Phylogenetic Analysis Article

Daphne Gould

Phylogenetic Analysis Article

In this report, I will be examining the relationship between common house pets: canis lupus familiaris (dog), felis catus (cat), gerbillinae (gerbil), gekko gecko (gecko) and cavia porcellus (guinea pig). I decided to do this experiment on house pets because I have both a dog and cats and I formerly had a lizard, gerbil, and gecko. Though they share similarities, these animals clearly have important distinctions from one another. The phylogenetic question that I am interested in investigating through this experiment is how genetic differences in common house pets could potentially explain differences and similarities in phenotypic structure. To start off, I analyzed the cytochrome oxidase subunit I COI gene. I decided to utilize this specific gene because of the fact that it is common to all of the animals which I am testing, and it is fairly indicative of evolutionary history and phylogenetic distinctions.
In this experiment, I analyzed the DNA sequences of the various organisms. I was able to obtain these DNA sequences from the very same website that the packet suggests (www.ncbi.nlm.nih.gov), as I have found that this is a reliable source for genetic information. I also used Clustal X and NJ Plot to carry out my analysis in sorting through DNA sequences and making trees. Once I got over the initial complications with downloading the program, everything was relatively easy to work with. Prior to doing this experiment, I hypothesized that dogs, cats, gerbils, and guinea pigs would all be closely related with the gecko as the outgroup. I presumed that the gecko would be the outgroup because it is the only reptile of the bunch, while gerbils, guinea pigs, cats, and dogs are all mammals. My hypothesis was true, but I did not specifically anticipate the way that it would branch off. Upon further analysis with the phylogenetic tree, it seems as though guinea pigs are also more closely related to gerbils and cats are slightly more closely related to dogs. This makes much sense, as dogs and cats are both larger, and gerbils and guinea pigs are both smaller in comparison. Similarly, gerbils and guinea pigs are also both rodents, which would explain genetic alikeness. It appears as though the time of divergence for the rodent line from the dog and cat like was within approximately half the time since the divergence of the gecko’s lineage. Their structural, phenotypic similarities to one another were quite representative of their genotypic similarities in the end.

According to the Scientific Journal Genome Research, one study produced significant research on the genetic makeup of a cat, comparing to that of several other mammals, such rodents and dogs. This research concluded that one source of similarities within these animals is their susceptibility to similar viruses. This is the reason why animals, such as rodents, are often test subjects for pharmaceutical products.Virus receptors are similar throughout most mammals, including the ones studied in this experiment. If I were to redo this experiment, I would most likely attempt to use a gene used to combat viruses to see if that affects the flow of phylogenetic similarities.

It is true that there is a substantial variation within the level of similarities shown between genes. That being said, I feel as though the COI genes is a good indicator of these genetic similarities.