Some of you are planning mate preference experiments that will involve observing matings in action. Others will do mate preference experiments in which mating is measured with crosses, or food preference experiments, or development time experiments. Get together with the people doing experiments similar to yours and discuss your projects. See if anyone has references or ideas that you can use. Critique each others' experiments, and see if there are things you can collaborate on.
If there is some aspect of your project that you should get started on today, get started on it.
Make a new vial of food (remember, it's 2 g of dry food plus 10 ml of water, with a few grains of yeast, like 5 or so, not a whole pinchful). Transfer the adult flies from your mixed population to it. If you have problems, because the food is goopy or the flies are clinging to the vial, put the vial on ice and then brush the flies out once they're chilled.
Last week, you aligned protein sequences of a gene from multiple species, estimated a phylogenetic tree using parsimony, and estimated the evolutionary steps that occurred at several amino acid sites. Look at your aligned sequences. Was there one sequence that was an oddball, very different from the other sequences? If so, talk to me about deleting it. Were there very few sites with amino acid variation? If so, talk to me about adding a more distantly related sequence. If you do delete or add a sequence, repeat the analysis from last week.
Another commonly used method for phylogeny estimation is neighbor joining. This is a two-step procedure; first you create a matrix of distances, then you use these distances for neighbor joining. Go to this this protdist server, which runs the protdist program of Phylip, and paste your Phylip-formatted protein sequences into the box. You can leave all the other parameters at their defaults. Run the program. From the output, copy the contents of the box labelled "Outfile." Then go to this neighbor joining server, paste your distance matrix into the box, and run. Copy the tree from the Neighbor output file box. Compare it with the tree you got with parsimony--are they different?
Copy the entire output from the neighbor.outtree box to a file; it will look like this:
(tribolium:0.13780,((bee:0.13935,nasonia:0.09797):0.04599, (Dmel:0.17192,(mosquito:0.18977,louse:0.22673):0.00543):0.00786):0.01046,human:0.22523);
Download the program NJplot from here and install it on your computer. Load the neighbor.outtree file into it and figure out how to draw a nice-looking tree. Be sure to figure out how to make your outgroup species be the outgroup.
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This page was last revised September 29, 2009. Its URL is http://udel.edu/~mcdonald/geneticslab8.html