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Reconstructing the evolution of traits in plant development studies

Reconstructing the evolution of traits in plant development studies
In a recent article published in December 2019 in Current Biology, researchers from the Plant Science Research Laboratory (LRSV - UMR University of Toulouse / CNRS / UPS) and the Station of Theoretical and Experimental Ecology (SETE - UMR CNRS / UPS) propose a guide for structuring comparative biology approaches with the aim of understanding plant diversity.

An incredible plant diversity is present on our planet. This diversity can be observed in a single group of closely related species, whether it be in form and function - the color of petals in flowering plants, the shape of fronds in ferns or the branching pattern in mosses for example. Diversity can also be found in more subtle traits, such as resistance to pathogens or the ability to recruit symbiotic microbes from the environment.

On the other hand, many plant traits can be highly conserved. For example, at the cellular and metabolic levels, entire biosynthetic pathways are present in all groups of plants. In addition, morphological traits such as vascular tissues have been conserved for hundreds of millions of years.


De gauche à droite. Tige et feuilles de l’angiosperme Medicago truncatula, sporophyte de la fougère Pteris vittata et gamétophyte de l’hépatique Marchantia paleacea.

The research community aiming at understanding plant traits by adopting an evolutionary point of view is growing. The authors of this article summarize a subset of the different aspects of evolutionary plant biology. They start by highlighting the importance of drawing conclusions based on accurate reconstructed phylogenies. Then, they provide a five-step guide for structuring comparative biology approaches.

As a preamble, the authors stress the need to consider the following point : all the living species are as much "evolved" as each other. Therefore, it would be better to call a taxonomic group by its name (flowering plants, moss, fern), rather than using arbitrary adjectives such "primitive", "higher" or "lower ".

Step 1: inferring trait evolution

Any study on the evolution of form and function (traits) should start by precisely defining the trait of interest. The objective of the first step is therefore to infer the evolution of the characters, by mainly focusing on living plant species. Fossils are not essential but, when available, greatly improve these inferences.

Step 2: the evolution of genes associated with the trait of interest

Once a gene of interest has been identified, the objective of the second step is to reconstruct the evolutionary history of this gene based on phylogenetic analysis, using the large databases of publically available genome sequences. In the end, comparisons between the phylogenies of the species and the phylogenies of the genes allow investigating genotype-phenotype relationships and the formulation of hypotheses. However, testing such hypotheses that are based on correlative predictions requires functional validation, which is detailed in the next two steps.

Step 3: Determining the evolution of biochemical properties

In the third step, the authors suggest studying the evolution of the biochemical properties of proteins encoded by the genes of interest, by performing interspecific complementation tests of mutants with orthologs from several clades of plants. For example, if a gene of a fern restores the morphological traits affected in a flowering plant mutant, it could be concluded that the important biochemical functions for this trait are conserved between flowering plants and ferns.

Step 4: Determining the evolution of a gene’s biological role

The conserved biochemical properties of a protein do not mean that its biological role itself is conserved. Testing the conservation of the biological role of a gene is generally carried out by generating mutants lacking the function of the corresponding gene in several species belonging to various taxonomic groups.

Step 5: Synthesizing the molecular evolution of the trait of interest

All of the previous steps are combined in a final step, thereby leading to a holistic understanding of the molecular evolution of the trait of interest. This inference is valid depending on the data available. Experimental validations in other species and the sequencing of a larger number of genomes is likely to provide refined scenarios.

Finally, the authors point out that humility is necessary on these subjects. Indeed, because we can only study living species at the genetic level, we always capture a simple snapshot of the phenotypes that have evolved. It is in this spirit that throughout the article, the researchers discuss the pitfalls to avoid when go into such studies, pitfalls illustrated by examples from the literature.

See also

Pierre-Marc Delaux & al. Reconstructing trait evolution in plant evo–devo studies. Current Biology 29, R1105–R1121, 2019