Week Eight: Host-Parasite coevolution

This laboratory focuses on the use of phylogenetic reconstruction to test explicit hypothesis in parasitology: do hosts and parasites coevolve and co-speciate? We will be focusing on one of the most important vector-borne infectious diseases in the world, malaria. The parasites responsible for malaria all belong to the genus Plasmodium, and we will be examining them along with their primate hosts.

A quick overview of the host range of Plasmodium reveals that the relationship between parasite and host is not one to one. Indeed, certain species of Plasmodium are capable infecting multiple primate hosts; certain hosts, in turn, are susceptible to more than one species of Plasmodium. These observations in themselves, however, do not address our hypothesis: parasites often have secondary hosts, but may still have been shaped by coevolving with their primary host.

In order to address this question, we need to construct a phylogenetic hypothesis for the parasites, and test the congruence of that phylogeny with a phylogenetic tree of hosts. As always, we need to establish the reliability of each of our trees in order to test them. As has been true throughout the course, the reliability of our results will depend on our choice of gene, the quality of our alignments, and on the model or models we use to guide our reconstructions.

For this lab, the task involves both the reconstruction of the host tree–in this case a primate tree–as well as of the Plasmodium tree. As usual, you will have a choice of genes or sequences on which to base your reconstruction. I am providing you with a couple of tables and figures that list the parasites, their primary and secondary hosts, and some preliminary host phylogenies.


I am also supplying you with some information that will guide you in constructing your trees.

Primate tree: I am attaching two files,

NCBI names
NCBI Numbers

that provide you with a large number of genes/sequences that can be used for the reconstruction of the primate tree. My suggestion is that groups of you tackle the reconstruction using nonoverlapping sets of genes, and then compare the resulting trees to assess their stability.

Plasmodium tree: I am supplying you with a list of Plasmodium species that might be of interest. Here, too, you can use any number of genes on which to base your phylogenetic reconstruction. My advice is to focus on one of the following: cytochrome B (mt), SSU 18S, or the merozoite surface protein. Split up as groups and tackle different sources of information so that we can compare the resulting trees.

In the end, we will be comparing the trees that emerge in order to assess their congruence. Our first test will rely on our eyeball, but we will subsequently do some more sophisticated analyses that take into account both the inherent uncertainty of the trees and the probability that a certain number of nodes/branches will match by chance alone.