We study polyploidy from various theoretical perspectives. Theory building and applying theoretical models from related field is a very valuable part of the cycle of scientific research, which complements our empirical research. By framing observations in a robust and transparent representation of the biological world, we can question our understanding in future research using our model systems. Our work seeks to identify fundamental mechanisms of polyploid establishment by leveraging various evolutionary and ecological theoretical frameworks through a combination of analytical, simulation and statistical modelling approaches:

1. Population Simulation and Population Genetics Models

We investigate the conditions that enable the establishment of polyploids and their effect on gene flow through incomplete reproductive barriers, so-called polyploid bridges (Kauai et al., 2023, Kauai et al., 2024). These models show us what patterns emerge from very simple mechanisms and, therefore, questions less obvious explanation.

2. Metabolic Theory of Ecology

Metabolic processes scale sublinearly with size. When polyploidy increases cell and body size, it should impact metabolism as well. The allometric scaling of metabolism reveals fundamental limits to biological rates with far-reaching consequences to individuals, populations and ecosystems. We study the relationship between polyploidy and metabolism in Dynamic Energy Budget simulation models (Milosavljevic et al., 2024) and validate this with our model systems.

3. Gene Regulatory Network simulations

Whole genome duplication doubles the number of each gene but also duplicates whole gene regulatory networks. We found that doubled gene regulatory networks are able to produce more extreme phenotypes that are, on average, beneficial in rapidly changing environments (Ebadi et al., 2023). For more information see Artificial Evolution.

4. Community Ecology Frameworks

Polyploids emerge in sympatry with their diploid progenitors and can establish by either outcompeting or by coexisting with that progenitor. Because competition is an undeniable process in communities, we can learn much from modern coexistence theory and contemporary niche theory, though, considering species barriers between polyploids and progenitors. We apply these frameworks in experiments with our model systems (Mortier, Van de Peer and Bonte, 2025).

Published papers:

• Ebadi, M. et al. (2023) ‘The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil’, Proceedings of the National Academy of Sciences, 120(41), p. e2307289120. Available at: https://doi.org/10.1073/pnas.2307289120.
• Kauai, F. et al. (2023) ‘Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems’, Proceedings of the Royal Society B, 290. Available at: https://doi.org/10.1098/rspb.2022.2456.
• Kauai, F. et al. (2024) ‘Interspecific transfer of genetic information through polyploid bridges’, Proceedings of the National Academy of Sciences, 121(21), p. e2400018121. Available at: https://doi.org/10.1073/pnas.2400018121.
• Milosavljevic, S. et al. (2024) ‘A metabolic perspective on polyploid invasion and the emergence of life histories: Insights from a mechanistic model’, American Journal of Botany, 111(8), p. e16387. Available at: https://doi.org/10.1002/ajb2.16387.
• Mortier, F., Van de Peer, Y. and Bonte, D. (2025) ‘Polyploid - diploid coexistence in the greater duckweed Spirodela polyrhiza’. bioRxiv, p. 2025.01.07.631665. Available at: https://doi.org/10.1101/2025.01.07.631665.