Individual phylogenetic methods
As we have discussed in class, individual phylogenetic methods are best suited to particular kinds of problems. For each of the following data sets, assess the suitability of maximum parsimony to that data set. Then do likewise for maximum likelihood. Clearly explain your reasoning in each case. (Note: some data sets may be suitable for both maximum parsimony and maximum likelihood, while other data sets may not be suitable for either method.) A researcher wants to reconstruct the evolutionary history of a 500-bp noncoding region. Her data consist of 15 DNA sequences representing a broad sample of eukaryotic organisms. A biomedical research group is studying the evolution of HIV (the virus that causes AIDS). Their data consist of 700 RNA sequences, each approximately 8 Mb long. In aIDition, the genomic region they are studying involves extensive recombination and transfer of genetic information from one strain to another. An ecologist wants to reconstruct the evolutionary history of the chytrid fungus currently infecting amphibian populations worldwide. His data consist of 10 samples from each of 50 populations, focusing on a 6-kb intron within a specific gene. Note that the chytrid epidemic is believed to have begun in the early to mid-1970s.
