Investigation #3

Hmm…Make some observations. Go to http://www.amnh.org/learn/pd/dinos/gallery.html 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.

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.

Download 3 of 4 files http://blogging4biology.edublogs.org/2010/08/28/college-board-lab-files Don’t open.

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.

Browse for one of the saved files

Don’t change the settings. Gene 1 Blast

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

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

Distance tree of results

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.

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