Gather relevant data from a genetic database, use the data to infer a phylogeny, and interpret your results.

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Project
The goals of this project are to:
1. build a phylogeny, so you know how they’re made,
2. interpret the output, so you know the constraints of phylogeny building, and
3. use the phylogeny to tell a story about life on Earth.
The goal is NOT to resolve a current mystery in phylogenetics or systematics.
For this project, you’ll choose creatures, gather relevant data from a genetic database, use the
data to infer a phylogeny, display/interpret your raw phylogeny, and use it to tell a story.
choose creatures
By the end of this project, you’ll construct a phylogeny that gives the relationships between
three groups of creatures. (Eg, a “group” could be octopuses, or cherry trees, or earthworms.)
Each group will be represented by 1-3 taxa, with at least 7 total taxa. (If you choose to add an
outgroup, that’s #8.) In the intro, you’ll compare the biology of these three groups—anything
you find interesting to compare and contrast. Later, when you’ve created a phylogeny, you’ll
use the phylogeny to tell any story you find interesting about the creatures.
gather data from genetic database
Dr. Jon Herron (another Bio354 instructor) made a video showing how to gather genetic data.
Watch the video here: http://evound.com/video-explainers/make-your-own-p…
You’ll have to decide what gene(s) and taxa are relevant for your project.
use the data to infer a phylogeny
This is also discussed in the video linked above. You’ll use a server called phylogeny.fr. Their
logo—a phylogeny emerging from a magic lamp—seems appropriate, since we won’t discuss
their exact phylogeny-building algorithm. (The concepts are covered in the pre-project.)
display/interpret your raw phylogeny
Phylogeny.fr will output a phylogeny with branch lengths indicating genetic distance, and
node numbers indicating bootstrap values (or similar) for the putative monophylies defined by
each node. You’ll display this “raw” phylogeny, and interpret it in your own words.
tell a story
When you get “raw” data from an experiment, you can display it many different ways,
depending on the story you want to tell. Similarly, a “raw” phylogeny can be simplified many
different ways. Your display should reflect what features are salient to your story. Your story
can be about a surprising homoplasy, a hypothesis about rates of evolution, a trait that seems
to transition easily, whatever you find interesting. It’s your story to tell.

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