Statement of the Problem:

Using BLAST information sources, where specifically is the unknown fossil specimen located on the cladogram?


According to our morphological observations, we believe that this fossil should be located close to the crocodilians and birds. By looking at the unknown fossil specimen, we believe that this fossil possessed long tail, actual backbone structure, and wing-like structures. However, since it seemed to have more-reptile like traits ( long tail, and body structure) we decided that the fossil is most closely related to the crocodilians than is to the bird.

Background Context:

Scientists have discovered an unknown fossil in China. Very little is actually known about the fossil; the only given information is that it contains soft tissue and DNA nucleotides. Thus, the main investigative objective of this lab is to find out where the organism fits on the cladogram, after analyzing 4 given genes through BLAST software. A Cladogram is a type of branching diagram that’s very useful to show cladistic relationships between a number of species. Common ancestry is used to determine how closely organisms are related. The more closer two organisms are on the cladogram, the more features they share. Analyzing all 4 genes, and determining which animals they’re located in can guide us through where this unknown fossil actually belongs.


Four main gene sequences found in the fossil are to be given to the student so that they can analyzed completely using BLAST software. These genes other animal's traits and proteins incorporated in the gene that will help deduce the characteristcs of the unknown organism. We must then identify the closest relatives of the fossil specimen gene sequences. The first gene was present in the Gallus gallus (chicken) is comprised of gene called Collagen type V Alpha-1. This collagen is significant because it's part of the fibrillar collagen family. The crocodile organism also has the same exact gene. This could mean that the unknown species shares a relation with the crocodiles and the birds. However, the most closest gene was indeed the Zebra finch gene and it's also alone with the unknown gene on one strand of the cladogram. The organization of the two genes display show that the unknown is most likely closest to the Zebra finch. The last gene is that of a fruit fly shared its gene with a wide variety of animals showing that it doesn't have the correct place for the unknown on the cladogram.

Using the information from the the cladogram, the student must then make a logical educated guess about which gene best describes the fossil. Using this knowledge, the four genes were listed in order from most important to least important:

Zebra Finch, Gallus Gallus, Crocodile, Fruit Fly.

Methodology and Experimental Design:

1. First, create an initial hypothesis, that indicates where you believe the fossil specimen is on the cladogram based on the observations of the rock containing in which the fossil is enclosed in.

2. Then, go to a BLAST link and download all four gene files.

3. Next, go to the BLAST home page and click on “Saved Strategies” at the left hand corner of the page.
4. Click on “Browse” and then select of one your downloaded gene files. After doing this, click view.

5. A screen will later show up, in which you can see that the gene sequence has already been selected. Scroll to the bottom, and then click BLAST.

6. A page with two major sections will appear next. The first section will include a display of the matching sequences. Other section is titled “Sequences producing significant alignments” .

7. Click on the first link, as generally what’s on the top is most similar and similarity decreases as you go down the list of sequences.

8. You will get a very detailed report which includes the species’ classification history, and the sequences that align with this gene.

9. You can also click on the “Distance Tree of Results” at the top of this page, to see a cladogram with species with similar sequences to your gene, and also understand how closely their matched genes align with your research gene.

Analyzing Results

Gene Sequence 1:

Unknown Organism Close to Birds

Gene 2:

Organism: Drosphila melanogaster ( fruit fly)


Nearest Relative: Fruit Fly

Location of Relative on Branch: On same branch of flies

Gene 3:

Unknown specimen is close to birds again.

Gene 4:

Organism: Mitochondrian Alligator sinensis ( Chinese alligator)

Protein produced by the sequence : NADH dehydrogenase subunit 6

Unknown close to alligator, crocodiles. etc..


This cladogram above represents the information presented in our hypothesis statement, that the fossil is most likely to be related closest to crocodilians than any other organisms.
After going through this lab, we concluded that the fossil is most likely to be most closely related to birds than the other organisms.

Conclusions and Interpretation of Results

Our final conclusion for the fossil was that it was most related to the birds/ the zebra finch. This is mainly due to the reason that the unknown gene sequence was shown to be emerged from birds common line of descent. If you look at the cladogram for the zebra finch, it shows how the unknown branched off from the bird species. Also, the gene sequence coded for a protein, which wasn't very present in a large variety of animals, thus making it the most important gene sequence. It was also found that there was a connection between the alligator and the gallus gallus because they both contained the collagen V, which was part of the fibrillar collagen family. Gallus gallus gave us an impression of the animal through Collagen V. Although the unknown animal had the same genes as the crocodile it was indeed still most likely a bird. The unknown species would go right before feathers on the birds branch of the cladogram, because this was not proven in the study. Our initial hypothesis was actually not very far from our result obtained after going through the experiment