Bias–variance tradeoffs in recombination rate estimation

In 2013, we and coauthors published a paper characterizing rates of recombination within the 2.1-megabase garnet-scalloped (g-sd) region of the Drosophila melanogaster X chromosome. To extract the signal of recombination in our high-throughput sequence data, we adopted a nonparametric smoothing procedure, reducing variance at the cost of biasing individual recombination rates. In doing so, we sacrificed accuracy to gain precision—precision that allowed us to detect recombination rate heterogeneity. Negotiating the bias–variance tradeoff enabled us to resolve significant variation in the frequency of crossing over across the garnet-scalloped region.