Kreitman and Hudson

Kreitman and Hudson [4] extended this approach by looking more carefully within the region to see where they could find differences between observed and expected levels of nucleotide sequence diversity. They used a ``sliding window'' of 100 silent base pairs in their calculations. By ``sliding window'' what they mean is that first they calculate statistics for bases 1-100, then for bases 2-101, then for bases 3-102, and so on until they hit the end of the sequence. It's rather like walking a chromosome for QTL mapping, and the results are rather pretty (Figure 1).

Figure 1: Sliding window analysis of nucleotide diversity in the Adh-Adh-dup region of Drosophila melanogaster. The arrow marks the position of the single nucleotide substitution distinguish Adh-F from Adh-S (from [4])

To me there are two particularly striking things about this figure. First, the position of the single nucleotide substitution responsible for the electrophoretic polymorphism is clearly evident. Second, the excess of polymorphism extends for only a 200-300 nucleotides in each direction. That means that the rate of recombination within the gene is high enough to randomize the nucleotide sequence variation farther away.