: +43 1 52177-311


  • 2008-2013: PhD, Vetmeduni Vienna, Austria: The genetic basis of adaptation in Drosophila melanogaster; Advisors: Prof. Christian Schlötterer & Prof. Thomas Flatt
  • 2004-2007: MSc (Magister rerum naturalis), Ecology, University of Vienna, Austria: The genetic structure of Slovakian Bee-eaters (Merops apiaster): Microsatellite differentiation between individuals and colonies; Advisors: Dr. Christian Schultze & Prof. Konrad Fiedler
  • 1999-2004: BSc (Bacchalaureus rerum naturalis), Biodiversity and Ecology, Karl Franzens University Graz, Austria

Professional History

  • Since July 2021: Bioinformatician at the Natural History Museum of Vienna, Austria
  • since 2019: Group Leader at Department of Cell and Developmental Biology, Medical University of Vienna, Austria
  • 2019 -2021: Group Leader at the Department of Evolutionary Biology and Environmental Studies with Prof. Wolf Blanckenhorn, University of Zürich, Switzerland
  • 2019: Bioinformatics specialist with Prof. Tadeusz Kawecki, Department of Ecology and Evolution, University of Lausanne, Switzerland
  • 2013-2018: Postdoctoral Research Associate with Prof. Thomas Flatt, Department of Ecology and Evolution, University of Lausanne, Switzerland & Department of Biology, Ecology and Evolution, University of Fribourg, Switzerland
  • 2008-2013: PhD Student with Prof. Christian Schlötterer, Institute for population genetics, Vetmeduni Vienna, Austria
  • 2007-2008: Research Assistant with Prof. Dr. Hans Winkler: Population genetic studies of migratory birds, European beavers and phylogeny of Piciformes, Konrad Lorenz Institute for Ethology, Austrian Academy of Sciences, Vienna, Austria


  • 2019-2022: WF standalone grant (P 32275; € 464.870,70): Keep cool: The Influence of Symbionts on Thermal Preference
  • 2016-2018: 3x ESEB STN Travel Awards
  • 2013: PhD diploma with distinction
  • 2009-2010: DOC-Fellowship, Austrian Academy of Science
  • 2008: Merit Scholarship, University of Vienna
  • 2008: Master thesis with distinction

Academic Teaching

Student and Postdoc Supervision
Postdoc (1); PhD students (3); master students (3)

Lectures and exercise courses
  • 2020: Ecology block course (Bio329); UZH Zürich (lecturer)
             Insect Reproduction block course (Bio310); UZH Zürich (main organizer & lecturer)
  • 2019: Animal behavior block course (Bio352); UZH ZÜRICH (lecturer)
             Evolution practicum (Bio116); UZH Zürich
  • 2017: Practical Course in Molecular Genetics (main organizer & lecturer)
              Drosophila Genetics TP, UNIL Lausanne
  • 2016: Practical Course in Molecular Genetics (main organizer & lecturer)
              Drosophila Genetics TP, UNIL Lausanne
  • 2015: Experimental Design Course; UNIL Lausanne (main lecturer)
              Drosophila Genetics TP, UNIL Lausanne (main organizer & lecturer)
  • 2015: NGS Workshop 2015: Introduction to bioinformatics with Python and data analysis using next generation sequencing (NGS), UNIL Lausanne (main organizer & main lecturer)
  • 2014: Experimental Design Course; UNIL Lausanne
             Bioinformatics TP, UNIL Lausanne
             Introduction to Scientific Writing, UNIL Lausanne
  • 2012: PhD student Introductory Course 2012: Introduction to bioinformatics programming with Python and data analysis using next generation sequencing (NGS), Vetmeduni Vienna (lecturer)
  • 2011: Introduction to Scientific Writing, UNIL Lausanne
              Einführung in die Biostatistik, Vetmeduni Vienna (main organizer)
               NGS Workshop 2011: De novo assembly, a brief introduction to ABySS, Vetmeduni Vienna (lecturer)

A complete list of my current peer-reviewed publications including manuscripts on preprint servers as well as H-Index can be found online on Google Scholar:,
Publications marked with an asterisk (*) indicate shared first authorship or co-correspondence.
Publications prefixed with a paragraph symbol (§) represent my five most important publications.

