reply: How was the Sdic gene fixed?

Nurminsky and Hartl reply — One hallmark of persistent strong background selection is a severe diminution of codon usage bias1,3. An example is the Drosophila gene rolled (gene 1 in Fig. 1), which is located in the centromeric heterochromatin of chromosome 2, where recombination is severely restricted. Other genes shown in Fig. 1are located near the base of the X chromosome. Genes 10 and 11 are AnnX and Cdic, respectively, which flank the Sdic gene4. As pointed out by Charlesworth and Charlesworth , gene 2, which is su(f), has much less DNA sequence variation than gene 17 (Zw). This difference is consistent with the discordant levels of codon usage bias and suggests strong background selection at su(f) but not at Zw. The degree of codon usage bias shows an extremely sharp increase as the gene locations progress outwards from su(f). The transition is near genes 5 (sol) and 6 (slgA), which are proximal to the Cdic-AnnXregion. Figure 1 Codon usage bias is scaled according to the effective number of codons7. The vertical axis is inverted because a smaller effective number of codons corresponds to a greater bias in codon usage. A similar pattern is seen with other measures of codon bias, such as the χ2/L statistic8 (data not shown). The genes and their accession numbers are: 1, rl (M95124); 2, su(f) (X62679); 3, S6kII (L28945); 4, fog (U03717); 5, sol (M64084); 6, slgA (L07330); 7, dod (U35140); 8, shakB (U17330); 9, run (X56432); 10, AnnX (M34069); 11, Cdic (AF070699); 12, Pbprp2 (U05981); 13, Pp4-19C (Y14213); 14, Mer (U49724); 15, Cdc42 (U11824); 16, Bap (X75910); and 17, Zw (M26673, M26674).