Martin Luther University Halle-Wittenberg

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Dr. Eckart Stolle


Dr. Eckart Stolle

room 6.06
Hoher Weg 8
06099 Ĥalle (Saale)

phone: (0049) 03455526502
fax: (0049) 03455527152
eckart.stolle --at--

GoogleScholar | GitHub | ORCID 0000-0001-7638-4061
ResearchGate | FigShare | ResearcherID G-3780-2011/Publons
member of the steering committee of the GBOP (genomic basis of phenotypic innovation in insect evolution) initiative for a DFG priority program. associated member of DFG research unit So-Long (FOR2281/2) between Freiburg, Mainz, Münster, Regensburg, Halle, Frankfurt, Groningen and Friborg.
thanks to our funders: DAAD, DFG, Marie-Curie-Actions, EASI-Genomics (European Union), the German and European Tax Payers!


  • 2020-01: new place: ZFMK Bonn (Head of Section Comparative Insect Genomics).
  • 2019-12: samples, papers and grants submitted =) and preparations started for my new post as Head of Section Insect Comparative genomics at the Leibniz Institute for Animal Biodiversity / Research Museum Alexander Koenig (Bonn). new email: e.stolle (at)
  • 2019-08: Bee microRNA preprint with Karen Kapheim et al. on BioRxiv
  • 2019-07: Thanks to EASI-Genomics for funding my proposal!
  • 2019-07: great SMBE conference in Manchester. Thanks SMBE for the financial support (Young Investigator Award)
  • 2019-05: 2 grants submitted! Oral Presentation at the SMBE conference! MolEcol paper with J Colgan and Y Wurm is now published
  • 2019-02: Joe's and Yannicks bumblebees, pesticides & RNAseq paper accepted in MolEcol!
  • 2019-01:thelytoky MBE paper is online
    (Media coverage: Eureka,ScienceDaily,,The Atlantic,upi,MSN ,VBIO ,IDW)
  • 2019-01:MBE paper (ant supergene expansion) is online
    G3 paper (alkali bee genome) is online
  • 2018-12: honeybee genomics paper accepted in MBE, ant supergene paper accepted in MBE, Alkali bee genome paper accepted in G3! grant submitted, now back to prepping another MS for submission, 1 minor revision and wait for another MS to come back from review.
  • 2018-11: watch out for our new honeybee paper, just got accepted @ MBE; also, our collab. work with QMUL got a minor revision and another collab. paper got submitted.
  • 2018-11: both paper revisions are back with MBE, 2 more papers from collaborations are submitted/on bioRxiv, grant proposal almost done, stingless bee assembly done
  • 2018-10: our ant genomics paper got a minor revision! Nanopore sequencing also is going good, got 17Gb on one flowcell (9.4.1 flowcell, LSK108 1D ligation kit)
  • 2018-09: our BioRXiv paper is in review. Our honeybee genomics paper got a major revision
  • 2018-09: finally started nanopore sequencing: stingless bee 2 runs @ 7.2/7.4 Gb = 50x. MaSuRCA assembly with 50x Illumina yield up to 4Mb N50, Canu still running, miniasm/racon/pilon about 2Mb N50, and all with BUSCO 96-98.6%. solitary bee nanopore sequencing @ 15x with relatively low Illumina coverage next, other bees coming soon
  • 2018-08: 2 talks at the international IUSSI meeting in Sao Paulo about our recent findings on the genetic basis of thelytoky in honeybees and on supergene evolution in fireants. thanks @ DAAD for the funding
  • 2018-05: talk at the Genomics of Social Insects meeting in Cold Spring Harbor/NY
  • Research Interests

    • Evolutionary Genomics of social insects
    • Insect phenotypic innovation and comparative genomics
    • Conservation Genomics
    • Chromosome and genome evolution in populations and species
    • Entomology, particularly Hymenoptera
    • short and long read DNA sequencing (Illumina, Ion Torrent, PacBio, Nanopore)
    • RNAseq, long read RNA sequencing
    • Epigenomics (DNA methylation, Chromatin modifications)
    • also intertested in Proteomics
    • RNAi, also intertested to apply CrisprCas
    • genome assembly and annotation
    • population scale approaches, genetic diversity, molecular evolution
    • regulatory networks

