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Beatriz Vicoso, Brian Charlesworth, Recombination Rates May Affect the Ratio of X to Autosomal Noncoding Polymorphism in African Populations of Drosophila melanogaster, Genetics, Volume 181, Issue 4, 1 April 2009, Pages 1699–1701, https://doi.org/10.1534/genetics.108.098004
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IN African populations of Drosophila melanogaster, the level of silent variability on the X chromosome often exceeds three-fourths of the autosomal value (the ratio expected for neutral equilibrium), suggesting that demographic or selective effects may influence variability (Andolfatto 2001; Kauer et al. 2002; Mousset and Derome 2004; Hutter et al. 2007; Pool and Nielsen 2007; Singh et al. 2007; Pool and Nielsen 2008). Although these sites are not completely neutral (Andolfatto 2005; Haddrill et al. 2005; Halligan and Keightley 2006), they are less constrained than coding sites and are often used as a neutral proxy.
The level of variability of neutral mutations can be affected by selection at neighboring sites: neutral variants will be removed from the population if they are linked to deleterious mutations or swept to fixation if they are linked to beneficial variants (Gordo and Charlesworth 2001). These effects are greatest when recombination rates are low, consistent with data on the relation between recombination and variability in D. melanogaster (Begun and Aquadro 1992; Shapiro et al. 2007). Differences in recombination rates between the X chromosome and the autosomes therefore could affect the relative values of X chromosomal and autosomal diversities in Drosophila. The expected magnitude of this difference depends on the type of selective effect involved (selective sweeps vs. background selection), on the location of the genes being compared (high vs. low recombination regions), and on the selection coefficients and dominance coefficients of the variants under selection. This makes the expected magnitude hard to predict, but we note that Charlesworth (1996, p. 139) showed that background selection could produce an effect on X-linked loci that yields a maximum diversity level for the highest recombining regions of the chromosome that was between 1.28 and 1.05 times that of an autosomal arm, depending on which arm is used for the comparison.
