V. Testing Hypotheses - Using Phylogenetic Trees (30 minutes)
Explain to students that molecular technology allows researchers to use DNA data to produce phylogenetic trees that provide another way to test hypotheses. Johnson, et al. used molecular data to generate phylogenetic trees to test how closely related different specimens from the different fish groups were to one another. Students will analyze one of the same phylogenetic trees that Johnson et. al used, a Maximum Likelihood (statistical method that searches for the tree that has the highest probability of accounting for the observed patterns; best estimate of the relationships of the taxa included) tree based on partial 16s ribosomal DNA sequences.
To get started and help students understand how patterns in the phylogenetic trees can be used to test the two hypotheses, have students complete An Exercise in Tree Interpretation on page 9 of the Student Research Notes. Guide students to take a careful look at which specimens share the closest common ancestor. They should determine that Tree One best supports the Single Clade Hypothesis and Tree Two best supports the Three Clade Hypothesis.
Have students look at the Phylogenetic Tree on page 10 of the Student Research Notes. Explain that this tree is generated from DNA samples taken from individual species of fish including those that have been classified in the three groups. Students should select a color for each group of fish (Tapetails, Whalefish, and Bignose fish) to create their own color-coded key, and then use the Deep Sea Fish Specimen Key to color-code the Whalefish, Tapetails, and Bignose fish species depicted on the tree.
Students should analyze the patterns revealed in each tree to explain which of the hypotheses this tree best supports. They should discover that the individual species of each group are distributed throughout the branches rather than forming distinct and separate groups (e.g. Tapetails are scattered throughout the tree). This pattern supports the Single Clade Hypothesis. The molecular evidence is consistent with the morphological evidence that these three groups of fish in fact belong to the same clade and represent females, males, and larvae.
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