Download 1 NAME DATE ______ PER ___ INVESTIGATION 3

1
NAME _____________________________________
DATE _____________ PER ___
INVESTIGATION 3: UNDERSTANDING
EVOLUTIONARY RELATIONSHIPS WITH
BLAST
Adapted from http://media.collegeboard.com/digitalServices/pdf/ap/bio-manual/CB_Bio_Lab_03_WEB_1_24_12.pdf and
http://www.ncbi.nlm.nih.gov/books/NBK21097/
1.
Observing and Asking Questions
a. List 3 characteristics of this fossilized organism.
b. List 3 modern day organisms that possess each of the
characteristics you listed.
Characteristic
Modern day organisms with
Characteristic
1.
2.
3.
Figure 2 includes the evolution of particular physical
structures called shared derived characters. Note that
the placement of the derived characters corresponds to
when (in a general, not a specific, sense) that character
evolved; every species above the character label
possesses that structure. For example, tigers and
gorillas have hair, but lampreys, sharks, salamanders,
and lizards do not have hair.
My-Nga Ingram AP Biology 2012
2
Max Score and E-Values
The Max Score gives an indication of how good the alignment is; the higher the score, the better the alignment.
In general terms, this score is calculated from a formula that takes into account the alignment of similar or
identical residues, the length of the sequence, as well as any gaps introduced to align the sequences.
The Expect value (E) is a parameter that describes the number of hits one can "expect" to see by chance when
searching a database of a particular size. Essentially, the E value describes the random background noise.
The lower the E-value, or the closer it is to zero, the more "significant" the match is. However, keep in mind
that virtually identical short alignments have relatively high E values. This is because the calculation of the E
value takes into account the length of the query sequence. These high E values make sense because shorter
sequences have a higher probability of occurring in the database purely by chance
2. Inferring and Hypothesizing
a. Based upon your analysis of the characteristics of this fossil, place the organism on the cladogram.
5. Data
Sequence 1 Query length: ________________
Results
Scientific Name
Common Name
Name and
Function of
Protein
First sequence
Second sequence
LAST sequence
My-Nga Ingram AP Biology 2012
Max Score
E-value
3
Sequence 2 Query length: ________________
Results
Scientific Name
Common Name
Name and
Function of
Protein
Max Score
E-value
Name and
Function of
Protein
Max Score
E-value
First sequence
Second sequence
LAST sequence
Sequence 3 Query length: ________________
Results
Scientific Name
Common Name
First sequence
Second sequence
LAST sequence
7. Discussion (Type and attach to back of this document.)
 State whether the newly acquired data supports/does not support your hypothesis.
 Restate key data that supports the above statement.
 Explain why the data supports/doesn’t support your hypothesis.
 Discuss why the max score is more significant than E-value in understanding where the fossil should be
assigned in the cladogram.
 Discuss how the functions of the proteins can help us understand evolutionary relationships.
(Connection)
 Discuss the significance of using BLAST in determining evolutionary relationships of newly discovered
fossils. (Connection)
My-Nga Ingram AP Biology 2012