MODULES’ STRUCTURE AND GOALS
The main goal of the task that you are about to undertake is to learn how to apply one of the most common methods scientists use to detect which transposable elements (TEs) are most likely to be adaptive; that is, recognizing which TEs present in Drosophila are most likely to affect adaptation to their local environment.
With this information, practical scientists would be able to find and characterize the functions of any genes found close TEs in the lab; and then determine how they affect adaptation to environmental stresses in comparison to those individuals that do not carry these insertions
For this purpose, you will need to become familiar with the theoretical concepts and practical tools presented in the following modules. In some of these modules, you will see a “Test yourself” section where you can practice different parts of the process and develop the skills needed to distinguish and classify TE induced mutations according to the level of importance; something which is of great interest to scientists studying adaptation. Finally, attached to the end of this document is Annex 1, where you can find a short summary of the TE candidates currently thought to be adaptive in Drosophila melanogaster.
- Module 1: things you should know
- DNA, Genes and Genomes
- Transposable Elements
- Population Genetics: things to take into account (the type of mutation, depending on its effect; natural selection, insertion frequencies, and recombination)
- Drosophila melanogaster: the main character
- Test yourself: QUIZ
- Module 2: Installation of Working Tools
- Why use a Statistic Package?
- R Installation
- RStudio Installation
- R Code Files
- Text Editor Installation
- Module 3: TE Visualization and Data Files: How to import files and variable distribution
- Flybase and GBrowse
- What is inside the data file?
- How to import the data file into R?
- Variables Distribution
- Test yourself: QUIZ
- Module 4: Generating Candidate Lists of Adaptive TEs
- Lists of Potentially Adaptive Candidate TEs: TEST YOURSELF
- Changing Parameters: TEST YOURSELF
- Check Lists: TEST YOURSELF
ANNEX 1: Current information about Drosophila melanogaster TEs candidate to be adaptive
Module 1 >