PhD students

Camilla Christensen

Title of the PhD project
Population genomics of archived shark samples

Supervisors
Einar Eg Nielsen, Michael B. Bennett and Jennifer Ovenden

Background of the project
Archived specimens held in museums and other natural history collections can provide a population genetic baseline, against which to assess potential negative consequences of recent changes in the environment. Thereby, offering an opportunity to track demographic and evolutionary consequences of climate change and other human-induced pressures. The recent advances in molecular genomics has made it possible to investigate genetic changes in many individuals sampled more than a century ago. However, few retrospective genomic analyses has comprised sharks. 

About the project
This PhD project is part of an international collaborative project, GenoJaws, involving the University of Queensland, Technical University of Denmark and Flinders University. The ambition of the project is to gain knowledge about population genetic parameters of the vulnerable sand tiger shark (Carcharias taurus) on a spatial and temporal scale. Performing genomic analysis on contemporary and historical samples will allow us to test for changes in abundance, effective population size, distribution and connectivity and ultimately make us capable of evaluating adaptive responses to environmental change and exploitation.

Perspectives
By tracking changes in genetic composition on a temporal scale, it is possible to find evidence of both distributional shifts and responses to selection. Ultimately, analysis of such records, taken over several years, can help us understand micro evolutionary processes. In addition, retrospective analysis can help making informed decisions for the protection and management of the current populations of sand tiger sharks.

Nina Strand

Title of the PhD project
DNAcatch: DNA based catch quantification for pelagic fisheries

Supervisors
Einar Eg Nielsen and Lars Magnus Wulff Jacobsen

Background of the PhD project
Inadequate bycatch assessment in fisheries can lead to declining spawning stock biomass and reduced recruitment, impacting both target and non-target species. In Denmark, the "bucket method" is currently used to document bycatch in pelagic fisheries, which typically have landings over 500 tons. This method involves sampling 10 kg of fish for every 25 tons at fish factories, with species composition determined manually by third-party observers. It is expensive, time-consuming, and requires taxonomic expertise, creating challenges in accuracy and cost-effectiveness. Environmental DNA (eDNA) analysis, which detects genetic material from organisms in environmental samples, offers a promising alternative. It can reduce time, costs, and workload, while eliminating the need for taxonomic expertise. Despite its potential, eDNA's widespread adoption in large-scale monitoring remains limited.

About the PhD project
The DNAcatch project aims to develop, evaluate, and implement eDNA-based methods for biomass quantification of bycatch in pelagic fisheries, enhancing fisheries management. Building on the pilot study DNAmix, which showed the feasibility of using eDNA for quantifying catch composition, this PhD project will focus on comparing molecular methods (dPCR vs. qPCR) for their impact on biomass estimations, developing eDNA-based methods for several target fisheries, and comparing these results with traditional methods.

Perspectives
Implementing eDNA-based methods for bycatch quantification in pelagic fisheries could improve fisheries management by providing more accurate, cost-effective, and scalable monitoring tools. By optimizing molecular techniques such as dPCR and metabarcoding, the project aims to improve the precision and sensitivity of bycatch detection, especially for rare species. The findings could lead to more effective management strategies, particularly for multispecies fisheries like sandeel. Ultimately, this research could support sustainable fisheries practices by enabling more accurate stock assessments. 

Previous PhD students within the research area Population Genetics (since 2020)

Paulina Urban
Practical implementations of the eDNA concept for marine resources monitoring

Homère J. Alves Monteiro
Applied population genomics in the native European flat oyster (Ostrea edulis)

Alice Manuzzi
Genomic analysis of DNA from archived shark jaws