Adventures in Phylogenetic Analysis

I thought I might take a moment to discuss the phylogenetic analysis lab/project that we do in AP Biology. I’ve done a version of it every year for the past three years, and each time I am increasingly happy with the work that my students do.

Here’s the general flow of the project:

1. Students spend a series of days learning how to conduct phylogenetic analysis. I’ve varied the mode that I use every year, but the general purpose is to get students familiar with the major tools that are used to access DNA/protein sequence data and analyze that data to construct phylogenetic trees. This is helped by the fact that by this point there are a lot of quality activities that I can use to “train” my students in these tools and techniques, AND the fact that there is an ever-increasing mountain of sequence data available for anyone with an internet connection to access. This year, I used three specific activities for training:
   • The AP Biology Lab Manual BLAST Analysis activity. I don’t love the “activity” portion of this document so much, but it does provide a very good, detailed, guide on how to access BLAST, feed sequence information in to it, and interpret the results that come back. It also has a nice open inquiry structure at the end, that allows me to foreshadow what students are going to be expected to do.
   • The HHMI “Comparing DNA Sequences to Determine Evolutionary Relationships Among Mollusks” Activity. This activity trains students on how to align sequence data, and then use that alignment to generate phylogenetic trees. The activity as presented uses a series of supplied sequences, and the offline programs Clustal and NJPlot. In Chromebook-land, “offline” programs don't quite mean the same thing. Fortunately, there’s an amazing website that runs alignment and renders trees from data that gets pasted/loaded in to the site’s landing page. So we use that instead of the offline programs, but the modification is minor and can easily be done on the fly. Again, this activity has a very nice open inquiry extension at the end of it, which enables me to bring the conversation back, once again, to what students are eventually going to be doing.
   • I also gave students the Marine Mammal Phylogeny activity from ngbw. Even though ngbw is dead, the activities can still be easily adapted to use the tools I outlined in the previous bullet. The document has a nice explanation of using uniprot to find protein sequences, which is really the only purpose I have in using it, outside of it serving as a third and final example of a possible workflow for students to use.
2. Once the training is done, I discuss the project with students: They are going to investigate any phylogenetic relationship that they are interested in. Essentially, they will try to answer the question "How is <organism> evolutionarily related to <organism>?"  To do this, I provide them with a planning document, and guidelines for the final work product (a class blog article). This discussed, students are turned loose to work on the project, generally in pairs.
3. We establish an agreeable deadline for the final product, and I make sure to give students a lot of opportunity for feedback and independent work up to that date. This is made much easier in Chromebook-land, where I can check in on student documents very easily, and collaboration is maximized in the google docs environment. I was even able to pop in when I was at a conference on 10/4 during lunch to see the work that students were doing in class in my absence. Our use of the Piazza Webforum, gave me a dedicated space to post resources as I found them, and allow students to write in with questions that could be addressed asynchronously. This year, I broadened the resources I provided to some suitable Reddit posts (I actually believe this last post was written by one of my students, given its date and the fact that it cites the specific hypothetical example I used in our class discussion of the project).
4. New for this year: We established a due date of 10/15 for the final product. Upon reading them, I noticed that many of them could benefit from some fine tuning, so I decided to implement another phase of reflective editing. I left comments on every article (some quite snarky). Students then worked for the next week to edit their articles to address my concerns, AND were required to reply to each comment that I left explaining how they addressed my critiques. The end results, posted to the class blog by today, are universally lovely examples of student work in this area.

Readers of this site know that this model of inquiry-centered student work is something that I deeply believe in. And I think the results of the process speak for themselves. Take a look at the diversity of the questions that students asked, and the caliber of the analyses that they conducted, and let me know what you think.  Please, let them know what you think, too. Comment on your favorites!.