What is Protein 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. Protein phylogeny involves comparing protein sequences between groups to infer the relatedness of the protein 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 Protein Phylogeny
Human ACNT3 protein was compared to seven different species - Arabidopsis, C. elegans, Fruit Flies, Chickens, Horses, Mice and Zebrafish- in order to obtain the phylogenetic trees below. Data was obtained through ClustalW2 and Phylogeny.fr which uses the MUSCLE program to perform analysis.
Analysis and Discussion
These two trees very quite a bit in the placement of the different species. Both trees seemed to agree that the mammals (horses, humans, and mice) formed one clade, however Tree 1 placed mice and horses on one node while Tree 2 placed humans and mice on the same node. Tree 2 seems more accurate since it grouped the vertebrates together and separate from the Arabidopsis (which is a plant). However it seems unusual that chickens, fruit flies, and nematodes form a clade that is completely different than zebrafish. Tree 1 suggests that zebrafish and chickens form their own branches, which seems reasonable, but it seems unlikely that the mammals share a node with invertebrates and Arabidopsis but not the other vertebrates.
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>.