Friday, 24 April 2015

Molecular phylogeny - a classroom example

During the winter term of 2014, I was able to carry out the teaching assignment of my postdoctoral adviser during his sabbatical leave. The course, Introduction to Plant Science, was an undergraduate class of approximately 80 students from various disciplines. This was a great opportunity for me to test and improve my teaching, presentation and communication skills. However, the best thing about it was that I could build my own lectures from scratch provided I covered what the syllabus outlined. But with three 50 min lectures per week for a total of four weeks (the course is co-taught, i.e. the other instructor covered the first four weeks) this meant a lot of work. Nonetheless, I decided to take this route because I knew I would present more naturally and, most importantly, I would have my own lecture material for the future.

One of my favourite lecture was an introduction to biological diversity and classification (see here). Besides talking about Carl Linnaeus, Charles Darwin and evolutionary trees, I decided to show an in-class example of how easy it is to build a simple molecular phylogeny of the green plants. The only thing we needed were gene sequences and a program that can calculate the phylogenetic tree.

For this in-class example, I decided to pick 14 species from various groups within the green plants (Viridiplantae). I also decided to use gene sequences that code for the enzyme RuBisCO, which is essential for carbon fixation in the leaves. I downloaded the sequences from the NCBI database saved them in a text file (see here) and pasted them into Robust Phylogenetic Analysis For The Non-Specialist after specifying the "One Click" option (thanks to Joan Laur for showing me this website). By accepting all the defaults, this is the tree you will get:


Fig. 1. Screen shot of the original tree as it comes out of the analysis.

Luckily one can flip the branches at the nodes without changing the meaning of the results. This helps to organize the tree a bit better and facilitates its interpretation. With a little bit of additional work in Adobe Illustrator, the result is a phylogenetic tree, which highlights monophyletic groups (or taxa) including the characteristics (synapomorphies) that define those groups.

Fig. 2. Molecular phylogeny of the Green Plants (Viridiplantae) using RuBisCO gene sequences including synapomorphies that define the five highlighted monophyletic groups: Green plants, Land plants, Vascular plants, Seed plants and  Flowering plants. The "Bryophytes" (red box) may not form a monophyletic group as a whole but each of the lineages (liverworts, mosses, hornworts) are considered monophyletic.

Do you have any comments or suggestions? Feel free to post them below!


References:

Simpson, M. (2010). Plant Systematics. 2nd Edition, Elsevier.

Thanukos, A. (2009). A name by any other tree. Evolution: Education and Outreach, 4, 303-309.

Gregory, T. R. (2008). Understanding evolutionary trees. Evolution: Education and Outreach, 1, 121-137.

Shaw, J. & Renzaglia, K. (2004). Phylogeny and diversification of bryophytes. American Journal of Botany, 91, 1557-1581. 

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