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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:

  1. 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
  1. Multiple sequence alignment
  2. Best-fit substitution models estimation
  3. Saturation test
  4. Merge the alignments
  5. 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:

  1. Tree comparison
  2. Bootstrap
  3. Divergence time estimation
  4. Coalescence analysis
  5. List trees
  6. Tree space
  7. 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).