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Stephan Hutter, Wolfgang Stephan, Reply to Beatriz Vicoso and Brian Charlesworth, Genetics, Volume 181, Issue 4, 1 April 2009, Page 1703, https://doi.org/10.1534/genetics.109.101212
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IN their letter to the editors, Vicoso and Charlesworth (2009, this issue) reanalyze our data set of X-linked and autosomal loci obtained from an African population of Drosophila melanogaster (Hutter et al. 2007) with regard to different estimators of recombination rate (Singh et al. 2005). They find that, on average, X-linked loci have higher effective recombination rates. This might influence the ratio of X-chromosomal to autosomal nucleotide diversity, as there is a well-known correlation between levels of recombination and nucleotide variability in D. melanogaster (e.g., Begun and Aquadro 1992). They therefore recalculate the ratio of X-linked to autosomal diversity using only loci with comparable rates of effective recombination and find that this ratio drops to 0.64, which is substantially lower than the 0.90 value that we report in our original study (Hutter et al. 2007), and even lower than the expectation of the standard neutral model (0.75). We would like to point out that this value was obtained by using the statistic π (Tajima 1983), which is more sensitive to deviations from the standard neutral model than Watterson's (1975) θW. Calculating diversity ratios using θW, we obtain a value of 0.71 for the data set used by Vicoso and Charlesworth (2009). Furthermore, if we account for possible biases in mutation rate by dividing θW by divergence to D. simulans, similar to the approach used in our original article (Hutter et al. 2007), the ratio increases to 0.73.
