Conor Wight

Mrs. Peterson
AP Biology
2/29/2016
BLAST Lab
Background
The Human Genome project, taking place between 1990-2003, was an
international research project that resulted in the identification and mapping of
approximately 20,000-25,000 genes that make up the human genome. In addition,
scientists involved in the Human Genome Project were able to map the genomes of the
fruit fly, mouse, Escherichia coli among others.
Having a better understanding of the human genome has several benefits. The first
is that it allows for a better understanding of genetic diseases by possessing the ability to
locate specific gene sequences. Outside of the human genome, the research is beneficial
in that the mapping of the genomes of other organisms assists in giving clearer
evolutionary ties between organisms. It was found that a great deal of the human genome
is near identical to those of other species.
Due to the impracticality and impossibility of scouring the entire genome of an
organism to find a specific sequence of genes, bioinformatics methods can be applied in
order to compare entire genomes and compare genetic components. One accessible
method is BLAST; through BLAST, one can plug in a gene sequence of interest and go
through an entire library of genomes to search for identical or similar sequences in a very
short amount of time.

Pre-lab questions

2. a. The percentage similarity in the

gene is always lower than the
percentage similiarty in the protein
because slightly different sequences of
genes will code for the same protein.
Different codons will produce the
same amino acid, which in turn
combine to form a protein. So, even if
the genome sequences are different,
the same proteins will be produced,
hence the difference in percentage
similarity.

Hypothesis
If the morphological observations of a long tail, four limbs and a reptilian head that all
point to a lizard-like creature are accurate, than the fossil specimen should be placed
above palatal valve close to the crocodilians.
Procedure
1. Download and save the 4 gene files onto your Computer Desktop.
Download files (See AP bio lab 3)
2. Follow procedures on pages S44-S48.
Observations

General observations; the fossil specimen shares a similar appearance with some type of
lizard species; this educated guess is based off of the long tail, presence of four limbs
with claw like appendages, and a head with a reptilian appearance.

Data Table
Gene
Sequence

1
2
3
4

Scientific
Gene
Name of
Name
Closest
Matching
Species
Gallus gallus Collagen

Max
Score

E Value

Common
Name of
Species

10129

0.0

Drosophilia
melanogaste
r
Taeniopygia
guttata

Transcript

4419

0.0

Red
Jungle
Fowl
Common
Fruit Fly

2120

0.0

Zebra
Finch

Alligator
sinesis

Complete
Genome

1768

0.0

Eastern
Chinese
Alligator

Observation
s From
Distance
Tree Results

Closest to
Flies
Closest to
birds and
turtles
Closest to
crocodile

Analysis
1. The species that is most closely related to the unknown fossil specimen are the
Red Jungle Fowl, based on the fact that it had the highest max score in relation to
the unkown species out of the 4 given gene sequences.

2. Based on the information gathered from BLAST, the new fossil species should be
placed above the trait of feathers and be put into the birds section of the
cladogram. This is based not only on its close relation to the Red Jungle Fowl, a
species of bird, but also to the Zebra Finch, another type of bird. Its relation to the
Zebra Finch is greater than it is to that of the Eastern Chinese Alligator, negating
the original idea that the unknown fossil specimen belongs in the reptilian
category.
Conclusion
1. No, the hypothesis was not supported by the data. The data made it clear that the
fossil specimen is more closely related to birds than it is to crocodiles, or other
species of reptile for that matter; the Eastern Chinese Alligator provided the
lowest Max Score of the 4 gene sequences, while the two species of bird
provided the highest and 3rd highest Max Scores.
2. All members of the group agree with the placement of the fossil specimen on the
cladogram.
3. The other data that can be collected from the fossil would be the rock that it is
encased in. Determining what strata of the Earth it was discovered in can help
scientists to estimate how long again the fossil existed, which would give them a
better understanding of where the creature should be placed in the evolutionary
timeline. Carbon dating can also be done on the fossil to be confident in the time
at which the fossil specimen was living above ground.