My research interests cover a variety of topics within phytoplankton/ protist ecology and evolution. Currently my research focus is on understanding the processes underlying speciation and biogeography in protists. My approach is to study these processes at the population level by investigating genetic diversity, population genetic and genomic structure, dispersal, and local adaptation. This research interest emerged from my PhD thesis work in which I studied the role of resting cysts to phytoplankton species and communities. I have also worked with competition among phytoplankton species, specifically allelochemical interactions.

Together with my research group and collaborators we are currently focusing on three main systems; a dinoflagellate species complex that has recently diverged into multiple species/ecotypes, a freshwater invasive nuisance species: Gonyostomum semen, and the toxin-producing cyanobacterium Microcystis.  Our approach is to use a combination of population genomics, transcriptome analyses, and experimental studies to address the specific research questions for each project.


Drivers of genetic differentiation in protist populations

This project is focused on the speciation event that has resultedOLYMPUS DIGITAL CAMERA in the formation of the two separate species Apocalathium malmogiense (marine) and Apocalathium aciculiferum (freshwater)(Logares et al. 2008). We are investigating both genetic divergence and reproductive barriers between these two, and the sibling species A. aff. malmogiense in the Antarctic lakes, as well as two closely related freshwater species. Our previous studies indicate that salinity is a major barrier to speciation (Logares et al. 2008, 2009, 2010) and that the two species are part of a recent adaptive radiation (Annenkova et al. 2015). Therefore, we are particularly interested in the response to salinity and differentiation at both the genetic and expression level. A population genomic approach (RAD-sequencing) is used to detect regions of selection and potential genes involved, in tandem with analyses of phenotypic variation of potential adaptive traits. In addition we are analyzing the transcriptomes of these species through the Marine Microbial Eukaryote Transcriptome Project funded by the Gordon and Betty Moore Foundation. The project is funded by the Swedish Research Council (Vetenskapsrådet).

Population genomics of the cyanobacterium Microcystis botrys

Aquatic environments are of enormous importance as natural resources of drinking water, fish production, and recreation. However, surface waters worldwide are threatened by toxic cyanobacterial algal blooms, which have detrimental effects on human health and aquatic biota. One of the most important toxic cyanobacteria in Swedish freshwater is the genus Microcystis. We know which species may be harmful, but cannot predict where and when blooms will be toxic due to inter-population and strain variation. In this project we will be using a population genomic approach to address this issue with the aim to understand temporal and spatial prevalence, and the underlying function of toxicity. Our overarching hypothesis is that toxic and non-toxic populations have emerged as a result of ecological differentiation. The project is financed by the Swedish Research Council Formas, and co-PI’s are Dr. Anna Godhe, Gothenburg University, and Dr. Catherine Legrand, Linneaus University.


Next-Generation microbial population genetics using single-cell genomics

The objective of this project is to study population genetics and genetic structure of phytoplankton based on single-cell genomics. Specifically, the focus will be on genomic variation in Gonyostomum semen (raphidophyceae), a harmful invasive microalga. Populations of Gonyostomum have expanded invasively across N. Europe, but populations in N. America are less invasive and display less disruptive phenotypes despite similar environments. A population genomic approach can be used to explore the detailed dispersal patterns, and to understand the genetic basis of the differentiation among populations. By using single-cell genome amplification, the effort and bias of algal culturing is circumvented.

This research project is part of SINGEK, a Marie Skłodowska-Curie Innovative Training Network devised to provide a unique and structured training programme to a new generation of scientists with the highest expertise in Single Cell Genomics, from the initial stages of cell sorting to genome sequencing and gene annotation, to the full exploitation of the data obtained. The network is composed of a multidisciplinary team of researchers from nine institutions, well connected and with high expertise in eukaryotic SCG. See the video or read on

Live to tell: Have phytoplankton evolved in response to environmental pollution during the last centuries?

In perturbed environments some species will go extinct while others persist (are resilient). The Baltic Sea is an ecosystem that is suffering from multiple stressors. In this system planktonic diatoms play a pivotal role as primary producers at the base of the food chain. Changes due to loss of diatom species may therefore cascade throughout the trophic web. We will study the underlying mechanisms of resilience (genetic adaptation or phenotypic plasticity) by using two diatom species from a cupper contaminated inlet. One species is a permanent resident of the area, whereas the other disappeared when [Cu2+] increased, but recolonized when water quality later improved. We will sample undisturbed sediment cores, date them by isotopes, and revive populations from before, during, and after the perturbation.  In ecotoxicological pollution induced tolerance tests we will quantify and compare the resilient and non-resilient species’ tolerance to cupper. Different populations isolated from diverse natural pollution regimes will be tested to infer the
importance of plasticity or genetic adaptation by tolerance selection experiments. This project is funded by the Research Council Formas with Dr. Anna Godhe as PI, and Karin Rengefors, Helena Filipsson, and Olof Berglund as co-PI’s.

Physical and biological dispersal barriers in invasive bloom-forming microalgae

Gonyostomum_cellFor several years we have been investigating the invasive freshwater phytoplankton species, Gonyostomum semen. This species is known as a nuisance species that forms frequent and dense blooms in boreal lakes. In previous work we have analyzed its population genetic structure, which supported the hypothesis of a recent expansion, as well as attempted to identify its dispersal barriers.  We found that physical dispersal barriers cannot alone account for the patterns observed, and that hydrological connectivity did not enhance gene flow. Instead we suggest that differentiation among microalgal populations might be explained by so called founder effects (see Publications). Founder or priority effects refer to the dominance of strains or species that arrive first to a new habitat. These are enhanced by short generation time, rapid local adaptation of the resident population, and large propagule banks that buffer against new immigrants. This research has implications for the understanding of the spreading of microalgae and microorganisms in general, as well as for predicting the occurrence of new algal blooms. The approach is to determine the importance of physical versus biological dispersal barriers by analyzing the genetic diversity patterns.