Research Assistant: Approaches to Reconstruct the Past Through Analysis of Ancient Environmental and Human Genomes

Introduction to the topic:

The Section for Geogenetics at the Globe Institute, University of Copenhagen, has a strong track record in generating and analyzing ancient DNA (aDNA). In this project, the focus is on the analysis and interpretation of aDNA from environmental samples and human remains, with the aim of reconstructing past ecosystems and human populations. By combining environmental and human genome analyses, this project will demonstrate how aDNA studies contribute to understanding evolutionary history, species adaptation, and human interactions with their environment.

Project details:

Research Assistants (RAs) will work with existing unpublished datasets and will not be directly involved in generation of new data in the wet lab. Instead, the project emphasizes experience with key techniques in ancient DNA research by handling, analyzing, and interpreting real, aDNA data from sources such as sediment cores and archaeological skeletal material. RAs will learn how to critically assess DNA authenticity and interpret genetic data to reconstruct past environments and human populations. By the end of the project, RAs will understand both the scientific and methodological challenges of working with ancient genetic material.

Some of the techniques and skills you will practice include:

Sequencing Data and Preprocessing: RAs will become familiar with the structure and characteristics of short-read sequencing data (e.g., Illumina) commonly used in aDNA studies. The project includes preprocessing steps such as adapter trimming, quality filtering, and an introduction to how biochemical treatments like UDG (Uracil-DNA Glycosylase) impact data characteristics, although RAs will not be directly involved in wet lab work.

Authentication and Quality Control: Ancient DNA presents unique challenges related to degradation and contamination. RAs will learn to authenticate aDNA sequences through read mapping, analysis of post-mortem damage patterns, and contamination screening. Tools such as mapDamage, MALT, and PALEOMIX will be used to verify data authenticity and assess the quality of the sequences.
Bioinformatics and Interpretation: Using established bioinformatics pipelines, RAs will apply population genetic methods such as principal component analysis (PCA), ADMIXTURE, and phylogenetic inference to investigate genetic diversity and population history. For environmental samples, metabarcoding and taxonomic assignment methods will be used to reconstruct past ecosystems. Emphasis will be placed on interpreting the results within ecological and evolutionary frameworks.

Selected relevant publications:

Kjær K.H., Winther Pedersen M., De Sanctis B., et al (2022). A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature, 612(7939), 283–291. doi: 10.1038/s41586-022-05453-y
Seguin-Orlando A., Korneliussen T.S., Sikora M., et al (2014). Genomic structure in Europeans dating back at least 36,200 years. Science, 346(6213), 1113–1118. doi: 10.1126/science.aaa0114

Prerequisites

One year of biology and one year of chemistry at the university level.

Additional application required

You must submit an additional application through the Online Registration portal.

All application materials must be submitted on the following dates by midnight in your time zone:

November 1 for spring semester applicants
May 1 for fall semester applicants

Complete your application through Student Registration.

Faculty

Thorfinn Sand Korneliussen

PhD (Statistical methods for population genetic inference based on low-depth sequencing data from modern and ancient DNA, Natural History Museum of Denmark, 2016). Associate Professor, Faculty of Health University of Copenhagen 2023-present. Tenure-track assistant professor, Natural History Museum, 2018-2023. With DIS since 2025.

Research Assistantship FAQ

Learn more about research at DIS.

: Earning authorship within the course of a semester is challenging. Exceptional Research Assistants may be considered for co-authorship, subject to evaluation from the supervising Research Mentor.

Though you may not ultimately become an author on a published paper, you will gain many practical skills and insights into the publication process.

: Many research projects last across several semesters, so not all RAs on the same project will conduct the same research.

: On average, students in 3-credit Research Assistantships spend at least 10 hours a week on research tasks. These 10 hours per week consist of a variety of different research-related tasks, including conducting a literature review, data collection, analyses, coding, documentation, and meetings with your mentor. You may decide on a particular block of time (consistent each week) for you to carry out the work, or adjust it on a week-by-week basis.

Students in a 6-credit Research Assistantships spend an average of 20 hours per week with lab and clinically based research tasks. You decide the exact meeting and lab times with your supervisor, but your schedule consists of classes at DIS two days a week, with two days a week in the lab.

There may be peak times in the research process where all Research Assistant students are expected to spend a few more hours, and then possibly fewer hours another week – to reflect the individual research project and process.

: Work for the 3-credit Research Assistantships may take place outside DIS, on your own time at a location of your choosing, or at DIS – this varies from project to project. The 6-credit research assistantships generally take place at labs in Copenhagen or Stockholm outside DIS.

: Students with a variety of academic backgrounds are encouraged to apply for the 3-credit Research Assistant course. While some courses do have prerequisites, many opportunities do not require prior research experience.

The 6-credit Research Assistant opportunity is designed for highly motivated students who have a strong science background within the field of interest and some basic research experience. The student must be willing to commit a large portion of their semester to an engaging opportunity involving hands-on research in universities and medical institutes in Copenhagen or Stockholm.

Introduction to the topic:

Project details:

Prerequisites

Additional application required

Faculty

Thorfinn Sand Korneliussen

Research Assistantship FAQ

Will I publish a research paper?

What exactly will I do?

What is the time commitment for a 3-credit or 6-credit Research Assistantship?

Where is the research work carried out?

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