Cladisticules

(September 20, 2013) I began my internship today!!! This year I am very lucky to be able to do intern on campus, which cut off all the travelling time:) Dr. Miller, who is my mentor, currently works in UCSD as a part of the CIPRES project (http://www.phylo.org/). He has been developing software and information technologies to assist biomedical research and now works with a supercomputer located in San Diego Supercomputer Center that maintains a database for phylogeneticic tree inference.

Last year, I wrote down for one of the reasons to apply for internship was to "widen my horizon," and here is the opportunity! All of my past experiences have more to do with molecular biology, such as growing cells and running PCRs in a lab. However, this year I get to learn biology in an evolutionary perspective. Dr. Miller raised a good point that studying phylogenetic trees is very critical for it allows us to take a step back and look at the organisms in the most fundamental view, to see a bigger picture of the biological world. I also learned many applications of phylogenetic trees, including predicting the properties of new pathogens, fighting against diseases that destroy food sources, and maintaining biodiversity. Nonetheless, I actually had had some experiences with some database such as BLAST and CLUSTAL before, which would help me through this course.

Different trees have different patterns, which I think are pretty impressive and very beautiful.
http://explorebio.wikispaces.com/The+Art+of+Phylogeny

After the introduction, we began a short exercise - to establish a simple cladogram.

1. There are 8 different species. We described each using different characters. The variants within a character is called character states. For example, the color of the abdomen is a character where as white / black abdomen are the character states.
   
2. Then we made a data matrix, with 0 meaning primary states and 1 being the developed states.
   
3. Based on the matrix, we constructed a Venn diagram.
   
4. Finally, we drew a cladogram based on the Venn diagram.
   

This exercise was actually really tricky because black abdomen rise up in two different places, which is called a homoplastic character. Although I had some basic background from AP Biology, this exercise was harder than expected. Luckily, we now have technologies that help us do this (which is what I will be learning!), and this was just to give me a taste of how long scientists used to spend on sorting out the evolutionary tree.

I definitely learned a lot, including many vocabs, during today's meeting. While Dr. Miller won't be here next week, he gave me a book Phylogenetic Trees Made Easy: A How-To Manual to read. My assignment is to learn to establish a phylogenetic trees on MEGA. Today was a great start and I am ready to explore the beauty of a phylogenetic tree!

Here is the link for the video Dr. Miller showed me during the introduction, and I thought it was pretty cool and well explained: http://archive.peabody.yale.edu/exhibits/treeoflife/film_discovering.html