Evolution of seed size in relation to dispersal agent
Background : In evolutionary biology, mathematics and phylogeny have recently become primordial tools. Different mathematical models are used to try to explain how species have evolved and differentiated during time, and as we gather more phenotipical and genomic data from research, it is primordial to learn how to use these new information to try to understand how evolution applies to species. In this study, we have used macroevolutive traits instead of microevolutive, meaning that the data are phenotypes and not punctual mutations. The concerned phenotype is seed size, measured in grams.
Goal : The objective of the study is to find out if the evolution of plant seed size in function of their dispersal agent is only due to genetic drift, or if it is under the influence of natural selection. To do so, we applied mathematical models on a phylogenetic tree of the seeds : The Brownian Motion (BM), which represents a model where only random mutations determine the seed size ; and the Ornstein-Uhlenbeck model (OU), which also takes the effect of natural selection into account. Using R, we learned how to code and optimize two complex mathematical models, to finally determine which model describes our data the most accurately.
Mathematical tools : Based on the work of Butler and King, we learned how to implement in R diverse statistical functions and optimization tools used to study the evolutionary models mentioned above. Using the R package Ape, we also learned how to manipulate phylogenetic information. Formulas and explanations of parameters can be seen in the presentations: for BM model, see mainly the midterm presentation, and for the OU model see mainly the final presentation
Biological aspects : This study allows to estimate which model (BM or OU) was more likely applied during evolution, and can be used to answer different phenotipical problems as ancestral reconstruction and future expectancies.
Results: With the implementation of both models that we developed, we were able to demonstrate that the OU theory fits better with our data than the simple genetic drift-based BM model, which means that selection has a significant effect on seeds size. See the end of our final presentation for more detailed results.
Supervisors : Anna Kostikova and Nicolas Salamin.
Students : Mathieu Seppey, Angela Etienne and Damien Romascano
Appendices :
Link towards our midterm presentation: File:SeedSize Midterm A4.pdf
Link towards our final presentation: File:Présentationfinale.pdf
Link towards an archive containing everything needed to run the project, source code and datas : File:SeedsSizeSourceCode.zip
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