Cophylogenies of mammals and their parasites/diseases
Due Friday, May 9th. Hand in a hard-copy of your results and be prepared to present your conclusions (about 15-20 minutes). As the final course presentation, these should more in-depth than previous presentations. Groups will be the same as last lab unless you would like to request a change.
In this lab you will investigate the co-phylogeny of a group of mammals and a parasite or virus group that infects them.
If you have a special interest in one of these topics let me know ASAP and the topic assignments can be changed.
- Group 1: Seth, Annette, Hillary. Parasites: apicomplexans, particularly Plasmodium species.
- Group 2: Huimin, Shanshan, Gregg, Feng. Parasite/virus: Lentivirae (immunodeficiency viruses). (Probably best to use gag/pol protein sequences; the dna sequences might be OK too).
- Group 3: Kristin, Sarah, Lindsey. Parasite: Anoplura (lice). (Cox1, EF1-alpha, and small subunit RNA genes are probably your only choices).
- Find and read some relevant literature for these parasite-host combinations on PubMed.
- Select genes from a group of parasites and another set of genes from their hosts. Try to get as many taxa as possible. You can use either DNA/cDNA sequences or proteins. You should select outgroups for each set.
- Create multiple alignments of your two sets of genes (using Clustalw, or TCoffee, or something else).
- Use at least two methods to create phylogenetic trees from the two gene sets.
- Do you results support a co-evolution of parasites with their hosts, or does it appear that there have been cross-host jumps? How could you quantify that?