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Name: _____________________________________________
AP Biology
Investigation 3 Lab Guide
Comparing DNA Sequences To Understand Evolutionary Relationships With BLAST
1. Read Background on pgs. S41-S43 in Lab Manual.
2. Lab Notebook:
Part I: Unknown Fossil
a. Pre-Lab: Answer Questions #1-2 on pg. S43-S44.
b. Purpose: To use BLAST to analyze the DNA from a fossil specimen found in Liaoning
Province, China
c. Hypothesis: Based on the morphological observations of this fossil, where do you
think this fossil belongs on the cladogram shown (See Figure 4 on pg. S45)? State
your hypothesis and draw a diagram in your lab notebook.
d. Procedure (Read pgs. S44-S48) – Download and save the 4 gene files onto your
Desktop.
e. Observations:
 List general observations and sketch fossil on pg. S44.
 Upload each gene sequence into BLAST. Follow directions in lab manual
(pgs. S45-S47 carefully!). For each gene sequence, record the name of the
species with the most similar sequence that matches , the name of the
gene product, and the Max Score and E Value for that particular gene.
 Look up (use Google, Bing, etc.) the common name of each of the species
that is listed.
 Now, on the gene summary page, look at the “Distance Tree of Results”.
Where does this gene fall on the phylogenetic tree? Record your
observations of each gene’s tree.
f.
Analysis of Results: (answer these questions in complete sentences in your
notebook)

Based on the BLAST results from each gene, which species are most closely
related to the unknown fossil specimen? Compare the Scores for each gene.
The one with the higher max score, the closer the alignment.

Based on this information, where should the new fossil species belong on
the cladogram? If necessary, re-draw the cladogram you created before.
g. Conclusion:

Was your hypothesis supported by the DNA data? Explain.
Designing and Conducting Your Investigation: Human Actin (Page S49)
1. Follow the instructions provided under “Example Procedure.” Besides other human
sequences, identify the top three other species that rank highly for similarity to the
human actin gene. Record your results in the chart below.
Scientific Name
Common Name
Max Score
Max Ident %
2. Based on the data you recorded above, construct a phylogeny illustrating the
evolutionary relationship between humans and the other three species identified by
your BLAST search of the actin gene.
3. Provide a reasonable explanation for why these organisms have such high similarity
in their DNA sequences.
4. Do some research on the Internet regarding human actin. What is the main function
of this protein?
Designing and Conducting Your Investigation
5. Begin a new investigation using one of the other genes suggested, or search for
another human gene of interest in the Entrez Gene database.
Identify your gene of interest: ______________________________________________________________
(Complete Questions 6-10 before running your BLAST analysis of your gene.)
6. What is the function in humans of the protein produced from that gene? (You may
need to do some additional research on the Internet to find this information.)
7. Would you expect to find the same protein in other organisms? If so, which ones?
Why?
8. Is it possible to find the same gene sequence in two different kinds of organisms’
DNA but not find the protein that is associated with that gene produced in both
organisms? Why?
9. If you found the same gene in all the organisms you test, what does this suggest
about the evolution of this gene in the history of life on Earth?
10. Does the use of DNA sequences in the study of evolutionary relationships mean that
other characteristics and lines of evidence for evolutionary relationships are
unimportant in such studies? Explain your answer.
Now, run the BLAST analysis on your selected protein.
11. Complete the following chart summarizing the results of the top five sequence
matches (omit other sequences from humans).
Scientific Name
Common Name
Max Score
Max Ident %
12. Based on the data you recorded above, construct a phylogeny illustrating the
evolutionary relationship between humans and the five other species identified by
your BLAST search of your selected gene.
13. How are the percentages discovered in the lab used by scientists?
14. Identify two research questions that could be answered using the Entrez Gene
database and BLAST analysis tools to compare nucleotide and protein sequences.