Data from: Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster

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.