A1AT+Discussion

The two trees showed similar groupings; the six (6) species at the top were the same for both trees (pan tronglodytes, pan paniscus, human, gorilla gorilla gorilla, and pongo abelii, and nomascus leucogenys, and the chlorocebus sabaeus was clearly separate from the main grouping of species. The last few species are dissimilar between the two (2) trees, because BLAST results were not ideal to allow for the exact same species to be utilized in the alignment. However, although the groupings are very similar, the phylogenic values are noticeably different. In the nucleotide tree, the pongo abelii and nomascus leucogeny had extremely low values of 41% and 53%, respectively, which is weak evidence for species similarity; however in the protein tree, only the human protein (62%) had a low value. One interesting note, the canis lupus in the nucleotide tree, which was originally chosen as the species out-group for the BLAST sequencing, was more similar, and even part of the in-group (seven similar species), than some of the other species expected to be similar. In the protein tree, the microcebus murinus was the out-group as expected from the BLAST sequencing. All species utilized in the phylogenic tree were compared to the tree of life database. Humans, gorilla species, pan species, and pongo species are in the family Hominidae and would be expected to show the greatest similarity, which was demonstrated in both phylogenic trees. The macaca species, cerocebus species, and chlorocebus species are in the family cercopithecidae and would be expected to show similarity to each other; however, they would be separate from the Hominidae family. Just like the Hominidae grouping, these species, formed their own groups in both the nucleotide tree and protein tree. The nomascus species is part of the family hylobatidae, separate from Hominidae and cercopithecidae. This was not apparent in the nucleotide and protein trees; the nomascus leucogenys was clearly grouped with the Hominidae grouping. However, while these species are in three (3) different families, they all belong to the same suborder of catarrhine, which may account for the similarity displayed in the trees. The microcebus species, part of the family cheirogaleidae, suborder strepsirrhine is separate from all the above and should demonstrate this same pattern on the phylogenic trees, which is apparent on the protein tree. The most interesting note is that the canis lupus, which is part of the family carnivora, and the order carnivora should be the most dissimilar from all the groupings, and yet, in the nucleotide tree, it actually forms a group with the Hominidae family.

Ultimately, the data provided results as expected. Both trees were similar to each other, both 3D structures were similar to each other, and the gene and protein tree showed results that would be expected based on relationships between the different species or families. Very few outliers were observed, but when observed, another connection could be made at the suborder or order level.

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