Original articles in peer-reviewed scientific journals

BETANCOURT NJ, RAJPUROHIT S, DURMAZ E, FABIAN DK, KAPUN M, FLATT T, & SCHMIDT P (2021). Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster. Molecular Ecology, 30: 2817-2830. doi:

KAPUN M*, NUNEZ JCB*, BOGAERTS-MÁRQUEZ M*, MURGA-MORENO J*, PARIS M*, OUTTEN J, … BERGLAND AO (2021). Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource. Molecular Biology and Evolution, (msab259). doi: 10.1093/molbev/msab259

§KAWECKI TJ, ERKOSAR B, DUPUIS C, HOLLIS B, STILLWELL RC, & KAPUN M (2021). The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila. Molecular Biology and Evolution, 18. doi: doi:10.1093/molbev/msab061

KAYA C, GENERALOVIC TN, STÅHLS G, HAUSER M, SAMAYOA AC, NUNES-SILVA CG, … KAPUN M, SANDROCK C (2021). Global population genetic structure and demographic trajectories of the black soldier fly, Hermetia illucens. BMC Biology, 19(1), 94. doi: 10.1186/s12915-021-01029-w

WALLACE MA, COFFMAN KA, GILBERT C, RAVINDRAN S, ALBERY GF, ABBOTT J, … KAPUN M … OBBARD DJ (2021). The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe. Virus Evolution, (veab031). doi: 10.1093/ve/veab031

KAPOPOULOU A*, KAPUN M*, PIEPER B*, PAVLIDIS P*, WILCHES R*, DUCHEN P*, … LAURENT S* (2020). Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster. Scientific Reports, 10(1), 22415. doi: 10.1038/s41598-020-79720-1

DURMAZ E, KERDAFFREC E, KATSIANIS G, KAPUN M*, & FLATT T*. (2020). How Selection Acts on Chromosomal Inversions. eLS (Encyclopedia of Life Sciences), in press

§KAPUN M*, BARRON MG*, et al. (2020). Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses. Molecular Biology and Evolution. 37, 2661–2678 (doi:10.1093/molbev/msaa120)

WANG Y, KAPUN M, KUENZEL S, BERGLAND AO, STAUBACH F. (2020). Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate. Environmental Microbiology Reports. 12, 220–228. (doi:10.1111/1758-2229.12826)

HOEDJES KM, HEUVEL J VAN DEN, KAPUN M, KELLER L, FLATT T, ZWAAN BJ. (2019). Distinct genomic signals of lifespan and life history evolution in response to postponed reproduction and larval diet in Drosophila. Evolution Letters. 3, 598-609. (doi:10.1002/evl3.143)

RAMAEKERS A, CLAEYS A, KAPUN M, MOUCHEL-VIELH E, POTIER D, WEINBERGER S, GRILLENZONI N, DARDALHON-CUMÉNAL D, YAN J, WOLF R, FLATT T, BUCHNER E, HASSAN BA. (2019). Altering the Temporal Regulation of One Transcription Factor Drives Evolutionary Trade-Offs between Head Sensory Organs. Developmental Cell. 50, 780-792. (doi:10.1016/j.devcel.2019.07.027)

DURMAZ E, RAJPUROHIT S, BETANCOURT N, FABIAN DK, KAPUN M, SCHMIDT PS, FLATT T (2019) A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life‐history adaptation in Drosophila. Evolution. 73, 1774-1792. (doi:10.1111/evo.13759)

FABIAN DK, GARSCHALL K, KLEPSATEL P, SANTOS-MATOS G, SUCENA É, KAPUN M, LEMAITRE B, SCHLÖTTERER C, ARKING R, FLATT T (2018) Evolution of longevity improves immunity in Drosophila. Evolution Letters. 2, 567-579. (doi:10.1002/evl3.89)

KAPUN M*, FLATT T*. The Evolutionary Significance of Inversion Polymorphisms in Drosophila melanogaster. (2018) Invited Review for a Special Issue in Molecular Ecology. 28, 1263-1282. (doi:10.1111/mec.14871)

MALLARD F, NOLTE V, TOBLER R, KAPUN M, SCHLÖTTERER C (2018) Rapid metabolic rewiring drives adaptation to novel thermal environments in Drosophila. Genome Biology, 19, 119. (doi:10.1186/s13059-018-1503-4)

