DOI: 10.5061/dryad.1pd2j
title: Data from: Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster

description: We considered genome-wide four-fold degenerate sites from an African
 Drosophila melanogaster population and compared them to short introns. To
 include divergence and to polarize the data, we used its close relatives
 Drosophila simulans, Drosophila sechellia, Drosophila erecta and
 Drosophila yakuba as outgroups. In D. melanogaster, the GC content at
 four-fold degenerate sites is higher than in short introns; compared to
 its relatives, more AT than GC is fixed. The former has been explained by
 codon usage bias (CUB) favouring GC; the latter by decreased intensity of
 directional selection or by increased mutation bias towards AT. With a
 biallelic equilibrium model, evidence for directional selection comes
 mostly from the GC-rich ancestral base composition. Together with a slight
 mutation bias, it leads to an asymmetry of the unpolarized allele
 frequency spectrum, from which directional selection is inferred. Using a
 quasi-equilibrium model and polarized spectra, however, only purifying and
 no directional selection is detected. Furthermore, polarized spectra are
 proportional to those of the presumably unselected short introns. As we
 have no evidence for a decrease in effective population size, relaxed CUB
 must be due to a reduction in the selection coefficient. Going beyond the
 biallelic model and considering all four bases, signs of directional
 selection are stronger. In contrast to short introns, complementary bases
 show strand specificity and allele frequency spectra depend on mutation
 directions. Hence, the traditional biallelic model to describe the
 evolution of four-fold degenerate sites should be replaced by more complex
 models assuming only quasi-equilibrium and accounting for all four bases.
description: Sequence alignment of
 fourfold degenerate sites of the 2L chromosome armWe 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 &lt; 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).alignment_2LSequence alignment of fourfold degenerate sites of the 2R chromosome armWe 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 &lt; 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).alignment_2RSequence alignment of fourfold degenerate sites of the 3L chromosome armWe 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 &lt; 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).alignment_3LSequence alignment of fourfold degenerate sites of the 3R chromosome armWe 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 &lt; 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).alignment_3R