Here's a picture of my three second year project students in front of their poster. Blerta Kolaj, Milu Jauregui, and Zarna Shah collaborated on this project to study the evolution of various members of the HSP70 gene family.
Eukaryotes contain at at least five or six versions of HSP70 genes. Two of them are present in single copies (mostly) and they were present in the common ancestor of all eukaryotes. One of these is the mitochondrial version, which is derived from the proteobacterium ancestor of mitochondria. The other is a version found in the endoplasmic reticulum (ER). The ER member of the HSP70 gene family (=BiP) arose very early in eukaryotic evolution.
A phylogenetic tree of either the mitochondrial gene or the ER gene should reveal the evolution of all eukaryotic species. The two trees should be identical provided the genes evolve independently and there has been no horizontal gene transfer. Furthermore, the two trees will root each other since they join at a common ancestral node representing the split between eukaryotes and prokaryotes. The purpose of the experiment is to test this hypothesis and see if we have enough examples of ER and mitochondrial genes to make duplicate trees. The problem is that we need an example of each gene in every species we test. The fact that we now have quite a few genome sequences means that this has become more feasible than in the past.
Blerta, Milu, and Zarna were able to add in one more set of sequences; the chloroplast members of the HSP70 gene family. These genes are derived from the cyanobacteria ancestor of chloroplasts so they provide independent confirmation of the eukaryotic tree for plants and algae. Unfortunately, there aren't very many examples of species that have sequenced versions of the chloroplast gene, the mitochondrial gene, and the ER gene.
Here's the tree.
As you can see, the relationship of most species (actually genes) in the mitochondrial and ER branches is very similar. This confirms that the two family members are evolving independently. Differences occur with the protists such as trypanosomes, Leishmania, plasmodia, and cryptosporidium. This is unfortunate since analysis of HSP70 genes could have helped resolve the relationship of protists, which is very controversial. At least we're sure of the roots of each major branch—that's a big step forward.
The chloroplast and mitochondrial clades are closer together than either is to the eukaryotic ER versions of the HSP70 family. This is not unexpected since both organelle genes are prokaryotic in origin. It suggests that the universal root is along the branch leading to the ER clade.
Now my students have to turn their attention to their individual projects. They have about six weeks to finish up. I'll post summaries of their work in May. I'm pretty excited about all three projects, we could end up answering some pretty important questions using the HSP70 database.