Chigozie Amonu
Mr. Hammer
AP Biology
24 October 2014
Phylogeny Analysis: Humans, Chimpanzees, and Zebrafish
For this phylogeny analysis, I studied one question: How closely related are humans (Homo sapiens), chimpanzees (Pan troglodytes), and zebrafish (Danio rerio)? To answer this question, I searched for a gene that I could use to compare all of these organisms. The gene I chose to execute this comparison was the ALX homeobox 1 gene, or the ALX1 gene. The ALX1 gene provides instructions for making a protein that is a member of the homeobox protein family. The ALX1 protein is necessary for normal development of the head and face, and particularly the formation of the eyes, nose, and mouth. The ALX1 protein is a transcription factor, which means that it attaches to DNA and controls the activity of certain genes. This protein controls the activity of genes that regulate cell growth and division (proliferation) and movement (migration), ensuring that cells grow and stop growing at specific times and that they are positioned correctly during development (ALX1 Gene). After gathering this information, I hypothesized that humans and chimpanzees would be more closely related when I used the ALX1 gene for comparison because humans and chimpanzees share more similar facial structures than zebrafish and humans or chimpanzees.
I gathered the nucleotide sequences from the NCBI website by searching the genus species of humans, chimpanzees, and zebrafish. After I obtained the nucleotide sequences, I aligned them using the ClustalX program. I created a phylogenetic tree with the data that I gathered from the ClustalX program. From this phylogenetic tree I observed how closely related humans (Homo sapiens) and chimpanzees (Pan troglodytes) were compared to zebrafish (Danio rerio). The phylogenetic tree showed that all these organisms shared a common ancestor. This observation concurs with the fact that these three organisms all have the ALX1 gene. The phylogenetic tree also showed that the zebrafish diverged from the common ancestor earlier than humans and chimpanzees. This shows that humans and chimpanzees are more closely related to each other than to zebrafish. This conclusion falls in line with research done by biologists at Wayne State University School of Medicine in Detroit, Michigan. These biologists used computer methods to analyze the amount of similarity between 97 important human and chimp genes and as many of the same gene sequences as are currently available for less-studied gorillas, orangutans, and Old World monkeys. The results suggested that within important sequence stretches of these functionally significant genes, humans and chimps share 99.4 percent identity (Pickrell). Humans and chimpanzees are almost 100 percent identical when comparing major genes, and this finding coincides with the phylogenetic tree that I created.
The biologists at Wayne State University School of Medicine in Detroit, Michigan are also arguing with new genetic evidence that lineages of chimps (Pan troglodytes) and humans (Homo sapiens) diverged so recently that chimps should be reclassed as Homo troglodytes. If this suggestion was actually implemented, chimps would be full members of our genus Homo, along with Neandertals, and all other human-like fossil species. "We humans appear as only slightly remodeled chimpanzee-like apes," says the study (Pickrell). The recent divergence of humans and chimpanzees would also explain the similarity between the ALX1 gene sequence of these organisms. All in all, my hypothesis was correct. Humans (Homo sapiens) and chimpanzees (Pan troglodytes) are more closely related than zebrafish (Danio rerio) to humans or chimpanzees.
Tree
Works Cited
"ALX1 Gene." Genetics Home Reference. N.p., Apr. 2014. Web. 22 Oct. 2014.
Pickrell, John. "Chimps Belong on Human Branch of Family Tree, Study Says." National
Geographic. National Geographic Society, 20 May 2003. Web. 23 Oct. 2014.
"Supplemental Content." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 22 Oct. 2014. <http://www.ncbi.nlm.nih.gov/nuccore/154813200?report=fasta>. (Homo sapiens ALX1)
"Supplemental Content." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 22 Oct. 2014. <http://www.ncbi.nlm.nih.gov/nuccore/113682306?report=fasta>. (Danio rerio ALX1)
"Using Nucleotide." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 22 Oct. 2014. <http://www.ncbi.nlm.nih.gov/nuccore>. (Pan troglodytes ALX1)
Why did you chose the human and chimpanzee? And how did you come up with using the Zebrafish as an outlying animal?
ReplyDeleteFrom prior knowledge, I knew that humans and chimpanzees were closely related. After I looked up a gene that humans and chimpanzees had in common (the ALX1 gene), I picked a random animal that also had that same gene, which turned out to be the Zebrafish. I wanted to see if there was another animal that could possibly be more closely related to the human than the chimpanzee when comparing the ALX1 gene. After I compared the DNA sequences of each animal, I concluded that the Zebrafish would be the outlying animal. However, before the comparison of the DNA sequences, I was pretty sure that the Zebrafish would be the outlying animal since chimpanzees and humans are closely related.
DeleteI really enjoyed reading your article. It was very informative and I appreciate how you have two outside sources to solidify your results of your phylogenetic tree. A question I would have would be, what other species could you have chose, instead of humans, to chose to do your analysis on? It would have been even more interesting to see a comparison done with all animals rather than with a human.
ReplyDeleteThank you! Originally, I actually wanted to compare mice, humans, and zebrafish. However, I never found the ALX1 gene sequence for mice, so I substituted mice with chimpanzees. I think it would be interesting to compare chimpanzees, mice, and zebrafish, though.
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