Rana's Phylogenetic Analysis Article

Rana Srouji

AP Biology

Mr. Hammer

October 23, 2014

Relationships of Organisms

Horses, domestic cats, zebra fish and sheep are all living organisms but are never really classified or thought of together.  Possibly because they tend to live in different habitats.  The zebra fish live in water, domestic cats are raised in homes, sheep are mainly found on farms, and horses are seen in wild grassy plains.  But according to the theory of evolution, they may be related through a common ancestor.  Which brings up the following question.  Of horses, domestic cats, zebra fish, and sheep, which are the most closely related?

In order to analyze this, I researched a gene that all of these organisms had in common.  All of them contained the gene that controls pigmentation.  It is the MC1R gene, or officially known as the alpha melanocyte stimulating hormone receptor, which supplies the instructions to make a protein called the melanocorotin 1 receptor.  This receptor, which is located on cells that produce the pigment melanin, plays a large role in normal pigmentation.  The melanin is what provides skin, hair, and eye color. Though I knew what gene to use as comparison for each organism, I had to find their sequences of the MC1R gene.  To do so, I used the http://www.ncbi.nlm.nih.gov/ website.  Looking under the category of Nucleotide, I put into the search bar the scientific name of each organism along with the shorthand gene name.  The scientific name of the horse is Equus caballus, the name of the zebra fish is Danio rerio, the name of the sheep is Ovis aries, and the name of the cat is Felis catus.  To choose which ones to use for the analysis, I looked for mRNA sequences of less than 1000 bases long, with the scientific name of the animal, and the gene name. After finding all the sequences necessary, I placed them onto a word document and then transferred them onto a text document.  From the text document I could then open the sequences onto the program ClustalX 2.1, which would align the sequences.  The alignment of the sequences allows for examining the differences to show evolutionary relationships among the organisms.  Finally, once they have been aligned, they were made into a tree.  Using the program NJplot, the horses, domestic cats, zebra fish, and sheep were put into a phylogenetic tree showing their relationships using the MC1R gene.

Thus, the results of the phylogenetic tree showed that the most closely related of the 4 organisms, through their MC1R genes, are the domestic cat and horse.  This is because they have the most recent common ancestor.  The zebra fish was used as the Out-group in this lab because it was least related to any of the other organisms. Since the zebra fish lives in water, while the other organisms live all live on land and breathe air, it would have the most distant common ancestor, as proven by the tree.  The phylogenetic tree also represents evolutionary relationships between the organisms.  It does this by connecting them through branches and branch points.  The domestic cat and horse have the closest branching points, then the sheep, and then the zebra fish.  A possible explanation for the fact that the domestic cat and the horse are the most closely related is that many horses are also domesticated.

To further explain this, a small amount of research has been implemented on the topic of how closely related the domestic cats and horses are.  Scientists have found that there are forelimb homologous structures in the domestic cat and horse.  Homologous structures are structures with different functions but all were inherited from the same common ancestor who had that body part.  The forelimbs have different forms and functions but the same bones are present in both organisms (Zimmerman 12).  This provides evidence for what the phylogenetic tree shows.  That the domestic cat and horse have a more recent common ancestor.

Of the Equus caballus, Felis catus, Ovis aries, and Danio rerio, the most closely related are the Equus caballus and the Felis catus. Evolution shows that all living organisms are linked genetically through common ancestors.  Many organisms evolve over time due to different selection pressures such as Natural selection, and even adaptive radiation.  They may become new species but still have diversified from the same original lineage.  Which could have been the cause for the relationship of the organisms that were studied in this experiment.  The phylogenetic tree showed the relationships of the 4 organisms.  The zebra fish least related to the rest of them, then the sheep, and the cat and horse are the most related due to their positions on the tree. 

Citations:
Zimmerman, Elwood C. "Possible Evidence of Rapid Evolution in Hawaiian Moths."Evolution 14.1 (1960): 137. Web. 23 Oct. 2014. <http://www.mhhe.com/biosci/genbio/raven6b/graphics/raven06b/other/raven06b_21.pdf>

Gene Sequences:
http://www.ncbi.nlm.nih.gov/nuccore/167621421?report=fasta
http://www.ncbi.nlm.nih.gov/nuccore/30725833?report=fasta
http://www.ncbi.nlm.nih.gov/nuccore/542133114?report=fasta
http://www.ncbi.nlm.nih.gov/nuccore/57163858?report=fasta

Phylogenetic Tree:
https://drive.google.com/file/d/0B2zcPPV2YgJ0TUxibm5oVEFWM28/view?usp=sharing

Gene information:
http://ghr.nlm.nih.gov/gene/MC1R