Andreas Wallberg research group

Population genomics and evolutionary genetics

Research topics

In our research we use genomics to study genetic variation in populations of terrestrial and marine species, including honeybees, krill and copepods.

By analyzing the patterns of genetic variation within and between populations, we can learn how different evolutionary processes, such as drift, dispersal, selection and adaptation, have shaped the genome and evolutionary history of species. These processes are particularly poorly understood for marine species, which are often difficult to sample, have complex life histories and high levels of variation.

• How is gene flow structured between populations in the open ocean? Do ocean currents influence the exchange of genetic material?

• Are hyper-abundant zooplankton largely unaffected by genetic drift? To what extent is observable genetic variation adaptive? Are populations genetically adapted to their local environments?

• How can we trace and explain the rapid expansion of genome content in many crustaceans?

• Do zooplankton, many with pivotal roles in ocean ecosystems, have the capacity to adapt at the genetic level to the changing climate? Which stocks are most at risk and what will the consequences be to marine food webs?

These are some of the major questions that we aim to answer. Our research is motivated by the dramatic changes and unclear future of our ocean ecosystems and the poor state of knowledge about some of the most common animal species on the planet.

Adaptation and evolution in the sea: ecological genomics in krill and copepods

Our program started in 2018 and has been awarded several national research grants to study keystone zooplankton: the shrimp-like krill (sv. lysräkor) and tiny Calanus copepods (sv. hoppkräftor). Planktonic crustaceans make up half of the planet’s animal biomass, and as major consumers of algae, and food for ecologically and commercially important mammals and fish, they are critical links between primary production and higher trophic levels. Distressingly, many krill and copepod species appear to decline due to ocean warming.

Genetic resources that could help us trace population dynamics and understand how these species will respond to continued change (through means of genetic adaptation, migration or extinction) are largely missing for these species. This is primarily because the genomes of these crustaceans tend to be large and complex, 2 to 14 times larger than the human genome, making them very challenging to assemble and study.

We aim at using state-of-the-art genomics and to understand how krill and copepods are adapted to the ocean environment and how they may respond to ongoing and future climate change. To this end, we use cutting-edge next-generation and third generation sequencing of DNA and RNA to assemble their genomes, annotate functional elements and map genetic variation.

We collaborate with an international network of marine ecologists to collect, sequence and analyze samples from across the world oceans. This entails visiting field stations or going on expeditions to find diverse material from different environments. Using bench-top minION Nanopore sequencers, or big iron Illumina or PromethION machines at SciLifeLab, we produce sequence data to assemble their genomes and transcriptomes and catalogue variation between populations and species. We then apply population and comparative genomics to uncover their evolutionary histories and identify the genetic mechanisms that underlie differentiation and adaptation.

Our current projects aim to:

• Assemble and annotate the reference genome of the Northern krill (Meganyctiphanes norvegica; 18 Gbp) and identify adaptive genetic variation across the range of this species by sequencing populations from warm and cold waters across the North Atlantic.
  
• Compare the rates of evolution across hundreds of transcriptomes sampled from many different species of krill in order to detect genes that appear to have evolved under positive selection and contributed to adaptation.
  
• Assemble the genome of an arctic Calanus copepod species in order to understand the neutral and adaptive processes underlying the diversity of genome sizes observed witihin this species.

Here are some popular science vlogs (in Swedish) from a recent field sampling campaign to the Indian and Southern Oceans.

Our group is developing new and fundamental genomics resources to better understand adaptation and evolution in the ocean, including the development of novel laboratory protocols and bioinformatics methods to accelerate analyses and research.