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:
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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.
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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