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PhD fellow in shotgun sequencing for comparative diet analysis of capercaillies

The EvoGenomics Group at the Natural History Museum of Denmark, Faculty of Science, University of Copenhagen is offering a fully funded PhD scholarship fellowship under the Plant.ID Horizon2020 European Training Network, starting April 2018 or as soon as possible thereafter.  
Plant.ID is recruiting 15 PhD fellows 
The EU H2020-ITN-ETN project Plant.ID that is based around the molecular identification of plants is a European training network aimed at providing 15 PhD fellows across nine European host institutions with excellent training through a network of leading academic experts, museums, governmental and industry partners in the field, using an intensive program with network-wide training events, intra-network supervision and secondments. Read more about the 15 individual PhD projects on 
PhD fellowship 4 will be based at the eDNA group at the EvoGenomics section at the Natural History Museum of Denmark. It houses the recently founded DNA reference database for Danish species, DNAmark, as well as state-of-the-art laboratories, high-throughput sequencing facilities and computational resources. Furthermore, the section offers a highly international and social environment. 
Project – Plant.ID PhD fellowship 4 
Diet analysis is a prerequisite to fully understand the biology of a species and the functioning of ecosystems. For animals, traditional diet analyses rely mostly on morphological identification of undigested remains in the faeces, but recent advances in metabarcoding have enabled using DNA of ingested foods to reconstruct diets. However, amplicon metabarcoding markers have limited resolution in species identification and the absence of complete sequence reference databases further limit accurate species identification. Recently, national DNA reference database projects have emerged, which create organelle genome reference data for each species: in the Alps (PhyloAlps), Norway (NorBOL) and Denmark (DNAmark). This PhD project will explore the optimal use of these novel and comprehensive reference databases for accurate species-level identification of plants in animal diets through a comparative shotgun sequencing diet study on capercailles (wood grouse) in the Alps and Norway. The project will involve fieldwork, laboratory preparation of collected faecal samples for shotgun sequencing and exploration/development of laboratory and bioinformatics protocols and workflows. Planned secondments will be at University of Oslo and University of Grenoble. 
Principal supervisor: Kristine Bohmann (Natural History Museum of Denmark). University of Copenhagen,, tel. +45 40750521. Co-supervision: Tom Gilbert (Copenhagen), Sanne Boessenkool (University of Oslo), and Eric Coissac (University of Grenoble, PhyloAlps project). Collaborators: Torbjørn Ekrem and Inger Greve Alsos (NorBOL).  
Who are we looking for? 
Marie Curie Training Networks offer a unique opportunity to get cutting-edge training in a multidisciplinary environment with a focus on academic and personal development of the PhD fellows. The supervisors in the network each provide specific competences and as part of the network you develop your skills and carry out research both independently and as part of a network of 15 PhD fellows. The consortium ensures cross-pollination and exchange of ideas through network-wide training events, summer schools and intersectoral secondments. As a PhD fellow in the Plant.ID network, you need to have good social skills and be willing to conduct the planned secondments and importantly be innovative and goal-oriented.  
  • Experience with molecular ecology, next generation sequencing, metabarcoding, environmental DNA and/or diet studies 
  • Capable of carrying out independent field work and sample collection 
  • Interest in bioinformatic processing of high-throughput sequence data 
  • Interest in developing protocols and workflows for the environmental DNA/molecular diet approaches of the future 
Job conditions 
The PhD student will be appointed under a 3-year employment contract with a competitive salary and mobility allowance at the host institution. The fellow is expected to start in April 2018. Additional funding for research and participation in courses, workshops, conferences, etc. is ensured. The PhD student will be enrolled in the PhD program of the Faculty of Science, University of Copenhagen, with the specific intent that it results in a PhD degree and scientific publications. 
Job description 
The position is available for a 3-year period. Your key tasks as a PhD student at SCIENCE/the Plant.ID network are: 
  • To manage and carry through your research project 
  • Attend PhD courses both within and outside the Plant.ID network 
  • Write scientific articles and your PhD thesis 
  • Participate in international congresses and Plant.ID network meetings 
  • Stay at the research institutions abroad for the secondments 
  • Work for the department 
  • Teach and disseminate your research 
Formal requirements  
Applicants should hold an MSc degree in Bioinformatics, Biology, Molecular Biology or similar with good results and good English skills (writing and speaking). As criteria for the assessment of your qualifications, emphasis will also be laid on previous publications (if any) and relevant work experience. 
EU eligibility criteria for candidates 
The applicant may be of any nationality but in order to be eligible for the positions the following criteria applies to all applicants: 
The applicant shall at the time of recruitment be eligible as an Early Stage Researcher (ESR) by being in the first four years of his/her research career and not have been awarded a doctoral degree.  
The applicant must not have resided or carried out his/her main activity in the country of the host institute for more than 12 months in the 3 years immediately prior to the recruitment. 
Plant.ID is recruiting 15 PhD students simultaneously and interested candidates are encouraged to apply for multiple projects within the network. Read more about the 15 individual PhD projects on  
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 312.879 including annual supplement (+ pension up to DKK 43.219). Negotiation for salary supplement is possible. 
Application procedure 
The application, in English, must be submitted electronically by clicking APPLY NOW below.  
By applying for PhD 4, you agree that your application can be transferred to other positions in the network for consideration. 
Please include  
  • Cover Letter, stating which PhD project you are applying for and detailing your motivation and background for applying for the specific PhD project (max. 2 pages) 
  • CV (max. 2 pages) including a list of publications (if any) 
  • Summary of last degree thesis (1 page) 
  • Diploma and transcripts of records (BSc and MSc) 
  • Full contact details (name, address, telephone & email) of 1-3 professional referees 
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 15.01.2018, 23:59 GMT +1. Applications received after the deadline for applications will not be considered.  
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 Assistant Professor, Kristine Bohmann, section for Evolutionary Genomics, Natural History Museum of Denmark,, Direct Phone: +45 40750521. 
General information about PhD programmes at SCIENCE is available at 

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Ansøgningsfrist: 15-01-2018
Ansættelsesdato: 04-04-2018
Arbejdstid: Fuldtid
Afdeling/Sted: Statens Natur Historiske Museum

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