Sequence alignment of fourfold degenerate sites of the 2L chromosome arm

We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns < 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).