Lucas Prost

Lucas Prost — PhD student
Joined the group in 2018

In November 2020 I obtained a PhD fellowship fundamental research from FWO (Fonds Wetenschappelijk Onderzoek) with the title “When Genomes Team Up”. The goal of the project is to investigate the immediate effects of allopolyploidization on fitness and gene expression. Allopolyploidization is an important phenomenon in plants that combines genome duplication and genome merging (i.e., polyploidization and hybridization). Allopolyploid plants have been described as “general purpose phenotype” by G. L. Stebbins, and indeed they seem to have a greater ability to exploit novel habitat than their diploid relatives. The most common hypothesis to explain this observation is the higher genetic diversity of allopolyploids, which they could use to respond to different conditions. Recently, this hypothesis has been reformulated in transcriptomic terms: allopolyploids can employ either adaptive homoeolog or either ecological parental expression level in response to environmental conditions, thus expanding their ecological amplitude across the parental niches. This hypothesis has been called the polyploid plasticity hypothesis in the literature, but I suggest the name of allopolyploid plasticity hypothesis.
Using the haploid species Chlamydomonas reinardtii, I intend to put this hypothesis to test in laboratory controlled conditions. I will merge different strains which will have evolved in different conditions during a laboratory adaptation experiment or which will come from different natural genetic clusters. These newly formed ‘allodiploid’ hybrids will be compared to their haploid parents for fitness and gene expression.

Birthdate: 5 February, 1995 (Obernai, France)

  • November 2020 – ...: FWO PhD Fellowship fundamental research (2 years, renewable once).
    Subject: “When Genomes Team Up: investigation of the immediate effects of alloploidization on fitness and gene expression”.
  • September 2018 – ...: Start of PhD in the team Bioinformatics and Evolutionary Genomics (VIB-UGent center for Plant Systems Biology).
    Topic: “Experimental evolution and evolutionary genomics – The effects of whole-genome duplication on plant evolution”.
  • September 2017 – June 2018: Master of Science in Evolutionary Biology (2nd year: Lille University, France / 1st year: Lund University, Sweden).
    Master’s thesis: “Genetic responses during an experimental evolution of Noccaea caerulescens in zinc-polluted conditions”.
  • September 2013 – June 2016: Bachelor of Science in Population and Organism Biology (Lille University, France).

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.
  2. Wu, T., Natran, A., Prost, L., Aydogdu Lohaus, E., Van de Peer, Y., & Bafort, Q. (2023). Studying whole-genome duplication using experimental evolution of Spirodela polyrhiza. In Polyploidy : methods and protocols (Vol. 2545, pp. 373–390). https://doi.org/10.1007/978-1-0716-2561-3_19
    In this chapter, we present the use of Spirodela polyrhiza in experiments designed to study the evolutionary impact of whole-genome duplication (WGD). We shortly introduce this duckweed species and explain why it is a suitable model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related duckweed experiment. These steps include strain selection, ploidy determination, different methods of making polyploid duckweeds, replication, culturing conditions, preservation, and the ways to quantify phenotypic and transcriptomic change.
  3. Bafort, Q., Prost, L., Aydogdu Lohaus, E., Van de Vloet, A., Casteleyn, G., Van de Peer, Y., & De Clerck, O. (2023). Studying whole-genome duplication using experimental evolution of Chlamydomonas. In Y. Van de Peer (Ed.), Polyploidy : methods and protocols (Vol. 2545, pp. 351–372). https://doi.org/10.1007/978-1-0716-2561-3_18
    In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related Chlamydomonas experiment. These steps include strain selection, ploidy determination, different methods of making diplo- and polyploid Chlamydomonas cells, replication, culturing conditions, preservation, and the ways to quantify phenotypic and genotypic change.