PhD fellow in beetle phylogenetics and big digital data from museum collections

Natural History Museum of Denmark
University of Copenhagen


Natural History Museum of Denmark (NHMD), Faculty of Science at University of Copenhagen is offering a PhD scholarship within the PHYLORAMA research project commencing 1 April 2021 or as soon as possible thereafter.

Description of the scientific environment
The PhD scholarship is part of a collaborative project “Expanding the Tree of Life through a digital view of museum collections (PHYLORAMA)” between the Department of Computer Science (DIKU) and Natural History Museum of Denmark (NHMD) at University of Copenhagen. As part of this research, DIKU will also offer two additional PhD scholarships with the foci on 1) Automated Visual Taxonomic Identification and Clustering of Insects and 2) 3D Reconstruction of Insect Fossils in Amber. Although each of three PhDs of PHYLORAMA will have certain foci within their respective domains, altogether they are geared towards improving the ways we explore insect phylogenies. Therefore, we call for applicants with the desire to go beyond their domain limits. Interactions and synergy among supervisors and students from the computer science and systematic entomology are at the core of PHYLORAMA. All PhD projects will contribute to the digitalization of the NHMD collections.

A PhD scholarship offered here will have main employment at NHMD and be embedded in the Section of Zoology, but some time will also be spent at DIKU. The NHMD offers a world class international research environment in systematic entomology, with English as official working language in addition to Danish. NHMD has one of the best entomological collections in Europe.

Project description
The Tree of Life (Phylogeny) is a fundamental concept for understanding biodiversity. Yet the position of more than one million insect species remains poorly known within the Tree of Life, partly because of their extreme diversity. Automated pipelines of phylogenomics cannot overcome this impediment alone because of various limitations. By combining computer vision with phylogenetics in entomology, we will explore a possibility of a high throughput pipeline that rapidly acquire images of millions of specimens, both recent and fossil, in the museum collections and cluster them via interpretable deep learning models into the Tree of Life clades based on phenotypes in combination with genomic data. The PHYLORAMA research project is a blend of systematic entomology and computer science, with classical elements from both domains and a shot for innovation in phylogenetic research in entomology by computer science.

Within the PHYLORAMA project, the NHMD seeks a highly motivated applicant for a PhD scholarship who will focus on reconstructing phylogeny of Staphylinidae rove beetles (or one of its large sub-clades). The phylogeny reconstruction will combine established methods of phylogenomics, morphology-based and total-evidence inference with the simultaneous exploration of new ways how to integrate morphological diversity of sampled lineages inferred from specimen images in the museum collections into the phylogenetic workflow.

Principal supervisor for the PhD project is Associate Professor, PhD., Alexey Solodovnikov, Natural History Museum of Denmark, asolodovnikov@snm.ku.dk, Direct Phone: +45 22 61 55 27.

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

  • Manage and carry through your research project
  • Attend PhD courses
  • Write scientific articles and your PhD thesis
  • Teach and disseminate your research
  • Stay at an external research institution for a few months, preferably abroad
  • Work for the department
Formal requirements
Applicants should hold a MSc degree in Biological sciences or other relevant area with a focus on zoology, entomology, or phylogenetics, or genomics, or a combination of any of those. The successful applicant is expected to have obtained outstanding grades during the MSc studies, and to be proficient in spoken and written English. As criteria for the assessment of your qualifications emphasis will also be put 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 331,125 (approx. €43,750) including annual supplement (+ pension at a minimum DKK 53,811). 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)
  • 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 31 January 2021, 23:59 GMT +1.

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 http://employment.ku.dk/faculty/recruitment-process/

Questions
For specific information about the PhD scholarship, please contact the principal supervisor Associate Professor, PhD., Alexey Solodovnikov, Natural History Museum of Denmark, asolodovnikov@snm.ku.dk, Direct Phone: +45 22 61 55 27.

General information about PhD programmes at SCIENCE is available at http://www.science.ku.dk/phd






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