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Open Ph.D. positions for 36 months

Open Ph.D. positions for 36 months
BaseClear In collaboration with Naturalis Biodiversity Center and the University of Leiden announces an opening for a fully funded PhD fellowship under the Plant.ID Horizon2020 European Training Network, starting April 2018.

Plant.ID is recruiting 15 PhD fellows
The EU H2020-ITN-ETN project Plant.ID on 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.

Project description
Monitoring of fresh water quality is traditionally done by microscopic determination of organisms in water aliquots, which is time consuming. Sequencing of environmental DNA (eDNA) is therefore increasingly used to supplement traditional surveys. DNA barcodes will be collected from museum specimens. Fresh water samples of different qualities will be sampled for eDNA. Metabarcodes and species identification obtained from high-throughput sequencing and species abundances from ddPCR analysis will subsequently be compared to results from traditional microscopy. Using aquarium assays and fossil ice cores, patterns of degradation of eDNA over time will be assessed to distinguish past from present biodiversity. Objective:Species-level identification and abundance of aquatic flora (higher plants, algae, diatoms) for fresh water quality assessment with genomic analysis of eDNA. Primary supervisor: Danny Duijsings, BaseClear, co-supervisors Walter Pirovano and Adalberto Costessi from BaseClear, Barbara Gravendeel and Arjen Speksnijder from Naturalis Biodiversity Center, and promotor Peter van Bodegom, University of Leiden. Planned secondments to Naturalis Biodiversity Center, University of Leiden and short visits to Diatomella.

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. Specific requirements for areas of previous degrees, planned secondments, and other expectations related to individual positions are listed in the detailed posting of each position. All candidates must be fluent in spoken and written English.

Job conditions
The PhD student will be appointed under an employment contract with a competitive salary and mobility allowance at the host institution. The fellow is expected to start in April 2017. Additional funding for research and participation in courses, workshops, conferences, etc. is ensured. PhD6 will be enrolled in the doctoral program of the University of Leiden.

Job description
Your key tasks as a PhD fellow in Plant.ID are:
- Manage and carry through your research project
- Take PhD courses within the Plant.ID network
- Write scientific articles and your PhD thesis
- Participate in international congresses and Plant.ID network meetings
- Stay at a research institution abroad for the secondment(s)
- Teach and disseminate your research

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

The following projects are included:
PhD 1 - Polyploid phylogenetics under the multi-species coalescent - University of Gothenburg
PhD 2 -Taxon identification and multispecies coalescent biodiversity assessments - University of Oslo
PhD 3 -Euphrasia: species delimitation in mega-diverse hemi-parasites - University of Copenhagen
PhD 4 -Shotgun sequencing for comparative diet analysis in capercaillie fowl -University of Copenhagen
PhD 5 -DNA barcoding and metabarcoding of herbal products for authentication -University of Oslo
PhD 6 -Metabarcoding of aquatic flora for fresh water quality monitoring - BaseClear, Degree Awarding University of Leiden
PhD 7 -Hayfever and software-automated pollen metabarcoding - Naturalis Biodiversity Center, Degree Awarding University of Oslo
PhD 8 -Paleogenomic annotation of historical Cinchona bark samples across time and space - University of Copenhagen
PhD 9 -Genomic barcoding of the succulent plant genus Aloe in trade - Royal Botanic Gardens Kew, Degree Awarding University of Copenhagen
PhD 10 -Orchid targets: Genomic barcoding to identify and trace traded orchids -University of Oslo
PhD 11 -Is mutational meltdown a threat in the mega diverse genus Begonia? - Royal Botanic Gardens Edinburgh, Degree Awarding University of Edinburgh
PhD 12 -Genomic barcoding to trace and identify illegally logged African trees -Botanic Garden Meise, Degree Awarding KU Leuven
PhD 13 -Bar-HRM traceability of toxic species in food and medicine - Centre for Research & Technology - Hellas, Degree Awarding Aristotle University of Thessaloniki
PhD 14 -Species, a taxonomic category distinct from the lineage concept - University of Gothenburg
PhD 15 -Logging forensics: mining ebony wood collections as references - Naturalis Biodiversity Center, Degree Awarding University of Leiden

Application procedure
All positions are announced on the Plant.ID website (, EURAXESS. Individual projects are announced at the hosting institution, and application received through the host institutions official application procedures will be considered.
To apply for PhD project 6, please see the full job advertisement and apply by January 15 2018 at

By applying for PhD 6, you agree that your application can be transferred to other positions in the network for consideration.

Application attachments
Motivation letter, max 2 pagesCV (max 2 pages) including a list of publications (if any)
Summary of last degree thesis (1 page)
Names and contact details of 3 referees, but no letters.

All announced positions will close on January 15th, and the evaluation process will start immediately with interviews of shortlisted candidates planned in February. All candidates will receive response. Questions regarding the recruitment can be sent to: Danny Duijsings,, or the project leader of Plant.ID, Hugo de Boer,
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