Rameia's Phylogeny Article

Phylogenetic Article

My question for my investigation is how are leopards(Panthera pardus) and tigers (panthera tigris) related to wild deer mice(Mus musculus)? My hypothesis is that the leopard and tiger are more closely related to each other than to the wild deer mouse, and that the wild deer mouse would be the outgroup organism.  This question was interesting to me at first because I was curious about how the leopard and tiger obtained their color patterns. Further down in my research it also interested me that the same gene that determines color patterns in the leopard and tiger is the same gene that colors a wild deer mouse, which is the Agouti gene.  Overall I was curious as to what genes and mutations in the genes were responsible for the colors and patterns of these organisms.

To figure out which genes are responsible for the color pattern of each organism, I initially used google to search for the names of the genes.  After discovering the gene name, I procceded to use www.ghr.nlm.gov to understand the specifics of the gene and how it works in organisms.  By doing this I also discovered that I would be using only protein sequences in order to compare the organisms I had chosen.  Knowing this I used www.ncbi.nlm.gov to find the protein sequences I would need in order to compare and create a phylogentic tree for all of the organisms.  By using the program Clusterx, I copy and pasted the sequences into a plain text file in order to align them.  After aligning the sequences, I was able to use Njplot to create a phylogenetic tree which compares the relationships off all the organisms I had chosen.

As you can see in the phylogenetic tree, it has came to the conclusion that the leopard and the wild deer mouse seem to have the most similarities with each other.  As seen in the phylogenetic tree the leopard and the mouse branched off of the tiger.  This means that the leopard and the mouse share the most recent common ancestor between all three organisms.  I believe my question of how the leopard and tiger are related to the wild deer mouse was answered, but I do not believe that my findings and the phylogenetic tree are an accurate representation of the evolutionary relationship between all three organisms. The tree shows that the tiger is the outgroup organism.  The leopard and tiger should be more closely related to each other than to the wild deer mouse.  I am basing this off of the fact the the leopard and tiger both share the same genus.  But, by using the Agouti gene which codes for the color pattern in all three organisms, it is possible that the protein sequence of the leopard and the wild deer mouse are more similar to each other in that sense.  

According to an article on www.dailymail.co.uk, scientists had discovered that the Agouti gene is responsible for the color pattern on the deer mice.  In the mice, the  Agouti gene is very active on the rodent's stomach where it causes a delay of the maturation of cells that produce pigment.  Scientists believe that this gene is also responsible for the color patterns of other vertebrates, such as the spots on a leopard, and the stripes on tigers and zebras.  Another article on www.blogspot.com states that the Agouti gene is found in variety of organisms that determines whether or not they have patterned fur.  The gene causes a range of pigmentation, for example the darkening of patches and fur, as well as giving a tiger its stripes.  Based on these articles, the phylogenetic tree that was made is an accurate representation of the relationship based on the Agouti gene of these three organisms.  But, if this is the case then all three organisms should come off of the same branch point and share the same recent common ancestor.  Again, the phylogenetic tree seems inaccurate in this sense.  

Improvements that could have been made to ensure the accuracy of the evolutionary relationships shown in the phylogenetic tree could have been to use longer protein sequences.  Using longer protein sequences could have been a make or break factor in the evolutionary relationships.  Even though all of the protein sequences were not the same length, using longer sequences as well as sequences with similar number of proteins could have provided more balance between the organisms.  Another improvement that could have been made is the addition of other organisms who also possess the Agouti gene.  This also could have gave the phylogenetic tree some balance, possibly creating a variety of outcomes.  

Works Cited

• The Blue Tiger Sightings - Unsolved Mysteries In The World. (n.d.). Retrieved October 24, 2014.
• Fiona Macrae for the Daily Mail. (n.d.). How the leopard REALLY got his spots: Scientists identify gene that determines patterns of colour on mice. Retrieved October 24, 2014.