What is Phylogeny?
Figure 1. A example of a phylogenetic tree
Phylogeny is a method to describe the evolutionary history of a species or population [1]. It is graphically represented by branched trees, a common evolutionary ancestor stemming to divergent organisms (see Fig. 1). The length of each branch indicates the number of genetic or phenotypic changes that have occurred in that branch. More can be read about the study of phylogeny here.
On this page, evolutionary history is predicted by similarity in protein sequence of Glo1 in several species. Proteins were identified as homologs to the human glyoxalase 1 protein (see protein homology page) and aligned in Clustal Omega. This program examines similarities in sequences and generates a phylogenetic tree [2].
On this page, evolutionary history is predicted by similarity in protein sequence of Glo1 in several species. Proteins were identified as homologs to the human glyoxalase 1 protein (see protein homology page) and aligned in Clustal Omega. This program examines similarities in sequences and generates a phylogenetic tree [2].
Clustal Omega Results for glyoxalase 1
Two different methods were employed for examining relatedness of glyoxalase 1 among different species: percent identity and neighbor joining. Percent identity refers to a quantitative measurement of the similarity between two sequences. Closely related species are expected to have a higher percent identity for a given sequence than would more distantly related species [3]. Neighbor joining focuses solely on common ancestors without the quantitative prediction of similarity, enabling trees to be built despite different rates of evolution between lineages [4].
Analysis and Discussion
Percent identity in homologs of human glyoxalase 1 (Figure 2) follow an expected tree of evolutionary divergence. The more closely related the species, the more closely related their glyoxalase protein in sequence, and predictably structure and function. Both trees built from Clustal Omega show yeast, arabidopsis, and drosophila as the most distantly related organisms from humans. This is reasonable considering yeast is classified in kingdom fungi, arabidopsis in plantae, and drosophila in the arthropoda phylum. Figure 3 represents this clearly as the three species are their own outgroup.
Both figures show the rodents (mouse and rat) fall into their own clade as expected. Other mammals branch off the common ancestor of the rodents, and a previous common ancestor links to the order of primates. This node encompasses the marmoset, orangutan, chimp, and human. Glyoxalase 1 in chimps is the most closely related to human glyoxalase 1, consistent with findings in homology (see homology page).
Both figures show the rodents (mouse and rat) fall into their own clade as expected. Other mammals branch off the common ancestor of the rodents, and a previous common ancestor links to the order of primates. This node encompasses the marmoset, orangutan, chimp, and human. Glyoxalase 1 in chimps is the most closely related to human glyoxalase 1, consistent with findings in homology (see homology page).
References
[1] "Learning with the ToL." Tree of Life: What Is Phylogeny. Tree of Life Project, 2004. Retrieved Feb. 19, 2013 from http://tolweb.org/tree/learn/concepts/whatisphylogeny.html
[2] Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75
[3] "Percent Identity of Genomic DNA Sequences, of Introns and Exons, and of Amino Acid Sequences." N.p., n.d. Web. 21 Feb. 2013.
[4] "Neighbor-joining Method." Neighbor-joining Method. N.p., n.d. Retrieved February 21, 2013 from http://www.icp.ucl.ac.be/~opperd/private/neighbor.html
[2] Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75
[3] "Percent Identity of Genomic DNA Sequences, of Introns and Exons, and of Amino Acid Sequences." N.p., n.d. Web. 21 Feb. 2013.
[4] "Neighbor-joining Method." Neighbor-joining Method. N.p., n.d. Retrieved February 21, 2013 from http://www.icp.ucl.ac.be/~opperd/private/neighbor.html
Site created by: Emma Baar
Last updated: 5-14-2013
University of Wisconsin - Madison
Last updated: 5-14-2013
University of Wisconsin - Madison