Download Investigation #3

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
Crocodilians
Palatal valve
Insects
Exposed
mouthparts
Birds
Great Apes
Opposable
feather thumbs
Crustaceans
Two-parted
limbs
Rodents
Two
specialized
incisors
fur
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/collegeboard-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
Gene
entered
Red bars compare
alignment with the
query.
Number of
results
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