This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
Genetic Phylogeny
Phylogeny refers to the relationships between species. These relationships are then used to create phylogenetic trees, which show the genetic connections and relationships between species through branches. In the past, these trees were based off of the similarity seen between physical features, such as size, color, and number of limbs. Due to the advancement of modern technology, trees are now created based on the similarity between genetic and protein sequences between species. Thus, this technique relies greatly on the study of homology as well [1]. These trees show the evolutionary history of life as the species diverge from a universal common ancestor.
|
A Few Phylogenic Trees of TOP3B
The two trees below were made through an online program called Clustal Omega. The FASTA sequences for the mRNA of each organism were entered all at once (the DNA FASTA sequences were not all available). Once these sequences are entered and aligned, there are numerous ways to construct a phylogenentic tree. The trees pictured here were created using the BLOSUM62 method. BLOSUM (BLock SUbstitution Matrix) 62 is based on a likelihood method, meaning that it looks for patterns of sequence similarity and then estimates the occurrence of each amino acid at each position. Amino acids that are more likely to be found in that position are given a higher likelihood score. These positional scores are added together for each sequence to create the tree [5]. The 62 part of BLOSUM62 means that all of the sequence patterns compared shared at least 62% amino acid identity [5]. Average Distance and Neighbor Joining are two slightly different distance based methods of tree construction. Here, distance refers to the degree of difference between sequences [3]. The Average Distance method compares the homologous sequences in a pair-wise manner and creates a rooted tree, meaning that all the organisms branch from a common ancestor, or a root. The Neighbor Joining method compares homologous sequences as well, but instead creates an unrooted tree, meaning the organisms do not branch out from a common ancestor [4,3]. This method creates the shortest branch length possible [2]. The 'Protein Phylogeny' page also mentions the Percent Identity method. However the PID method failed to create trees with the mRNA sequences. Thus, only BLOSUM62 was used.
Analysis
The first and second trees are identical, which makes sense as they both use the Neighbor Joining method. However, I think that the third tree makes the most logical sense. In the first and second, the section of branches from chimp and human to zebra fish has both an order and grouping that is to be expected. The order goes from most complex organism to the simplest in the section, that being zebrafish. Next, the two plant species (plant means Arabidopsis thaliana) are grouped together, which is also to be expected. The two interesting and unexpected parts are the random side branches for the fly and worm. Based on their cellularity and organ systems, I expected these to grouped into the section with the other animals. This is why I think the third tree is more logical, as all the animals are grouped together. Furthermore, it meets the same logical standards of order as the first two.
References
[example tree] http://www.ib.bioninja.com.au/options/option-d-evolution-2/d5-phylogeny-and-systematic.html
[1] What is phylogenetics? Created Jan. 2001. Retrieved Feb. 2014. http://www.cs.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec08/node2.html
[2] Calculations of trees from alignment. Retrieved Feb. 2014. http://www.jalview.org/help/html/calculations/tree.html
[3] Chuang Peng. Distance based methods in phylogenetic tree construction. Morehouse College Department of Math. Retrieved Feb. 2014. http://biochem218.stanford.edu/Projects%202007/Peng1.pdf
[4] Irit Orr. Introduction to Phylogenetic Analysis. Retrieved Feb 2014. http://bip.weizmann.ac.il/education/course/introbioinfo/03/lect12/phylogenetics.pdf
[5] Chuck Staben. BLOSUM 62 Substitution Matrix. Created Sept. 1998. Retrieved Feb. 2014. http://www.uky.edu/Classes/BIO/520/BIO520WWW/blosum62.htm
[1] What is phylogenetics? Created Jan. 2001. Retrieved Feb. 2014. http://www.cs.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec08/node2.html
[2] Calculations of trees from alignment. Retrieved Feb. 2014. http://www.jalview.org/help/html/calculations/tree.html
[3] Chuang Peng. Distance based methods in phylogenetic tree construction. Morehouse College Department of Math. Retrieved Feb. 2014. http://biochem218.stanford.edu/Projects%202007/Peng1.pdf
[4] Irit Orr. Introduction to Phylogenetic Analysis. Retrieved Feb 2014. http://bip.weizmann.ac.il/education/course/introbioinfo/03/lect12/phylogenetics.pdf
[5] Chuck Staben. BLOSUM 62 Substitution Matrix. Created Sept. 1998. Retrieved Feb. 2014. http://www.uky.edu/Classes/BIO/520/BIO520WWW/blosum62.htm