PhD fellow in evolutionary ecology and comparative genomics of citrus-associated Colletotrichum fungi

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The Applied Evolutionary Ecology (AEE) group at Department of Plant and Environmental Sciences (PLEN), Section for Organismal Biology at the University of Copenhagen is advertising a PhD scholarship in comparative genomics and evolutionary ecology of plant-associated Colletotrichum fungi starting August 1st 2021 or as soon as possible thereafter.

Description of the scientific environment
The AEE group studies the evolutionary effects of organism interactions, which is of fundamental significance in ecology, evolution, agriculture and human health. We use fungi as model systems as they represent a diverse group of organisms that play a crucial role in all ecosystem processes. Group activities span how antagonistic (pathogenic) and beneficial (mutualistic) fungal symbionts are shaped by host ecology and evolution, how ecological and evolutionary factors determine the species-range partners interact with, and how new species interactions are established, for example through partner-shifts. We mainly use molecular and applied bioinformatics coupled with experimental work. Our work is fundamental in nature, but of applied significance for example for biological control and pathogen host shifts. More information can be found on the webpage of Applied Evolutionary Ecology.

Project description
The position is advertised in connection to a newly established research project “From plants to animals – understanding inter-kingdom host-shifts of fungal pathogens”, funded by the Carlsberg Foundation. Overall, the project will use the fungal genus Colletotrichum, which contains hemibiotrophic phytopathogens that are highly variable in host and tissue specificities, as model system to study wide host colonization’s of fungal pathogens. The PhD candidate will conduct independent research to assess patterns of cryptic genetic variation in several Colletotrichum species found in Brazilian citrus plantations and analyse how genomic population diversity varies relative to endophytism and plant-pathogenicity. The PhD candidate is expected to participate in the detailed design of experiments and analyses, and the work will involve both comparative genomic, population genomic and experimental mycological techniques. The project will involve close collaboration with a postdoc within the group and project partners in Germany and Brazil. A longer research stay at University of Sao Paulo in Brazil must be expected.

Principal supervisor isAssociate Professor Henrik H. De Fine Licht,Section for Organismal Biology, Department of Plant and Environmental Sciences, hhdefinelicht@plen.ku.dkDirect Phone: +45 35320097.

Co-supervisor will be Associate Professor Birgit Jensen, Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen.


  • Experience working in a microbiological laboratory, preferably with fungi, is required
  • Experience with population genetics and evolutionary biology
  • Experience with standard molecular biological techniques (eg. DNA/RNA extraction, PCR/qPCR, sequencing, etc.) is expected
  • Experience working with plant pathogenic fungi is an advantage but not a requirement
  • Experience with analysis of next generation sequencing data and/or comparative/population genomics is preferred
  • Relevant scientific publications in reputable journals is advantageous, but not a requirement

Inquiries about the position can be made to Principal Supervisor: Assoc. Prof. Henrik H. De Fine Licht, Department of Plant and Environmental Science. E-mail: Phone: +45 35320097.

Job description
The position is available for a 3-year period and your key tasks as a PhD student at SCIENCE are:

  • To manage and carry through your research project
  • Attend PhD courses
  • Write scientific articles and your PhD thesisTeach and disseminate your research
  • To stay at an external research institution for a few months, preferably abroad
  • Work for the department

Formal requirements
Applicants should hold an MSc degree in biology, biotechnology, microbiology, microbial ecology or a similar degree from other relevant research fields with good results and good English skills. As criteria for the assessment of your qualifications, emphasis will also be laid on previous publications (if any) and relevant work experience.

Terms of employment
The position is covered by the Memorandum on Job Structure for Academic Staff.

Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

The starting salary is currently at a minimum DKK 330,817 (approx. €44,108) including annual supplement (+ pension at a minimum DKK 53,761). Negotiation for salary supplement is possible.

Application Procedure

The application, in English, must be submitted electronically by clicking APPLY NOW below.

Please include

  • Cover Letter, detailing your motivation and background for applying for this PhD project.
  • CV
  • Diploma and transcripts of records (BSc and MSc)
  • Acceptance Letter for the relevant MSc Programme at SCIENCE, if any
  • Other information for consideration, e.g. list of publications (if any)
  • 1-3 reference letters (if any)

Reference letters must be uploaded by the applicant him/herself. The recruiting person must NOT  obtain reference letters which content is not known to the applicant him/herself. This is against Danish law.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

The deadline for applications is 11 April 2021, 23:59 GMT +2.

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee. Afterwards an assessment committee will be appointed to evaluate the selected applications. The applicants will be notified of the composition of the committee and the final selection of a successful candidate will be made by the Head of Department, based on the recommendations of the assessment committee and the interview committee.

The main criterion for selection will be the research potential of the applicant and the above mentioned skills. The successful candidate will then be requested to formally apply for enrolment as a PhD student at the PhD school of Science. You can read more about the recruitment process at

For specific information about the PhD scholarship, please contact the principal supervisor Associate Professor Henrik H. De Fine Licht, Section for Organismal Biology, Department of Plant and Environmental Sciences, hhdefinelicht@plen.ku.dkDirect Phone: +45 35320097.

General information about PhD programmes at SCIENCE is available at



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