Novikova Lab – Ecological Genomics: Discovering the Secrets of Adaptation

Polina Novikova heads the Ecological Genomics Lab at the VIB-UGent Center for Plant Systems Biology (PSB) and is an Associate Professor at the Department of Plant Biotechnology and Bioinformatics at Ghent University since 2025. Previously she led a research group at the Max Planck Institute for Plant Breeding Research (Cologne). Her group investigates how organisms adapt to different environments.

It appears that organisms with additional genomes (polyploids) often are associated with extreme conditions. Polyploids possess multiple copies of normal genome, resulting from one or even a series of whole-genome duplications. While this may sound unusual, polyploidy is widespread in nature, particularly among plants, including many crop species. Throughout history, humans have often selected polyploid plants because they exhibit desirable traits, like enlarged fruits and biomass. However, polyploidy also occurs naturally, and understanding its role in adaptation is a central focus of the Novikova Lab.

Her research group use genomic information to disentangle why polyploidy may be so beneficial. Reconstruction of historical information allows to track multiple polyploidization events in the North. Matching ecological conditions across the world with genetic variation reveals adaptive mutations. Finally, comparison of adaptive strategies between polyploid and regular diploid organisms shows why sometimes many copies of each gene is better than one. Yet the main question stands: why polyploids are frequently associated with stressful and extreme habitats? It remains unclear whether environmental stress promotes the formation of polyploids, whether polyploids are inherently better to survive in such conditions or can adapt faster, or whether all these processes contribute. There are several ways to approach this problem.

Uneven distribution

“Although polyploidy is abundant, it is unevenly distributed across the Tree of Life, evolutionary time and geographical space,” Novikova tells. The Novikova research group use these distributions as a clue to identify the forces driving natural selection in regular and extreme environments.

“My team investigates the relationship between adaptation and polyploidy to understand the molecular mechanisms that enable organisms to function with duplicated genomes, developing new traits and overcoming harmful organismal side effects. To assess polyploidization bursts and declines we rely on large population datasets, which provide information about both time and spatial distribution of poliploidization events. We study diploid–tetraploid species complexes in both plants and animals spread across a wide range of environments: for example (1) Arabidopsis lyrata plants distributed across the Northern hemisphere and adapted to the Arctic, (2) Australian frogs Neobatrachus, adapted to extremely arid desert zones, (3) the globally distributed genus Potamogeton, polyploid flowering plants which, like dolphins, came back to life in water. Our research addresses fundamental questions: how do environmental and genetic factors influence the formation of polyploids? What determines the successful establishment of new polyploid lineages? Do diploid and polyploid species evolve different adaptive strategies? And what processes drive the eventual return to a diploid state over evolutionary time?

Environmental conditions

Along with large population datasets Novikova Lab use common garden experiments. In common gardens the plants are grown in controlled conditions, allowing to understand the genetic adaptation and separate effects of different environments. For example, growing in the North requires from plants not only tolerating cold, but also being adapted to season changes and high soil humidity. Thus, when the researchers discover mutations, which may be responsible for specific adaptation, common garden experiments are used to proof their findings.

Multidisciplinary research

The research process in the lab covers all aspects, starting from the field work and expeditions, work with ready collections from herbaria and museums, lab work to extract DNA and sequence the samples and finally lots of computational work requiring high-performance clusters to assemble full genomes and analyse population-scale datasets. Beyond research, the group actively engages with the international scientific community through conferences, collaborations, and the exchange of ideas that help advance the field of ecological genomics.