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Phylogenetic TreesAP Biology

Evolution

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Phylogenetic TreesBy Bob Cooper and Mark Eberhard

+Learning Objectives

Use gel electrophoresis to create DNA and/or amino acid seuquences

Use DNA and amino acid sequence to create a matrix

Use a matrix to create a phylogenetic tree

Use national databases for DNA and protein sequences and online tools (such as Evoseq and Phylogeny FR) to create phylogenetic trees

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

Students will be able to

+Part 1 – Introduction to Phylogenic Trees(1 Day) Conduct the Great Clad Race using the runners

Relate the Great Cad Race with runners to the evolution of selected vertebrates

Create a 3D model of a tree based on the vertebrates cards Use the model to illustrate how groups can rotate around

each node Use the model to interpret evolutionary relationships

+Part 2 – The Basic Math Behind the Tree(1 day) Analyze a given DNA or Amino Acid Sequences

Determine number of differences

Create a matrix based on the differences in the sequence

Using your data matrix create a phylogenetic tree

Using a given data matrix, such as Evoseq, to create a phylogenetic tree

Students complete a series of practice scenarios/problems

+Part 3 - Create Your Own Sequences to Build a Tree(2-3 Days)

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)

Introduce students to national databases – NCBI, Genebank, UniProt, etc.

Introduce students to online analysis tools – Molecular Workbench, Phylogeny FR, etc.

Use these national data bases and online tools to answer scientific questions 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 HHMI Anole Lizard Phylogeny

+Assessment

Students develop their own research question Students use national databases and tree building

programs to help answer their research question Students create a poster presentation of their work to share

with their peers

Testing Assessment 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

Provide a tree and ask questions about evolutionary relationships- students would need to be able to read the tree to answer