Caul Pearson
Mohn
AP Biology, Hour 4
22 February 2015

The Relationships of Rodents to Rabbits
Introduction:
Rodents (of the order Rodentia) are the most diverse of all mammals with over 2000 species. They are often seen as invasive pests, but rodents are an interesting order as many live socially and have complex methods of communication. Species of rodents are quite varied with the smallest, the Pygmy Jerboa, weighing under an ounce and the largest being the Capybara which can weigh up to 115 pounds. They are characterized by a pair of incisors on their upper and lower jaws that continuously grow. Hares are often confused as being a type of rodent but they are actually of the order Lagomorpha. Even though they are of a separate order, hares share many of the common characteristics of rodents including whiskers and large buckteeth. The observable similarity between hares and rodents begs the question; how closely related are rabbits to rodents?

Methods:
To discover the closeness of the relationships of the rodents, the research looked at the Cytochrome Oxidase Subunit I (COI) gene. This gene is commonly used to identify animal species because its mutation rate allows scientists to distinguish closely related animals and many other eukaryotes. The mutation rate is too slow in plants to be distinguish species.

The species of rodents that were compared to the rabbit(Oryctolagus cuniculus) were the squirrel(Sciuridae), the rat(Rattus), the capybara(Hydrochoerus hydrochaeris), the mouse(mus), the beaver(Castor) and the chipmunk(Tamias). The bottlenose dolphin(Tursiops) was used as an outgroup.

To gather the COI sequences for the different species the researcher went to the website: http://www.ncbi.nlm.nih.gov/nuccore. To find these COI sequence the researcher used the scientific name of the animal in the search box then typed COI after the name. After the results appeared the FASTA link was clicked on. The text of each FASTA link was copied into a .txt file, leaving a space between each copied animals COI.

The ClustalX software which can be found at http://www.clustal.org/download/current/, was then opened. The .txt file was then opened which loaded the sequences into the software. To make sure the COI genes were matched up the researcher then clicked on the Alignment tab and clicked on Do Complete Alignment. After this was done, the Trees tab was clicked on and Draw Tree was selected which created a filetype of .ph.

After the .ph file was created with ClustalX, NJplot, which can be found here: http://pbil.univ-lion1.fr/software/njplot.html, was used to display the Phylogenetic Tree. To do this the .ph file was opened and the tree was displayed. A screen shot was then taken of the tree which is displayed below.

Results:

As show in the tree the out group which is the dolphin does not share the more recent common ancestor that the rodents share. According to the tree the closest related species to the rabbit is the Capybara. The mouse and rat were the most closely related but they also share a common ancestor with the Chipmunk. The squirrel shares a common ancestor with the Beaver and they share a common ancestor with the rest of the rodents plus the