Molecular Evolution Analyses

In the context of my Ph.D., I am studying the molecular evolution of the mud snail genus Ecrobia. Five Ecrobia species are included in this study:

1. Ecrobia grimmi (Ecgr)
2. Ecrobia maritima (Ecma)
3. Ecrobia spalatiana (Ecspa)
4. Ecrobia ventrosa (Ecve)
5. Ecrobia truncata (Ectr)

And two outgroups:

1. Peringia ulvae (Peul)
2. Salenthydrobia ferrerii (Safe)

Data

My data include two mitochondrial markers:

1. Cytochrome c oxidase subunit I (COI): 359 individuals
2. 16S ribosomal RNA (r16S): 74 individuals

And one nuclear marker:

3. Internal transcribed spacer 2 (ITS2): 46 individuals

Prerequisites

To estimate maximum likelihood trees with RAxML, this program needs to be previously installed, and the path of the executable needs to be given.

Installing

I set the working directory to source file location.

Steps

The whole script is still under progress. The following steps are already included:

1. Import DNA sequences (including outgroups)
2. Exploratory data analyses

• Base frequency
• Base frequency for each individual
• Base frequency between genes for all species pooled - WIP

3. Multiple sequence alignment
4. Best-fit substitution models estimation
5. Saturation test
6. Merge the alignments
7. Infer trees

• Brute force
• Evolutionary distances
• Distance-based phylogenetic methods
• Maximum parsimony
• Maximum likelihood methods
• Bayesian inference
• Codon model - WIP
• The class 'phylo' - WIP
• Visualization methods - WIP
• Plot trees - WIP

The following steps are not included yet:

8. Tree comparison
9. Bootstrap
10. Divergence time estimation
11. Coalescence analysis
12. List trees
13. Tree space
14. phytools

Written and Compiled With

• Sublime Text 2 version 2.0.2
• R version 3.4.1
• RStudio version 1.1.419

Author

• Justine Vandendorpe

Funding

My project is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642973.

Acknowledgments

This script was started during the course Phylogenetic Analysis Using R organized by Transmitting Science in March 2017. I would like to thank Emmanuel Paradis and Klaus Schliep for teaching during this course. I also found a lot of information in Emmanuel Paradis's book 'Analysis of Phylogenetics and Evolution with R' (Second Edition).