This page was produced as an assignment for Genetics 564, an undergraduate capstone course at The University of Wisconsin - Madison.
What is Phylogeny?
Phylogeny is the evolutionary history of a species or a group of related species [1]. It is a way of systematically organizing organisms by their most recent common ancestors with the use of fossil, molecular, and genetic data. These relationships are shown in the branches of phylogenetic trees (Fig. 1)
We can use our knowledge of phylogeny to identify similarities in Amyloid Precursor Protein between different organisms. To accomplish this we begin by compiling a word document of the amino acid sequences for all homologues containing the gene for Amyloid Precursor Protein (APP). Then we perform a sequential alignment using the online program Clustal Omega. The same program is used to generate phylogenetic trees. For further instructions on how to make a Phylogenetic Tree visit Anna Lisa Doebly's website.
APP4 Protein Sequences and Alignments
Figure 3. The above FASTA sequences were compiled using the NCBI database.
Figure 4. The program Clustal Omega was used to generate this sequence alignment. Based on the alignment analysis of the amino acid sequence for APP across 12 model organisms, APP appears to be well conserved.
APP4 Phylogenetic Tree
Discussion
Previously on the Homology page we compared the percent identity of APP across various organisms. By analyzing the protein sequences we are able to further characterize the similarities between organisms that have the APP gene. By observing the phylogenetic trees generated from this analysis we can conclude that all model organisms except Drosophila and C. elegans have very similar protein structure.
References
Images
Figure 1. https://en.wikipedia.org/wiki/Phylogenetic_tree
Figure 2. https://learning.hccs.edu/faculty/toyin.babarinde/biol1407/lecture-presentation/chapter-26
[1] Reece, J. et al., 2011. Lecture Presentations for Campbell Biology, Ninth Edition. Accessed by https://learning.hccs.edu/faculty/toyin.babarinde/biol1407/lecture-presentation/chapter-26
Figure 1. https://en.wikipedia.org/wiki/Phylogenetic_tree
Figure 2. https://learning.hccs.edu/faculty/toyin.babarinde/biol1407/lecture-presentation/chapter-26
[1] Reece, J. et al., 2011. Lecture Presentations for Campbell Biology, Ninth Edition. Accessed by https://learning.hccs.edu/faculty/toyin.babarinde/biol1407/lecture-presentation/chapter-26