What is DNA phylogeny
Phylogeny is the study of the relatedness of groups of organisms through molecular sequencing and physical characteristics (1). These groups of organisms can be different populations of the same species or different species. Gene phylogeny involves comparing DNA sequences between groups to infer the relatedness of the gene in question. This information can then be used to construct a phylogenetic tree (Figure 1).
Figure 1. The root of a phylogenetic tree is the common ancestor from which all the other species were derived. Each branch defines the relatedness between taxa (species) while the branch length represents the number of changes that occurred in that branch. Branches can be further divided by nodes (which can be either extinct or still alive) in to taxa. When two or more taxa share a common ancestor it is referred to as a clade.
ACTN3 Gene Phylogeny
Human ACNT3 protein was compared to five different species - Fruit Flies, Chickens, Horses, Mice and Zebrafish- in order to obtain the phylogenetic trees below (Figure 2). Data was obtained through ClustalW2. I was unable to add more model organism such as nematodes or plants because there weren't sequences in the database.
I was only able to create a tree through ClustalW2 since the DNA sequences were very long and other programs I tried couldn't align them. Throughout the class I have come to realize that ClustalW2 is not my favorite sequence alignment and phylogeny creating tool for the ACTN3 gene/protein so it didn't surprise me that my tree was different than I had expected. I think that it's strange the the Fruit Fly gene is more similarly related to the Zebrafish and the mouse than the chicken is. I also think it's odd that the mammals aren't on the same branch, especially since my DNA homology (as seen here) shows that the mouse and the human gene are the most identical and the horse and fruit fly are the least identical. Overall I am not confident in this tree and I think it could have benefitted from more model organism DNA sequences (which I was unable to find).
1. "Learning with the ToL." Tree of Life: What Is Phylogeny. Tree of Life Project, 2004. Web. 17 Feb. 2013. <http://tolweb.org/tree/learn/concepts/whatisphylogeny.html>.