Introduction: In this lab, I will be addressing the question ‘How can bioinformatics be used as a

tool to determine evolutionary relationships and to better understand genetic diseases?

Background Context: The previous lessons covered the concept of evolution, which refers to
alterations in the genetic makeup of a population over time. Evolution suggests that species
have originated from a shared ancestor, and phylogeny is the field that explores the
evolutionary history of life. Cladograms are diagrams employed in phylogeny that group multiple
species together using clades, which consist of an organism and all of its descendants, based
on shared physical characteristics. These diagrams can be useful in placing unknown
organisms by making hypotheses about their positions based on visual comparisons.
Bioinformatics, particularly the Basic Local Alignment Search Tool (BLAST), can support these
hypotheses by comparing the genetic makeup of the unknown organism to known species.

Hypothesis: The fossil will fall between crocodillians an great apes with a high chance of it being
a vertebrate.

Analyzing Results:

Gene 1:
1. Gallup gallus collagen (chicken) has the most similar gene sequence
2. The species is located within the bird clade on the cladogram.
3. The gene sequence is 100% similar.
4. The Anas platyrhynchos collagen (domestic duck) has the next most similar gene
sequence to the gene of interest.

Gene 2:
1. Drosophila melanogaster shaker (fruit fly) has the most similar gene sequence
2. The species is located within the insect clade on the cladogram.
3. The gene sequence is 92% similar.
4. The drosophila melanogaster (fruit fly) has the next most similar gene sequence to the
gene of interest.

Gene 3:
1. Taehlopygia guttata (zebra finch) has the most similar gene sequence
2. The species is located within the bird clade on the caldogram.
3. The gene sequence is 99% similar.
4. The geospiza fortis (medium ground finch) has the next most similar gene sequence to
the gene of interest.

Gene 4:
1. Alligator sinensis (Chinese Aligator) has the most similar gene sequence
2. The species is located within the crocodilians clade on the caldogram.
3. The gene sequence is 100% similar
Conclusion: These results support that my hypothesis was correct because the species seems
most related to a chicken since it had the highest max score which means its genes were the
most similar to the unknown species. Despite this the species also had 100% similar genes with
lower max scores with the zebra finch (another bird) and the Chinese Alligator. This shows that
there is some common ancestry with both birds and crocodilians which prevents the species
from being completely in either the crocodilian section or the bird section. Therefore, the species
has to be below both of those sections but still in the same clade as those two due to the strong
similarity. Additionally, in this case the fruit fly similarity gene has nothing to do with the
placement of the unknown species into the cladogram. This is because the organism is already
proven to be vertebrae and only has similarity in that gene because it is common in all
heterotrophs. One way that would improve this experiment would be to give all the genes equal
parameters because I noticed that the only gene that had the parameter of optimizing for highly
similar sequences was the first one which I thought was not an equal judgment of all four genes.