Felipe Kauai PEREIRA

Felipe Kauai PEREIRA — PhD student
Joined the group in 2021

The pioneering work of Ronald Fisher, Sewall Wright and others on population and evolutionary genetics has inspired many theoretical computer scientists to pursue the implementation of theoretical evolutionary biology into optimisation algorithms. These algorithms can in turn provide valuable insights on how one can go about simulating and studying real biological phenomena. As a forest engineer with a master's degree in the field of evolutionary computation, I aspire to develop models that simulate the eco-evolutionary dynamics of populations. By doing so I try to understand key processes driving the distribution of biodiversity on the planet. Specifically, I am interested in understanding how polyploid organisms can emerge and persist among diploid populations, and how such emergence disturbs the entire system in time and space.

Publications

  1. Mortier, F., Bafort, Q., Milosavljević, S., Pereira, F. K., Prost, L., Van de Peer, Y., & Bonte, D. (2024). Understanding polyploid establishment : temporary persistence or stable coexistence? OIKOS. https://doi.org/10.1111/oik.09929
    Polyploidy, resulting from whole-genome duplication (WGD), is ubiquitous in nature and reportedly associated with extreme environments and biological invasions. However, WGD usually comes with great costs, raising questions about the establishment chance of newly formed polyploids. The surprisingly high number of polyploid and mixed-ploidy species observed in nature may be a consequence of their continuous emergence or may reflect stable polyploid persistence and even coexistence with the ancestral ploidy under certain circumstances. However, empirical studies on contemporary polyploid establishment often neglect the cost-benefit balances of polyploid characteristics, tradeoffs between phenotypic characteristics, intercytotype interactions, recurrent polyploid formation, and stochastic processes. Here, we advocate for considering population-level success, combining the aforementioned factors that affect polyploid establishment and long-term coexistence with their ancestors. We approach the paradox of polyploid establishment despite high costs from a modern coexistence theory perspective and give an overview of the diversity of mechanisms and their timing that may potentially enable stable rather than transient persistence.
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  2. Pereira, F. K., Mortier, F., Milosavljević, S., Van de Peer, Y., & Bonte, D. (2023). Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 290(1995). https://doi.org/10.1098/rspb.2022.2456
    Polyploidy, i.e. the occurrence of multiple sets of chromosomes, is regarded as an important phenomenon in plant ecology and evolution, with all flowering plants likely having a polyploid ancestry. Owing to genome shock, minority cytotype exclusion and reduced fertility, polyploids emerging in diploid populations are expected to face significant challenges to successful establishment. Their establishment and persistence are often explained by possible fitness or niche differences that would relieve the competitive pressure with diploid progenitors. Experimental evidence for such advantages is, however, not unambiguous, and considerable niche overlap exists among most polyploid species and their diploid counterparts. Here, we develop a neutral spatially explicit eco-evolutionary model to understand whether neutral processes can explain the eco-evolutionary patterns of polyploids. We present a general mechanism for polyploid establishment by showing that sexually reproducing organisms assemble in space in an iterative manner, reducing frequency-dependent mating disadvantages and overcoming potential reduced fertility issues. Moreover, we construct a mechanistic theoretical framework that allows us to understand the long-term evolution of mixed-ploidy populations and show that our model is remarkably consistent with recent phylogenomic estimates of species extinctions in the Brassicaceae family.
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