Polina Novikova

Polina Novikova — Postdoc
Joined the group in 2016

Molecular adaptation to polyploidy in plant and animal systems

  • September 2016 - present Postdoctoral researcher, Bioinformatics & Evolutionary Genomics group of Y. Van de Peer, Department of Plant Systems Biology, VIB, Gent, Belgium.
  • 2011 - 2016 PhD student, Population Genetics group of Dr. M. Nordborg, Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
  • 2011 - 2016 Associate PhD student, Vienna Graduate School of Population Genetics, University of Veterinary Medicine, Vienna Austria
  • 2009 - 2010 Biotechnologist, Department of Cell Culture, Stem Cell Bank Pokrovski, St. Petersburg, Russia.
  • 2004 - 2009 Diploma student, supervisor - Dr. P.M. Krasilnikov, Department of Biophysics, Moscow State University, Moscow, Russia.


  1. Burns, R., Mandáková, T., Gunis, J., Soto-Jiménez, L. M., Liu, C., Lysak, M. A., … Nordborg, M. (2021). Gradual evolution of allopolyploidy in Arabidopsis suecica. NATURE ECOLOGY & EVOLUTION, 5(10), 1367–1381. https://doi.org/10.1038/s41559-021-01525-w
    Arabidopsis suecica is a natural allotetraploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. Comparative analysis of genome and transcriptome data shows no evidence for major genomic changes linked to structural and functional alterations in A. suecica but reveals changes to the meiotic machinery and cyto-nuclear processes. Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.
  2. Novikova, P., Brennan, I. G., Booker, W., Mahony, M., Doughty, P., Lemmon, A. R., … Donnellan, S. C. (2020). Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLOS GENETICS, 16(5). https://doi.org/10.1371/journal.pgen.1008769
    Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.
  3. Burns, R., & Novikova, P. (2020). Parallel adaptation to climate above the 35th parallel. MOLECULAR ECOLOGY. https://doi.org/10.1111/mec.15391
    Independent or parallel evolution of similar traits is key to understanding the genetics and limitations of adaptation. Adaptation from the same genetic changes in different populations defines parallel evolution. Such genetic changes can derive from standing ancestral variation or de novo mutations and excludes instances of adaptive introgression. In this issue of Molecular Ecology, Walden et al.(2020) investigate the scale of parallel climate adaptation from standing genetic variation between two North American Arabidopsis lyrata lineages, each formed by a distinct evolutionary history during the last glacial cycle. By identifying adaptive variants correlated with three ecologically significant climatic gradients, they show that instead of the same genetic variants or even genes, parallel evolution is only observed at the level of biological processes. The evolution of independent adaptive variants to climate in two genetically close lineages is explained by their different post-glacial demographic histories. Separate glacial refugia and strong population bottlenecks were probably sufficient to change the landscape of shared allele frequencies, hindering the possibility of parallel evolution.
  4. Zhang, T., Qiao, Q., Novikova, P., Wang, Q., Yue, J., Guan, Y., … Qiong, L. (2019). Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116(14), 7137–7146. https://doi.org/10.1073/pnas.1817580116
    Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica’s adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.
  5. Bossuyt, F., Schulte, L. M., Maex, M., Janssenswillen, S., Novikova, P., Biju, S., … Van Bocxlaer, I. (2019). Multiple independent recruitment of sodefrin precursor-like factors in anuran sexually dimorphic glands. MOLECULAR BIOLOGY AND EVOLUTION, 36(9), 1921–1930. https://doi.org/10.1093/molbev/msz115
    Chemical signaling in animals often plays a central role in eliciting a variety of responses during reproductive interactions between males and females. One of the best-known vertebrate courtship pheromone systems is sodefrin precursor-like factors (SPFs), a family of two-domain three-finger proteins with a female-receptivity enhancing function, currently only known from salamanders. The oldest divergence between active components in a single salamander species dates back to the Late Paleozoic, indicating that these proteins potentially gained a pheromone function earlier in amphibian evolution. Here, we combined whole transcriptome sequencing, proteomics, histology, and molecular phylogenetics in a comparative approach to investigate SPF occurrence in male breeding glands across the evolutionary tree of anurans (frogs and toads). Our study shows that multiple families of both terrestrially and aquatically reproducing frogs have substantially increased expression levels of SPFs in male breeding glands. This suggests that multiple anuran lineages make use of SPFs to complement acoustic and visual sexual signaling during courtship. Comparative analyses show that anurans independently recruited these proteins each time the gland location on the male’s body allowed efficient transmission of the secretion to the female’s nares.
  6. Novikova, P., Hohmann, N., & Van de Peer, Y. (2018). Polyploid Arabidopsis species originated around recent glaciation maxima. CURRENT OPINION IN PLANT BIOLOGY, 42, 8–15. https://doi.org/10.1016/j.pbi.2018.01.005
    Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary history of plants, however they do not seem to be uniformly distributed along the time axis. For example, many of the detected ancient whole-genome duplications (WGDs) seem to cluster around the K/Pg boundary (similar to 66 Mya), which corresponds to a drastic climate change event and a mass extinction. Here, we discuss more recent polyploidy events using Arabidopsis as the most developed plant model at the level of the entire genus. We review the history of the origin of allotetraploid species A. suecica and A. kamchatica, and tetraploid lineages of A. lyrata, A. arenosa and A. thaliana, and discuss potential adaptive advantages. Also, we highlight an association between recent glacial maxima and estimated times of origins of polyploidy in Arabidopsis. Such association might further support a link between polyploidy and environmental challenge, which has been observed now for different time scales and for both ancient and recent polyploids.

