Nida's Phylogenetic Analysis

Nida Ali

Mr. Hammer

AP  Biology

October 24, 2014

Phylogenetic Analysis

      Are humans more closely related to mice, chickens or black spotted frogs in terms of their genetic makeup? Within this analysis, the TYR gene is analyzed among the protein sequences. This gene provides specific instructions on how to construct the enzyme tyrosinase, which is located in specialized cells called melanocytes that are responsible for producing the pigment melanin. This pigment is the substance that provides the color for skin, hair and eyes. In order to distinguish a similarity among the several different species of homo sapiens (humans), mus (mice), Gallus gallus domesticus (chickens) and black spotted frogs, The TYR gene was selected as the basis of analysis to determine the degree of relatedness among the organisms homo sapiens (humans), mus (mice), gallus glasus domesticus (chickens), and the pelophylax nigromaculatus (black spotted frogs).

      Because humans, mice, chickens, and black spotted frogs all had DNA containing the TYR gene, I chose to compare the sequences from these particular species. I decided to compare humans to mice because 95% of mice’s genome is similar to humans, displaying an abundant amount of similarities. In addition, mice have a similar order in chromosomes as humans. Considering the fact that mice have similar digestive systems, metabolism, circulation and immune defenses, determining whether or not mice would display similar production of melanin pigment due to the TYR gene was a relevant consideration (Office of Science Education- Mice and Humans Are Biologically Similar). Furthermore, humans and chickens contain a number of similarities in their genes as well. More than half of chicken genes are similar to those of humans. On average, 75% of corresponding pairs are present among humans and chickens (Researchers Compare Chicken, Human Genomes). Based on this fact, I wanted to determine whether or not the TYR gene was within that 75% similarity.

      Considering the fact that humans and frogs share a similar body plan, such as their skeletons, organ systems and their location, size and purpose, concluding whether or not these two species contain a similar gene is worth analyzing (The Frog Skeletons vs. Human Skeletons).

To start, I began my research by determining the animals that I wanted to compare and find similarities among. Then I found the TYR gene to base my results off of. I decided to go with this gene mainly because it is an essential to producing pigment in our hair, eyes and skin. After I figured out what gene I wanted to base my analysis on, I began to research whether or not this gene was present in the animals I originally chose for this analysis. At first, I decided to switch which animals I wanted to compare, but finally I decided to determine which species are most similar to each other among the ones I chose including homo sapiens (humans), mus (mice), Gallus gallus domesticus (chickens) or the pelophylax nigromaculatus (black spotted frogs).  Next, after choosing and analyzing for protein sequences, I began to use the software, ClustalX, in order to align and compare DNA sequences. This program was downloaded onto my computer in order to compare the sequences of humans, mice, chickens and black spotted frogs. After finishing the complete alignment, I chose the “draw tree” feature in order to construct a cladogram.

One common ancestor among these species is presented in the cladogram above. The cladogram above reads, in order from top to bottom, as mouse, human, chicken, and black spotted frog. In comparison to the TYR gene, humans and mice are equally related. Since mice and humans have over 95% of genetic similarities, they are listed closely together, which suggests that they are closely related through the TYR gene. Chicken, mice and humans are much more closely related to each other than to the black spotted frog. There are more similarities than differences among the mice, human and chicken. The black spotted frog is represented as an outgroup due lack of many similarities it has with the other three monophyletic groups of organisms. This cladogram matches evidence showing the relationship and similarity among humans, mice, chickens and black spotted frogs.  

The results of my findings corroborated Winstead’s conclusions from his research. More similarities rather than differences are seen among humans and mice. Over 700 mouse genes are grouped in the same order as in humans. Researchers at Celera Genomics in Rockville, Maryland recognized the vast implications of using the mouse as a model organism for researching human health and disease, commenting that “even researchers who are not mouse geneticists will find tremendous value from examining the sequence” (Winstead).

Researchers compared chickens genomes to those of humans and came to the same conclusion as I discovered: that these two species share more than half of their genes. Humans and chickens roughly the same number of genes, but the chicken genome is slightly smaller than those of humans. A slight discrepancy was seen within this source. The source stated that humans and chickens contain 60% similarity in terms of genes, whereas 75% of similarity was stated from another article, from which I based my research. The alignment of chicken and human genes were off of 2,000 chicken genes, adding onto the slight 25-40% difference seen between these two species (Spencer).

To add, Rochester's ‘Jumping Frog Lab’ results were comparable to the results I concluded within my analysis.  Emphasized Rochester's results, he stated how humans and frogs share several features in the earliest stages of their development, such as the development of the nervous, skeletal, and immune systems, which is similar in both humans and frogs. What I found out within his research was that similarities between these two species also derive among genes related to proteins, such as the MHC (major histocompatibility complex) protein. This protein allows for organisms to detect and control cancerous cells (The Frog Skeletons vs. Human Skeletons) .

To conclude, homo sapiens and mus were the most closely related species. The level of similarity among these two species were seen mainly through their DNA sequences. The TYR gene added onto the 95% similarity. Within my results, the tyrosinase enzyme in humans and mice provides similar construction and production of providing pigment in hair, eyes and skin. More similarities than differences were seen among chickens and humans. Roughly 70% of similarities were mainly seen within the DNA sequences. The slight differences were in result to the added 2,000 human genes in the sequence. Lastly, humans and black spotted frogs contain minimum similarities among their genetic makeup while comparing the TYR gene. Only specific organs and its location, size and purpose, among these two species addressed the similarity. In essence, my research concluded that homo sapiens and mus were most similar to each other than among the other animals in this study.

Works Cited

"The Frog Skeletons vs. Human Skeletons" HowStuffWorks. N.p., n.d. Web. 24 Oct. 2014.

"Office of Science Education- Mice and Humans Are Biologically Similar." Office of Science Education - Animals In Research - Amazing Facts - Mice and Humans Are Biologically Similar. N.p., n.d. Web. 24 Oct. 2014.

"Researchers Compare Chicken, Human Genomes: Analysis Of First Avian Genome Uncovers Differences Between Birds And Mammals." ScienceDaily. ScienceDaily, n.d. Web. 24 Oct. 2014.

Rochester. "Genome Sequence Marks Big Leap Forward for Frog Researchers." - News Room. N.p., n.d. Web. 23 Oct. 2014.

Spencer. "2004 Release: Researchers Compare Chicken, Human Genomes." 2004 Release: Researchers Compare Chicken, Human Genomes. N.p., n.d. Web. 23 Oct. 2014.

Winstead. "Humans and Mice Together at Last." Humans and Mice Together at Last. N.p., 31 May 2002. Web. 23 Oct. 2014.