Population Genetics

Main themes within Population Genetics research

DTU Aqua's research into population genetics has five main themes: 

• Stock identification 
  Using cutting edge molecular genomic tools we describe the genetic integrity and distribution of fish populations (stocks) for a high number of species across their geographical distribution. For example, we outline how many populations of cod there are in the Baltic Sea/North Sea region and of native salmon in continental Europe. At the same time we estimate the extent of genetic exchange between populations and determine the distribution and (genetically effective) size of local populations, now and historically.
  
  
• Traceability and monitoring 
  Based on genomic information we develop high resolution, fast and cost efficient methods for tracing the species and population or geographical origin of individual fish and fish products. These tools are applied for forensic purposes; however, another key applied aspect is to estimate proportions of different local populations contributing to “mixed stock” fisheries. For example, we can determine the migratory behavior and contribution of different North Atlantic herring and Baltic Sea cod populations to mixed fisheries with very high precision in close to real-time. In freshwater systems similar tools are used to determine the stocked or wild origin of salmonids and to monitor the number of breeding individuals in restored habitats.
  
  
• Adaptations to the local environment and aquaculture conditions 
  We examine whether local wild or farmed populations are genetically adapted to their environments. We identify genes or gene regions subject to natural or artificial selection and investigate the genomic background of traits of importance for survival and reproduction. This knowledge is used for understanding the fundamental processes that determine population structure and the fitness of wild and aquaculture fish in both natural and farm environments. Importantly, this key knowledge is also applied as practical management tools, e.g. to identify the origin of individual fish and to predict the impact of releases aimed at rebuilding endangered or locally extinct populations.
  
  
• Impact of climate change and fisheries on aquatic resources 
  We examine effects of climate change and fisheries on the distribution, abundance and genetic composition of wild marine and freshwater populations. We have leading experience in analyzing DNA from historical fish samples (scales, otoliths and bones) collected over decades and sometimes even centuries. We use these analyses to determine whether populations become locally extinct, alter their distribution and/or adapt genetically in response to exploitation and global change. For example, we have shown that different population responses to both climate and fishing were of major importance for the collapse of the historical cod fishery in West Greenland.
  
  
• Environmental DNA (e-DNA)
  We develop methods for monitoring aquatic resources using DNA from water samples and other complex samples, such as fish silage or stomach content. The aim is to be able to determine the presence/absence and relative abundance of keystone, rare or invasive species in both freshwater and marine habitats. We are pursuing opportunities for developing high resolution, high throughput and automated systems that will allow these tools to be employed in a number of situations for routine monitoring. 

Why do we do research into Population Genetics?

Modern DNA technology can provide a number of key insights for sustainable management of exploited aquatic resources, biodiversity conservation, aquaculture and ecosystem monitoring. Thus there is high demand and broad application for new genetic tools and methods targeting the generation of new knowledge and systematic monitoring of aquatic resources from species to individuals. 

Specifically, genetic tools provide superior species identification for all life stages (e.g. eggs or larvae) and processed fish products (e.g. fish filets). They allow delineation of local populations, their distributions, migrations and relative contribution to fisheries, the knowledge of which is a prerequisite for modern ecosystem based fisheries management. In addition, genetic tools allow the determination of provenance of individual fish and fish products (including from aquaculture) and are therefore powerful tools for fighting IUU (Illegal, Unregulated and Unreported) fishing worldwide. 

Genetic diversity is the fuel that secures the health and resilience of populations and is therefore an essential part of biodiversity conservation. DNA based methods allow monitoring of the genetic status of populations. By using systematic monitoring of genetic diversity it is possible to evaluate the health and resilience of populations towards external stressors such as climate and fishing as well as interactions with escaped or released fish from aquaculture.

New DNA applications such as e-DNA can, in principle, be used for monitoring the distribution and relative abundance of all aquatic organisms from virus to whales from water samples. When properly developed and implemented these approaches have wide applications as fast and cost-efficient methods for ecosystem monitoring at all trophic levels, a prerequisite for ecosystem based management of marine resources. This does not only include exploited species, but also key ecosystem species (e.g. plankton), as well as protected and invasive species, all of which can be monitored without sampling the organism itself. Similar tools can be applied to study stomach content and mixed processed fish products to determine the species composition when morphological data are not available.

What is the research used for? 

DNA based methods are increasingly applied for species identification in cases where morphological data is limited or lacking, or where precise species identification requires highly specialized taxonomic insights. We collaborate with the Danish Veterinary and Food Administration and the Danish Fisheries Agency (fisheries control and enforcement) on the development and application of methods to identify illegal trade of fish and fish products at both species and population levels. In addition we are contracted by a number of private companies and NGO’s to deliver similar analyses.

Population genetic analyses of contemporary and historical samples of commercially and recreationally important fish species are used to identify biologically meaningful management units and determine the population composition of fish catches in order to avoid overexploitation of small and vulnerable populations. Our research is used by the International Council for Exploration of the Sea (ICES) in order to provide advice on both the short and long term sustainable management of key species such as cod, herring, plaice, salmon and brown trout. 

Insights from DNA analysis plays an important role in establishing the genetic status and health of populations through investigating levels of genetic diversity, effective population sizes, genetic changes imposed by e.g. climate and fishing and introgression by fish from aquaculture. Also here analysis of historical material plays a key role. Our research is extensively used in the monitoring and management of populations of species with high conservation status, such as the small, unique populations of Atlantic salmon and North Sea houting in Denmark, but also for evaluating the genetic quality of material used for marine and freshwater enhancement of e.g. flounder, turbot and brown trout.

Analysis of e-DNA has been shown to be highly effective for monitoring the occurrence and distribution for both freshwater and marine fish. Most of our effort in this field is currently devoted to the development of tools and methods. However, we are currently testing systems for practical monitoring of whitefish spawning distribution and larval abundance in rivers through e-DNA analysis. This will provide more detailed qualitative and quantitative insights and be much less time consuming than previously applied manual methods.