    Evolutionary Genomics of social insects

    Sociality is one of the major transition of life and social species such as bees, wasps and ants are major players in terrestrial ecosystems. Furthermore they provide important ecosystem and agricultural services, such as pollination. We are interested how the extremely complex insect societies are regulated on a molecular level and what are the evolutionary processes facilitating the origin and shaping sociality. We use cutting-edge molecular and genomics approaches to address major questions and topics:
    • genetic and regulatory basis of caste determination
    • evolutionary genomics signature of eusociality
    • population dynamics and genetics of social insects, including mating behavior
    • origin and molecular underpinnings of social parasitism, i.e. loss of sociality
    • genomic architecture of major transitions, i.e. chromosomal inversions and degenerative expansion of social chromosomes in polygynous fire ants

    Insect phenotypic innovation and comparative genomics

    Insects are by far the most speciose group of higher eukaryotes and have evolved a tremendous diversity in behavioral, physiological and morphological adaptations. However, apart from a few insect model organsims, we know comparatively little about the genomic basis of phenotypic innovations in insects. Thereforewe aim to shed light into the genome evolution and molecular mechanisms shaping or shaped by new phenotypes, such as:
    • special reproductive strategies such as parthenogenesis
    • sex determination and sexual dimorphisms
    • parasitism and its associated changes in multiple morphological and behavioral traits
    • adaptations to extreme environments or diets
    • general population genomic effects and signatures of selection

    Conservation Genomics

    Many insect and pollinator species are declining due to habitat loss or homogenization. Some species are more affected than others, but some species always had small population sizes and survived yet without big problems. A decline can have a profound impact on the genetic composition of a species or population due to detrimental effects of genetic drift, loss of adaptability to changing environments and increased levels of inbreeding. We know little about the population size and genetic diversity limits a population or species can tolerate. Thus, we are investigating extreme cases with modern sequencing technologies to answer the following questions:
    • Which species are in decline and why?
    • How is decline and fragmentation of populations impacting the genetic diversity?
    • What are the limits for a population's genetic diversity and size?
    • How is genetic diversity shaped in extremely rare species?
    • What are mechanisms of inbreeding avoidance in subtropical stingless bees?
    • How genetically diverse (concurrent and historic) is the extremely isolated German population of Camptopoeum frontale, a specialist (oligolectic) bee species?
    • How can genetic information support the evaluation of the conservation status of species for Red Data Books?


    See also [Google Scholar]
    1. Brain microRNA expression associated with social evolution in bees (submitted)
      Kapheim K, Jones BM, Søvik E, Stolle E, Waterhouse RM, Bloch G, Ben-Shahar Y
      BioRxiv, doi: , 2019
    2. Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees
      Colgan T, Fletcher I, Arce A, Gill R, Ramos Rodrigues A, Stolle E, Chittka L, Wurm Y
      Molecular Ecology, 28(8):1964–1974, 2019
    3. A single SNP turns a social honey bee (Apis mellifera) worker into a selfish parasite
      Aumer D°, Stolle E°*, Allsopp M, Mumoki F, Pirk CWW, Moritz RFA*
      Molecular Biology and Evolution, 36(3): 516–526, 2019
    4. Degenerative expansion of a young supergene
      Stolle E°,Pracana R°, Howard P, Paris CI, Brown SJ, Castillo-Carrillo CA, Rossitter SJ , Y Wurm°
      Molecular Biology and Evolution, 36 (3): 553–561, 2019
      bioRxiv 2018: doi:
    5. Draft genome assembly and population genetics of an agricultural pollinator, the solitary alkali bee (Halictidae: Nomia melanderi)
      Kapheim KM, Pan H, Li C, Blatti C, Harpur BA, Ioannidis P, Jones BM, Kent CF, Ruzzante L, Sloofman L, Stolle E, Waterhouse RM, Zayed A, Zhang G, Wcislo WT
      G3, 9(3): 625–634, 2019
      bioRxiv doi: 2018
    6. Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins
      Pracana R*, Levantis I*, Martinez-Ruiz C, Stolle E, Priyam A, Y Wurm°
      Evolution Letters 1-4: 199–210, 2017
    7. Microsatellite analysis supports the existence of three cryptic species within the bumble bee Bombus lucorum sensu lato
      McKendrick L°, Provan J, Fitzpatrick U, Brown MJF, Murray TE, Stolle E, Paxton RJ
      Conservation Genetics 18(3): 573–584, 2017
    8. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living
      Kapheim KM*°, Pan H*,.., Stolle E,.., Robinson GE, Zhang G
      Science 348(6239): 1139-1143, 2015
    9. The genomes of two key bumblebee species with primitive eusocial organization
      Sadd BM°,.., Stolle E,.., Schmid-Hempel P, Worley K°
      Genome Biology 16:76, 2015
    10. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima
      Chipman AD,.., Stolle E,.., Richards S°
      PLoS Biology 12(11): e1002005, 2014
    11. Finding the missing honey bee genes: lessons learned from a genome upgrade
      Elsik CG°, Worley K°,.., Stolle E,.., Gibbs R
      BMC Genomics 15:86, 2014
    12. RESTseq – Efficient Benchtop Population Genomics with RESTriction fragment SEQuencing
      Stolle E°, Moritz RFA
      PLoS ONE 8(5): e63960, 2013
    13. Patterns of Evolutionary Conservation of Microsatellites (SSRs) Suggest a Faster Rate of Genome Evolution in Hymenoptera Than in Diptera
      Stolle E°, Kidner JH, Moritz RFA
      Genome Biology and Evolution 5(1): 151–162, 2013
    14. Alternative splicing of a single transcription factor drives selfish reproductive behavior in honeybee workers (Apis mellifera)
      Jarosch A°, Stolle E, Crewe RM, Moritz RFA
      PNAS 108(37): 15282-15287, 2011
    15. A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758) reveals slow genome and chromosome evolution in the Apidae
      Stolle E°, Wilfert L, Schmid-Hempel R, Schmid-Hempel P, Kube M, Reinhardt R, Moritz RFA
      BMC Genomics 15:86, 2011
    16. Estimating the Density of Honeybee Colonies across Their Natural Range to Fill the Gap in Pollinator Decline Censuses
      Jaffé R°, Dietemann V, Allsopp MH, Costa C, Crewe RM, Dall’Olio R, de la Rúa P, El-Niweiri MAA, Fries I, Kezic N, Meusel MS, Paxton RJ, Shaibi T, Stolle E, Moritz RFA
      Conservation Biology 24(2):583-593, 2010
    17. Novel microsatellite DNA loci for Bombus terrestris (Linnaeus, 1758)
      Stolle E°, Rohde M, Vautrin D, Solignac M, Schmid-Hempel R, Schmid-Hempel P, Moritz RFA
      Molecular Ecology Resources 9(5): 1345-1352, 2009
    18. Flower visitors in a natural population of Arabidopsis thaliana
      Hoffmann MH°, Bremer M, Schneider K, Burger F, Stolle E, Moritz G
      Plant Biology 5(5): 491-494, 2003

