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Evolution
Phylogenetic Trees
AP Biology
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Phylogenetic Trees
By Bob Cooper and Mark Eberhard
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Learning Objectives
Students will be able to
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Use gel electrophoresis to create DNA and/or amino acid
seuquences
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Use DNA and amino acid sequence to create a matrix
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Use a matrix to create a phylogenetic tree
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Use national databases for DNA and protein sequences and
online tools (such as Evoseq and Phylogeny FR) to create
phylogenetic trees
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Use national databases for DNA and protein sequences and
online tools (such as Evoseq and Phylogeny FR) to answer
provided research questions and/or student generated
research questions
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Part 1 – Introduction to Phylogenic Trees
(1 Day)
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Conduct the Great Clad Race using the runners
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Relate the Great Cad Race with runners to the evolution of
selected vertebrates
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Create a 3D model of a tree based on the vertebrates cards
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Use the model to illustrate how groups can rotate around each
node
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Use the model to interpret evolutionary relationships
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Part 2 – The Basic Math Behind the Tree
(1 day)
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Analyze a given DNA or Amino Acid Sequences
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Determine number of differences
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Create a matrix based on the differences in the sequence
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Using your data matrix create a phylogenetic tree
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Using a given data matrix, such as Evoseq, to create a
phylogenetic tree
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Students complete a series of practice scenarios/problems
+ Part 3 - Create Your Own Sequences to Build a
Tree
(2-3 Days)
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Bio-Rad – Comparative Proteomics Kit
 Extract protein from muscle tissue of a variety of fish
 Use protein electrophoresis to create and analyze protein
profiles
 Use the protein profiles students generated to create a
matrix
 Use student generated matrix to build a phylogenetic tree
that shows evolutionary relationship of the various fish
used
+ Part 4 - Answer Research Questions Using Bioinformatics
(1-2 days)
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Introduce students to national databases – NCBI, Genebank, UniProt, etc.
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Introduce students to online analysis tools – Molecular Workbench, Phylogeny
FR, etc.
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Use these national data bases and online tools to answer scientific questions
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Whales, Walruses, and Seals, Oh My
 Did marine mammals evolve from a single ancestor who returned to the ocean, or
were there distinct return events from separate ancestors?
Polar Bears and Giant Panda Ancestory
Bats are Bugs  Bats are Birds – protein analysis
Where Do Humans Fit In? – DNA analysis
Should Birds be Considered a Type of Reptile? – protein analysis
Return to Later in the Course / Throughout the Year
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HHMI Anole Lizard Phylogeny
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Assessment
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Students develop their own research question
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Students use national databases and tree building programs to
help answer their research question
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Students create a poster presentation of their work to share with
their peers
Testing Assessment
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Provide a image of a gel for a DNA or amino acid sequence and
they have to create a matrix and draw a tree based on the gel
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Provide a tree and ask questions about evolutionary relationshipsstudents would need to be able to read the tree to answer