Wednesday, April 18, 2012

Teaching phylogenetics


Repost from a blog I wrote here.

As career scientists, I think we have two main roles:

1. To conduct good research
2. To communicate the findings

I consider public science outreach to be a responsibility that falls under "communication". If the general public is not informed about the basic background of science, how can we hope for them to understand and support current research? In an effort to further basic science education, several of us from the Nielsen lab have been volunteering our time and talents to teach at the local high school. My contribution was a lesson on Phylogenetics. If you're very interested in this topic, please see the University of California Museum of Paleontology's website on Phylogenetic Resources.

I put together a simple set of activities to introduce the concept of phylogenetic trees, address how we build the trees, and discuss ways in which they are useful. I tried to make it as hands-on as possible, and was supported by several wonderful colleagues who also volunteered their time to assist with the small group activities.



The lesson started with an explanation of what a phylogenetic tree is, and how it is used to represent the relationship between individuals or species. We also discussed how switching the order of labels might or might not affect the information in the tree.



The students then broke into groups to work on an exercise to see if they could apply the lesson about interpreting phylogenetic trees. We then had a second section where we discussed how phylogenetic trees are made. After some discussion where students suggested using physical features or environment differences to build a tree I passed out a tree and a set of species, and asked the students to estimate the relationships between the species using their knowledge about the morphology of the species. Afterwards I had each group come to the front, show their grouping, and explain the logic behind their decision.



Then I described how many scientists now also use information from DNA sequences to learn about the relationships between species. Each group was given three different "gene" sequence alignments, with one sequence per species (species names were encoded by numbers to prevent biases from the last section), and asked to determine the relationship between the species based off of differences between the DNA sequences.



Afterwards I had another student come up to the front and draw the relationship between species based off the DNA sequences (everyone in the class agreed with the tree), and then I revealed the true species names. We compared the tree built with DNA sequences to the tree estimated from morphological traits and discussed differences/similarities between them.



In the last section of class we discussed the following topics:
- Of the three "gene" sequences, one had many informative sites, and one had only two informative sites (and did not give a highly resolved tree). Why might this be?
- What are the applications of phylogenetic trees? For example, being able to determine the history of infectious viruses, like avian flu.

Please feel free to email me (mwilsonsayres at berkeley.edu) if you'd like a copy of the lesson plan and materials I made for this project.

4 comments:

Rich said...

Looks like fun, Melissa. Have you seen this neat little introduction to phylogenetics:

http://www.bioone.org/doi/abs/10.1662/0002-7685%282003%29065%5B0679:TGCR%5D2.0.CO%3B2

mathbionerd said...

It was a lot of fun, and useful for me to figure out a concise way to teach the concept.

I hadn't seen that - thanks for sharing!

Rich said...

If you're interested in learning more about teaching phylogenetics, check this out: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092386/

\self promotion...

mathbionerd said...

Thanks :)