    other publications (selected)

    Interested to join the lab?

    If you are interested to join the lab for a Masters or PhD project, please contact us.
    Unless otherwise stated, we currently have no open positions, but support applications to external funding, e.g.


    • 2017 University Halle, PostDoc/Researcher/Assistant
    • 2017 short-term Lecturer, Queen Mary University of London
    • 2015-2017 Marie-Curie IEF Fellow, Queen Mary University of London, ant evolutionary genomics group of Dr. Y. Wurm
    • 2014-15 DAAD PostDoc, Queen Mary University of London, group of Y. Wurm
    • 2014 visiting scientist University of Buenos Aires, Argentina
    • 2014 visiting professor University Sao Paulo, Brazil
    • 2011-2014 research assistant BioSolutions GmbH, Halle
    • 2013 PhD, University Halle, Molecular Ecology group of Prof. R. Moritz
    • 2007-2010 research assistant University Halle, Molecular Ecology group of Prof. R. Moritz
    • 2007 Diploma (Biology), University Halle
    • 2006 research visit South Africa, Univ. of Pretoria


    • Bachelor/Lehramt (Biologie,Geographie,Biochemie,Bioinformatik): Grundpraktikum Zoologie (Vorlesungen, Praktikum, Prüfungen)
    • Master (Biology): General Zoology (Evolutionary & Population Genomics, Lectures, paper seminar, research project)
    • Bachelor/Lehramt (Biologie): Verhaltensbiologie/Behavioral Genetics (Vorlesungen, Praktikum)

    Location of our lab

    Institut für Biologie, Hoher Weg 8, 06120 Halle, Germany
    North tract of the building, 6th floor, AG Allgemeine Zoologie (Prof. Dr. R. Paxton)
    To get here by public transport, take Tram number 7 towards "Kröllwitz" (Tram stop under the "bridge", has a ticket machine) from the Main Train Station until stop "Louise Otto Peters Straße" (the ride takes about 15-20 minutes, its the second stop after crossing the Saale river)), where you cross the street into "Am Birkenwäldchen" and follow it straight through the little walkway and the end until the Institute building (ca 5 min walk)

    Institut für Biologie, Hoher Weg 8, 06120 Halle, Germany