TRUITT A, KAPUN M, KAUR R, MILLER W (2018) Wolbachia infections modify temperature preference in Drosophila melanogaster. Environmental Microbiology. 21, 3259-3268. (doi:10.1111/1462-2920.14347)

DURMAZ E, BENSON C, KAPUN M, SCHMIDT PS, FLATT T (2018) A Chromosomal Inversion Polymorphism Underpins Latitudinal Clines in Survival Traits. Journal of Evolutionary Biology. 31, 1354-1364. (doi:10.1111/jeb.13310)

BEHRMAN E, HOWICK VM, KAPUN M, STAUBACH F, BERGLAND AO, PETROV DA, LAZZARO BP, SCHMIDT PS (2018) Rapid seasonal adaptation in innate immunity of wild Drosophila melanogaster. Proceedings of the Royal Society of London B. 285, 20172599. (doi:10.1098/rspb.2017.2599)

KAPUN M*, SCHMIDT C*, DURMAZ E, SCHMIDT PS, FLATT T (2016) Parallel effects of the inversion In(3R)Payne on body size across the North American and Australian clines in Drosophila melanogaster. Journal of Evolutionary Biology, 29, 1059-1072

§KAPUN M, FABIAN DK, GOUDET J, FLATT T (2016): Genomic Evidence for Adaptive Inversion Clines in Drosophila melanogaster. Molecular Biology and Evolution, 33, 1317-1336

RANE RV, RAKO L, KAPUN M, LEE SF, HOFFMANN AA (2015). Genomic evidence for role of inversion 3RP of Drosophila melanogaster in facilitating climate change adaptation. Molecular Ecology, 24, 2423-2432

SZKIBA D, KAPUN M, VON HAESELER A, GALLACH M (2014). SNP2GO: Functional Analysis of Genome-Wide Association Studies. Genetics, 197, 285–289

§KAPUN M, VAN SCHALKWYK H, MCALLISTER B, FLATT T AND SCHLÖTTERER C (2014). Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster. Molecular Ecology, 23, 1813–1827

FABIAN DK*, KAPUN M*, NOLTE V, KOFLER R, SCHMIDT P, SCHLÖTTERER C, FLATT T (2012) Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America. Molecular Ecology, 21, 4748–4769

OROZCO-TERWENGEL P*, KAPUN M*, NOLTE V*, KOFLER R, FLATT T, SCHLÖTTERER C (2012) Adaptation of Drosophila to novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Molecular Ecology, 21, 4931–4941

KAPUN M, DAROLOVÁ A, KRIŠTOFIK J, MAHR K, HOI H (2011): Distinct colour morphs in nestling European Bee-eaters Merops apiaster: is there an adaptive value? Journal of Ornithology, 152, 1001-1005

KAPUN M, NOLTE V, FLATT T, SCHLÖTTERER C (2010): Host Range and Specificity of the Drosophila C Virus. PLoS ONE, 5, 3043–3046


Books, Book sections

HAUDRY A, LAURENT S, KAPUN M (2020): Population Genomics on the Fly: Recent Advances in Drosophila. in Dutheil J, editor. 2020. Statistical Population Genomics, Methods in Molecular Biology. Springer US. (doi:10.1007/978-1-0716-0199-0. ISBN: 978-1-07-160199-0)

Central Research Laboratories

De Mattia Willy
Project researcher
Duda Michael
Project researcher
Fischer Iris
Project researcher
Haring Elisabeth
Head of department
Helmer Nikolaus
Project researcher
Kirchner Sandra
Project researcher
Kruckenhauser Luise
Staff scientist
Leeb Christoph
Project researcher
Macek Oliver
Project researcher, Myriapoda collection assistant
Pail Victoria
Project researcher
Reier Susanne
Project researcher
Schoder Sabine
project researcher
Schubert Hannah
Project researcher
Schwahofer Paula
Project researcher
Sittenthaler Marcia
Administration, Technician, Projekt researcher
Szucsich Nikolaus
Wanka Alexandra Julia
Technician (CRL) / Office (2nd Zoology)
Wegner Wencke
Operator for microanalysis
Wolf Paul
Project researcher