This is just something to get you thinking over the holiday, to make sure your brains don’t totally ossify. There is a specific reason for asking this: I want to relate it to a blog post I read last night. And, hey, you’ve got nothing better to do than think about phylogenetics whilst you’re digesting your chocolate, have you?
Imagine that you’ve done the following experiment. You have take a single isolate of a phage (a bacterial virus), split it into 5 populations, and grown each of them on one of two bacterial species (two on a strain of E. coli and three on a strain of Salmonella typhimurium), and a higher temperature than they are use to. You culture these populations for 11 days, and find that their fitness in their new environment is higher than their ancestor’s, but fitness on the other host is no better than the ancestor’s (evidence for local adaptation). You also sample and completely sequence one isolate from each population.
So, what would you expect the estimated phylogeny from these sequences to look like? Remember, the true phylogeny is a star. Just to help – yes, there is a signal in the data.
As an added bonus, you cultivate one of the E. coli-grown strains on E. coli, and take one of the S. typhimurium-grown strains and split it into 3 populations: one you continue to grow on S. typhimurium, the other two you grow on E. coli. After 22 days, you sample an isolate from each population. You find that the fitness of the isolates on their new hosts has increased, so that all isolates have roughly the same fitness on the host they have been growing on. Again, you sequence the whole genome of each isolate (hey, these are phages so it’s not too difficult!).
Again, what would you expect the estimated phylogeny from these sequences to look like? And yes, there is a signal in the data.
There are “right” answers, but I’m as interested in seeing whether and how people analyse this and come to their answers. I’ll comment a bit about them when a few people have had their say, and can also answer any questions. There’s one particular reason for this, plus a couple of other aspects that I (at least) find interesting.