Other publications

  1. Lee, Cheng-Ruei, Hannes Svardal, Ashley Farlow, Moises Exposito-Alonso, Wei Ding, Polina Novikova, Carlos Alonso-Blanco, Detlef Weigel, and Magnus Nordborg. “On the Post-Glacial Spread of Human Commensal Arabidopsis Thaliana.” 2017 Nature Communications 8 (February): 14458.

  2. Rabanal, FA, Nizhynska V, Mandáková T, Novikova PY, Lysak MA, Mott R, and Nordborg M. “Unstable Inheritance of 45S rRNA Genes in Arabidopsis Thaliana.” 2017 G3:Genes|Genomes|Genetics, February, g3.117.040204.

  3. Novikova PY, Tsuchimatsu T, Simon S, Nizhynska V, Voronin V, Burns R, Fedorenko OM, Holm S, Säll T, Prat E, Marande W, Castric V, Nordborg M. “Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis Suecica.” Molecular Biology and Evolution, January 2017.

  4. Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, et al. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics. 2016;48(9):1077-82.

  5. Alonso-Blanco, C., Andrade, J., Becker, C., Bemm, F., Bergelson, J., Borgwardt, K.M., Cao, J., Chae, E., Dezwaan, T.M., Ding, D.J., Ecker, J.R., Exposito-Alonso, M., Farlow, A., Fitz, J., Gan, X., Grimm, D.G., Hancock, A.M., Henz, SR., Holm, S., Horton, M., Jarsulic, M., Kerstetter, R.A., Korte, A., Korte, P., Lanz, C., Lee, C.R., Meng, D., Michael, T.P., Mott, R., Muliyati, N.W., Nägele, T., Nagler, M., Nizhynska, V., Nordborg, M., Novikova, P.Y., Pico, A.R., Platzer, U., Rabanal, F.A., Rodríguez, A., Rowan, B.A., Salomé, P.A., Schmid, M., Schmitz, G., Seren, U., Sperone, F.G., Sudkamp, M., Svardal, H., Tanzer, M.M., Todd, J.A., Volchenboum, S.L., Wang, X., Wang, X., Wang, X., Weckwerth, W., Weigel, D., Zhou, X. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell. 2016;166(2):481-91.

  6. He F, Arce AL, Schmitz G, Koornneef M, Novikova P, Beyer A, et al. The Footprint of Polygenic Adaptation on Stress-Responsive Cis-Regulatory Divergence in the Arabidopsis Genus. Molecular Biology and Evolution. 2016;33(8):2088-101.

  7. Muir G, Ruiz-Duarte P, Hohmann N, Mable BK, Novikova P, Schmickl R, et al. Exogenous selection rather than cytonuclear incompatibilities shapes asymmetrical fitness of reciprocal Arabidopsis hybrids. Ecology and Evolution. 2015;5(8):1734-45.

  8. Novikova PY and Krasilnikov PM. Molecular Modelling of the Reactive Configuration of Peroxidised Lipid and Αlfa-Tocopherol in the Membrane. Cell Biophysics. 2009;54(4): 476–80.