Joshua Everett's Phylogenetic Anaylsis Article

Joshua Everett

AP Biology  

Mr. Hammer

October 24, 2014

Phylogenetic Analysis Article

For this phylogenetic lab, I studied different species of animals that I thought would be similar to one another, not only based on appearance but on the type of gene they all had in common. The question I was addressing in this lab is how are Mus musculus (house mouse), Pan troglodytes (chimpanzees), and Sus scrofa (wild boars) similar to Ambystoma mexicanum (Mexican salamander). To make this comparison, I looked at the msh homeobox 1 gene, also known as MSX1 in each of these species. The MSX1 gene provides instructions to make a protein that regulates the activity of other genes. Specifically, the MSX1 gene controls the normal development of fingernails, toenails, teeth, and other structures of the mouth. I formulated this question based on interesting characteristics of these species like their differences in appearances and their homologous structures. In prior knowledge, I was aware that humans and chimpanzees are very similar to each other not only through their shared structures but also through their DNA sequences. In this lab, however, I wanted to find another species of organisms that were also similar to chimpanzees. Although none of the species I chose to analyze in my lab seem very similar based on their appearance, structures, and ecological locations, that is what makes this lab interesting. This lab will reveal how similar these different species really are to one another based on the MSX1 gene that they all share.

In order to compare the Mexican salamander, the mouse, the chimpanzee, and the wild boar, I decided to compare their nucleotide sequences, or specifically their mRNA sequences. The MSX1 gene is found on the short end of chromosome four at position 16.2. Because this gene is found on a chromosome and is found from base pair 4,859,664 and 4,863,935, it would make more sense to compare these species based on their nucleotide sequences rather than, possibly, protein sequences (http://ghr.nlm.nih.gov/gene/MSX1). Before I performed my experiment I looked up organisms that had the MSX1 gene and I picked the ones that I knew the least information about. I did this because I wanted to be able to discover something new and interesting about these species instead discovering information I already had prior knowledge about. After I found my different species, I found each of their mRNA sequences by using the NCBI database that could be found at http://www.ncbi.nlm.nih.gov/nuccore. In order to align these sequences to view similarities and differences between all these types of organisms and to draw a phylogenetic tree, I used the program ClustalX2. To view the results in a phylogenetic tree, I used the program njplot to view the phylogenetic tree which allowed me to form conclusions and make inferences on the relatedness of these species.

After forming conclusions and making inferences, my results showed that chimpanzees and wild boars are more similar in the way that they develop teeth, fingernails, and toenails from the MSX1 gene. According to my phylogenetic tree, it seems are if chimpanzees and wild boars share a more recent ancestor than the mouse and the Mexican salamander. The Mexican salamander is the outgroup in my tree which means that they are the least similar to the chimpanzee, mouse, and wild boar. The mouse, however, is more similar to the chimpanzee and the wild boar than the Mexican salamander. The reason in which the mouse is not as similar to the chimpanzee and wild boar is because I am able to infer from the phylogenetic tree that they have a less recent common ancestor. The chimpanzee and the wild boar branch off at a more recent point which could mean that they have a more recent common ancestor which makes them more similar. My question is answered from the phylogenetic tree because it shows that the mouse, the chimpanzee, and the wild boar are not closely related to the Mexican salamander. The most closely related species, however,  are the chimpanzee and the wild boar.

Chimpanzees and wild boars, also known as wild pigs, are the two most closely related species based off of the phylogenetic tree. There is a report that was done by John Hewitt that supports that chimpanzees and wild pigs could actually be more related than what individuals might think. Dr. Eugene McCarthy specializes in hybridization in animals and he hypothesized that it would be possible for a male boar (Sus scrofa) and a female chimpanzee (Pan troglodytes) to cross and reproduce and have offspring. McCarthy proposes that” hybridization between pigs and apes produced the earliest hominids millions of years ago and that subsequent mating within this hybrid swarm eventually led to the various hominid types and to modern humans” (http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html). Scientists believe that humans arose from multiple generations of chimpanzee crossings and or reproducing. McCarthy is newly introducing that wild pigs could have contributed to the earliest hominids as well, based on nucleotide sequence data comparisons (http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html). The fact that wild pigs and chimpanzees are able to reproduce and have hybrid offspring, means that both species of organisms would have to be similar in a way in which they had compatible reproductive parts. Another hypothesis that McCarthy proposed was that chimps and wild pigs had separate crosses that led to the production of separate hominids (http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html). If pigs and chimps cross separately and produce hominids, regardless of the differences between them, scientists and other individuals can deduce that wild pigs are similar to chimpanzees because of the similar organisms that can be produced by both of them. This report would support the results from the experiment because it proves that wild boars and chimpanzees are indeed similar as represented by the phylogenetic tree.

An experiment was performed to see if a mouse, a chimpanzee, and a wild boar are closely related to a Mexican salamander. Nucleotide sequences were found using the NCBI database and  data comparisons were done between all the organisms using ClustalX2. A phylogenetic tree was made from njplot  and the results came back revealing that chimpanzees and wild boars are the most closely related and that the Mexican salamander is the outgroup, or least similar out of the four species. The mouse was similar to the chimpanzee and wild boar but a more recent common ancestor was shared between the chimp and the wild boar which made the ultimate difference between the two groups. The conclusion that chimpanzees and wild boars are more closely related and similar is supported by the hypotheses made by Dr. Eugene McCarthy about hybridization in animals. Overall this experiment proved that comparing DNA sequences or other types of sequences can lead to formations of phylogenetic trees which can reveal common ancestry and relatedness among species of organisms.

Phylogenetic Tree:

https://docs.google.com/document/d/1oSbQSqXWk0lBaO993JiMu8Ze6UK7yCOv8fZx4ET0gn8/pub

Work Cited

Hewitt, J. (2013, July 3). A chimp-pig hybrid origin for humans? Retrieved October 24, 2014, from http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html

MSX1 gene. (2014, October 20). Retrieved October 24, 2014, from http://ghr.nlm.nih.gov/gene/MSX1