PhD at DTU Aqua
The PhD programme at DTU Aqua educates future researchers within the institute's research areas for a career in academia or business.
PhD students
PhD students and projects at DTU Aqua within the research area Population Genetics.
Camilla Christensen
Title of the PhD project
Population genomics of archived shark samples
Supervisors
Einar Eg Nielsen, DTU Aqua and Michael B. Bennett and Jennifer Ovenden, The University of Queensland
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.
Daniel Anthony Hancock
Title of the PhD project
Climate change population genomics
Supervisors
Jakob Hemmer-Hansen and Dorte Bekkevold, DTU Aqua
Background of the project
A rapidly changing climate will have a major impact on the distribution, evolution and persistence of species, with marine ecosystems being particularly vulnerable, facing gradual threats like ocean acidification, temperature shifts, and alterations in currents, as well as immediate crises such as marine heatwaves. Considering these challenges, climate vulnerability assessments that account for nuanced, population-specific responses such as divergent range shifts and local adaptation, as well as highlighting potential maladaptation to future environments are becoming increasingly important. Such assessments are crucial for proper evaluation and mitigation of the impacts of climate change on the persistence of species of economic and ecological importance.
About the project
The objective of this project is to evaluate the risks associated with climate change to marine species in the Kattegat-Skagerrak transition zone. To achieve this, genomic and climatic data will be integrated in a comparative approach across multiple aquatic taxa to make predictions about evolutionary responses to climate change. This will involve spatial and evolutionary modelling to predict the connectivity, future distribution and adaptive capacity of populations, as well as investigating genetic vulnerability metrics such as mutational load, genetic diversity and inbreeding.
Perspectives
This PhD is part of the Interreg Øresund-Kattegat-Skagerrak BlueBioClimate project, which aims to facilitate cross-border co-operation for climate-adapted management of aquatic biodiversity. Through collaboration with project partners across the region and national and regional resource management practitioners, it aims to provide guidance for the prioritization of effective conservation strategies in aquatic ecosystems, to ensure ecosystem resilience and safeguard natural resources.
Nina Strand
Title of the PhD project
DNA based catch quantification for pelagic fisheries (DNAcatch)
Supervisors
Einar Eg Nielsen and Lars Magnus Wulff Jacobsen, DTU Aqua
Background of the 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 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.
Karoline Bruun Degn
Title of the PhD project
Assessing biodiversity at offshore wind farms using eDNA (WINDDNA)
Supervisors
Einar Eg Nielsen and Lars Magnus Wulff Jacobsen, DTU Aqua
Background of the project
The transition to sustainable energy is a crucial part of global efforts to combat climate change. Offshore wind farms are set to expand significantly as part of this green transition. For instance, the Esbjerg Declaration by Danish authorities aim to increase wind power production in the North Sea by tenfold by 2050. However, this expansion raises concerns about potential disruptions to marine ecosystems. To address these concerns, political goals have shifted from “No Net Loss” to “Marine Net Gain” in biodiversity, meaning offshore wind farms should enhance rather than harm marine ecosystems.
About the project
This PhD project focuses on using environmental DNA (eDNA) metabarcoding techniques to monitor marine biodiversity around offshore wind farms. By employing advanced autonomous robotic instruments for in situ eDNA sampling and DNA analysis, the project aims to achieve high spatial and temporal resolution. Techniques such as 3rd generation sequencing, digital PCR (dPCR), and oceanographic modeling will be applied. Sampling will primarily take place around the offshore wind farm Horns Rev II located in the North Sea and at the Ørsted windfarm off the coast of Anholt. The overarching goal is to develop a robust, cost-efficient eDNA-based tool for offshore biodiversity monitoring and marine environmental impact assessment.
Perspectives
We hope to transform eDNA from a basic science concept into a practical monitoring tool that can be adopted by the industry and national authorities. In that way we can ensure that the establishment of wind farms contributes positively to marine biodiversity and supports nature-based solutions for artificial reef structures.
Previous PhD students within the research area Population Genetics
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
Alan Le Moan
Comparative population genomics provides insights on the evolutionary history of marine fishes
Brian Klitgaard Hansen
Novel DNA methods and instrumentation for species monitoring in fisheries
Thomas Frank-Gopolos
Adaptive differences between wild and farmed trout: linking traits with genomic variation
Nina Overgaard Therkildsen
Insights from the past: Retrospective monitoring of genetic variation in Atlantic cod (Gadus morhua)
Kristian Meier
The molecular basis of local adaptation in brown trout
Morten Tønsberg Limborg
Population structure and adaptation in fishes. Insights from clupeid and salmonid species