Difference between revisions of "Evolution of seed size in relation to dispersal agent"
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Here is an archive containing everything needed to run the project, source code and datas : [[Media:SeedsSizeSourceCode.zip]] | Here is an archive containing everything needed to run the project, source code and datas : [[Media:SeedsSizeSourceCode.zip]] | ||
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| + | '''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, the students will use macroevolutive traits instead of microevolutive, meaning that the data are phenotypes and not puntucal mutations. The concerned phenotype is seed size, measured in grams. | ||
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| + | '''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, the students will apply 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, the students will learn how to code and optimize two complex mathematical models, to finally determine which model describes our data the most accurately. | ||
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| + | '''Mathematical tools''' : Based on the work of Butler and King, students will learn how to implement in R diverse statistical functions and optimization tools used to study the evolutionary models mentioned above. Using the R package Ape, students will also be able to learn how to manipulate phylogenetic information. | ||
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| + | '''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. | ||
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| + | '''Supervisors''': Anna Kostikova and Nicolas Salamin. | ||
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| + | '''Students''' : Mathieu Seppey, Angela Etienne and Damien Romascano | ||
Revision as of 11:48, 5 June 2013
Here is an archive containing everything needed to run the project, source code and datas : Media:SeedsSizeSourceCode.zip
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, the students will use macroevolutive traits instead of microevolutive, meaning that the data are phenotypes and not puntucal 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, the students will apply 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, the students will learn 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, students will learn how to implement in R diverse statistical functions and optimization tools used to study the evolutionary models mentioned above. Using the R package Ape, students will also be able to learn how to manipulate phylogenetic information.
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.
Supervisors: Anna Kostikova and Nicolas Salamin.
Students : Mathieu Seppey, Angela Etienne and Damien Romascano
