PhD students

PhD students within the research area Population Genetics.

Camilla ChristensenCamilla Christensen


Title of PhD project

Population genomics of archived shark samples

Supervisors

Einar Eg Nielsen, Michael B. Bennett and Jennifer Ovenden

Background of 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. 

Perspective

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.

Homère Alves MonteiroHomère Alves Monteiro


Title of PhD project

Applied population genomics in European flat oyster (Ostrea edulis

Supervisors

Jakob Hemmer-Hansen, Dorte Bekkevold and Camille Saurel 

Background of project

The flat oyster Ostrea edulis represents a valued food source since the Romans, and a luxury good nowadays. It has been overfished and heavily impacted by disease outbreaks. In contrast with the pacific oyster Crassostrea gigas, where the whole genome sequencing enabled novel and more powerful genetic population studies of the species, the flat oyster has not got the same consideration yet. In Denmark, the current distribution is confined to the Limfjorden. In Norway, records have been reported as far north as the Nordland region, which likely represents the northernmost distribution limit of the species. In Sweden, flat oysters are observable in the north of the Swedish Skagerrak coast and show sustainable populations in relatively good health in contrast with other European flat oyster's locations.

About the project

We aim to gain insights into the European flat oyster natural genomic diversity, with a particular focus on the Scandinavian populations, and to develop genetic knowledge of the species as a practical tool to inform aquaculture production and restoration projects. To achieve these goals we will perform an analysis of genome-wide markers at an unparalleled level of geographical and genomic detail. Expected results are knowledge on 1) Genetic diversity of the Scandinavian natural flat oyster, with comparison among populations from the species' entire distribution range, and 2) Genetic practical tools applicable to aquaculture and restoration programs.

Perspective

This large sampling campaign and subsequent genetic diversity analysis will permit an assessment of the putative population structure, local adaptation, and effects from translocations of O. edulis in Scandinavia. As well as providing genetic input resulting in a set of recommendations/guidelines for the flat oyster aquaculture and restoration.

Paulina UrbanPaulina Urban 


Title of PhD project

Analysis of environmental DNA, “eDNA” from marine organisms

Supervisors

Einar Eg Nielsen and Dorte Bekkevold

Background

Environmental DNA (eDNA) describes all DNA molecules found in an environmental sample, e.g. water, soil or air, that originated from organisms present in that environment. Consequently, analysis of eDNA can be used for monitoring of species or species assemblages. This would likely save time, costs, and workload for such procedures. So far, eDNA implementations for large scale monitoring projects conducted by management institutions, such as fisheries institutes, are limited. This includes both single species monitoring, of e.g. invasive species, and monitoring of species assemblages, e.g. for bycatch estimations. One of the reasons for this might be the need for quantitative estimates for such applications. In order to use eDNA for quantitative estimates, eDNA behavior needs to be better understood, and the molecular methods applied need to be calibrated and validated.

Project

My PhD project aims at facilitating practical implementations of eDNA based methods for monitoring of single species and species assemblages in management and industry. To archive this, on the one hand I will develop methods for eDNA-based quantitative assessment of species assemblages that could be used for by-catch estimations in fisheries. On the other, I will assess and advance methods for monitoring single species, e.g. invasive species that would enable fast monitoring of their spread in ecosystems.

Perspective

Results gained from this PhD project will improve the understanding of eDNA ecology and behavior, and improve the molecular methods applied on eDNA for different monitoring goals. If successful, the methods developed throughout the PhD will come at hand to applied areas such as management, and industry, which need frequent species monitoring.

Previous PhD students (since 2020)


Alice Manuzzi

Genomic analysis of DNA from archived shark jaws
Go to DTU Orbit to download thesis