Drosophila melanogaster and D. simulans are two closely related species with a similar distribution range. Many studies suggested that D. melanogaster has a smaller effective population size than D. simulans. As most evidence was derived from non-African populations, we readdressed this question by sequencing 10 X-linked loci in five African D. simulans and six African D. melanogaster populations. Contrary to previous results, we found no evidence for higher variability, and thus larger effective population size, in D. simulans. Our observation of similar levels of variability of both species will have important implications for the interpretation of patterns of molecular evolution.
DROSOPHILA melanogaster and D. simulans are two closely related species, which have a similar, but not identical, distribution range and demographic history (David and Capy 1988;Irvin et al. 1998;Capy and Gibert 2004;Lachaise and Silvain 2004). This species pair has been used in numerous comparative studies highlighting their similarities and differences. One of the central conclusions emerging from these studies was that the effective population size (N e ) differs between the two species, with D. simulans having the larger size.The level of neutral polymorphism which scales with effective population size was found to be higher in D. simulans than in D. melanogaster (Aquadro et al. 1988;Aquadro 1992;Moriyama and Powell 1996). In contrast, due to the higher efficacy of selection in large populations, nonneutral characters are expected to be less variable in the species with the larger population size. Consistent with D. simulans having a larger effective population size, D. melanogaster was repeatedly found to harbor higher levels of nonsynonymous polymorphism (Moriyama and Powell 1996;Morton et al. 2004). Similarly, the efficacy of selection for synonymous codon usage is expected to depend on population size, with selection being more effective in larger populations (Muto and Osawa 1987;Akashi 1995). Concordant with a smaller population size, and thus relaxed selective constraint, the D. melanogaster lineage has fixed a much higher number of unpreferred codons than the D. simulans lineage (Akashi 1995(Akashi , 1996(Akashi , 1997Akashi and Schaeffer 1997;Akashi et al. 1998;McVean and Vieira 2001). Allozymes which evolve under selective constraints, have consistently been shown to be much less variable in D. simulans than in D. melanogaster Singh et al. 1987;Choudhary et al. 1992). Finally, morphological data that can be directly interpreted as reflecting adaptive constraints also support the picture of lower variability and less differentiation between worldwide D. simulans than D. melanogaster populations ½reviewed in Capy and Gibert (2004).Unfortunately, the majority of data, from which evidence for different effective population sizes of D. simulans and D. melanogaster was derived, is based on comparisons of non-African populations ½e.g., Moriyama and Powell (1996). Given that both species underwent changes in effective p...