Check your mixed vial, and if it has a decent number of adults, transfer them to a food vial. If you tranferred adults last Thursday, remove them and count them.
Work on you individual project.
Last week you looked at the Ka/Ks ratio, as one way of detecting the effects of selection. Today you'll use a different technique, the McDonald-Kreitman test. This compares the divergence between species with the polymorphism within species, so you'll need DNA sequence data for multiple alleles of a gene. A good place to get this is from the Drosophila Polymorphism Database. Go there and search for data on the gene you've been working on for the last couple weeks. Enter "Drosophila melanogaster" in the "Organisms" box, and enter the symbol for your gene in the "Genes" box. (Don't enter the allele number, just the gene symbol; "sn", not "sn3", for example). Then scroll down and hit "Run search".
If you don't get an output, it may mean that there isn't sequence polymorphism data for your gene. In that case, change "Num. Synonymous sites" to 30 and "Num. of sequences" to 10, then run the search again. You should get a list of about 327 polymorphic sets. Scroll through the list until you find the gene that is alphabetically closest to your last name. Click on the link for "CDS", then click on the link for "FASTA align." This should give you the coding sequence for multiple alleles of the gene. Copy this into a file. Also click on the link for "McDonald-Kreitman test", and write down the numbers in the 2x2 table, plus the chi-square and P-values.
Take one of the alleles and BLAST it against the Drosophila yakuba genome. Get the coding sequence for the best matching gene and add it to your file of D. melanogaster sequences. Then run the file through ClustalW, save the output in Phylip format, and read it into DNAsp. Get the McDonald-Kreitman results from DNAsp. They will be different from the results from the Drosophila Polymorphism Database, as the DPDB compares D. melanogaster polymorphism to divergence vs. D. simulans.
Get the codon bias index for your new gene in D. melanogaster and D. yakuba, as well.
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This page was last revised October 13, 2010. Its URL is http://udel.edu/~mcdonald/geneticslab13.html