Polymorphism and divergence along the D. melanogaster branch, divergence along the D. simulans branch, and results of D. melanogaster McDonald–Kreitman tests for each of the five DCC genes

mel/simaD. melanogaster branchD. simulans branch
Geneπ (N/S)ansimdNdSNpolyNfixSpolySfixFETbNpolyNfixSpolySfixFETb
mle0.000/0.000NA0.010/0.0100.047/0.0541183331 .00NANANANANA
  • π, nucleotide diversity; N, nonsynonymous; S, synonymous; nsim, D. simulans sample size (for D. melanogaster, n = 10 for all); d, divergence; poly, polymorphism; fix, fixations; FET, Fisher's exact test P-value).

  • a Ten inbred lines of D. melanogaster (North Carolina, T. Mackay) were sequenced directly to obtain polymorphism data from each of the five core protein-coding loci in the DCC. For D. simulans, sequences were obtained from a population genomic data set, which consists of light-shotgun sequencing (one to two times coverage) of six lines syntenically aligned to D. melanogaster v4 assembly, and were used for population data for all five DCC genes (Begun et al. 2007). These D. simulans data were subjected to extensive quality control ( Levels of nucleotide diversity (π) were estimated as in Nei (1987) and Weir (1990). The numbers of silent and replacement sites were estimated using the method of Nei and Gojobori (1986). The pathway between two codons was calculated as the average number of silent and replacement changes from all possible paths between the pair. Lineage-specific divergence was estimated by maximum likelihood using PAML v3.14 (Yang 1997). PAML was run in batch mode using a BioPerl wrapper (Stajich et al. 2002) for codeml with codon frequencies estimated from the data. Sequence data for this article have been submitted to GenBank under accession nos. EU167087EU167150.

  • b To test for adaptive protein evolution, we used the McDonald–Kreitman test (McDonald and Kreitman 1991), which determines whether the number of fixations relative to polymorphisms for synonymous and nonsynonymous sites deviates from neutral expectations. We used parsimony to infer whether a fixation occurred on the D. melanogaster or the D. simulans branch, restricting our attention to codons that varied at a single position among the three species. The syntenic alignment of D. yakuba was used to polarize changes to the D. melanogaster or D. simulans branch (Begun et al. 2007). For msl3 and mof, which had borderline significant McDonald–Kreitman tests for the D. simulans lineage, 10 additional inbred lines were sequenced (Winters, CA, S. Nuzhdin).