1. Investigation #3

2. Hmm…Make some observations.
Go to for a high resolution photo.
This fossil was found near Liaoning Province China.
Where does this organism “belong” in the cladogram on the next page?
DNA sequence of several genes was obtained. Use this to place the organism.

3. Fossil Cladogram Great Apes Rodents Crocodilians Birds Opposable
thumbs
Palatal valve
feather
Two specialized incisors
Insects
Crustaceans
fur
Exposed
mouthparts
Two-parted limbs
vertebrae
heterotroph
From page S45 AP Biology Investigative Labs from the College Board.

4. Download 3 of 4 files
Don’t open.

5. http://blast.ncbi.nlm.nih.gov/Blast.cgi Click on saved strategies
Many data base choices. This exercise uses nucleotide blast to compare the fossil sequence to known organisms.

6. Browse for one of the saved files

7. Don’t change the settings.
Gene 1
Blast

8. Analysis Number of results Gene entered
Red bars compare alignment with the query.

9. Scroll down. Listed in order of similarity
This score refers to gaps and substitutions. Higher=more similar alignment
E value is the likelihood a match occurred by chance. Lower the number the better the match.
Refer to other data bases

10. Distance tree of results

11. Repeat with other genes
Think about your hypothesis in response to the question: Where does the fossil fit on your cladogram?
Remember:
The higher the score, the closer the alignment.
The lower the e value, the closer the alignment.
Sequences with e values less than 1e-04 (1 x 10-4) can be though of as related
See page S48 for additional questions and some thoughts on designing your own investigation.
From the College Board AP Biology Investigative Labs.

12. Find a gene of interest http://www.ncbi.nlm.nih.gov/gene