Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. Yun S. Song^1,2, Andrew Chan¹, Paul Jenkins³. 1) Department of EECS, University of California, Berkeley, CA, USA; 2) Department of Statistics, University of California, Berkeley, CA, USA; 3) Department of Statistics, University of Warwick, Coventry, UK.

   Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. To address this challenge, we have developed a new computational method which allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome. As an application, we have performed a genome-wide analysis of genetic variation data for two Drosophila melanogaster populations, one from North America (Raleigh, USA) and the other from Africa (Gikongoro, Rwanda). Our study shows that fine-scale recombination rate variation is widespread throughout the D. melanogaster genome, across all chromosomes and in both populations. At the fine-scale, a conservative, systematic search for evidence of recombination hotspots suggests the existence of a handful of putative hotspots each with at least a tenfold increase in intensity over the background rate. We have compared the estimated recombination maps in the two populations and quantified the extent to which recombination rates are conserved. In general, similarity is observed at very broad scales, but substantial differences are seen at fine scales. The average recombination rate of the X chromosome appears to be higher than that of the autosomes in both populations, and this pattern is much more pronounced in the African population than the North American population. We have also examined the correlation between various genomic features, including recombination rates, diversity, divergence, GC content, gene content, and sequence quality; the most notable difference between D. melanogaster and humans is in the correlation between recombination and diversity.