The Pattern of Polymorphism on Human

Polymorphism data from 20 partially resequenced copies of human chromosome 21—more than 20,000 polymorphic sites—were analyzed. The allele-frequency distribution shows no deviation from the simplest population genetic model with a constant population size (although we show that our analysis has no power to detect population growth). The average rate of recombination per site is estimated to be roughly one-half of the rate of mutation per site, again in agreement with simple model predictions. However, sliding-window analyses of the amount of polymorphism and the extent of linkage disequilibrium (LD) show significant deviations from standard models. This could be due to the history of selection or demographic change, but it is impossible to draw strong conclusions without much better knowledge of variation in the relationship between genetic and physical distance along the chromosome. [Supplemental material is available online at www.genome.org.] There are essentially two reasons for studying the pattern of genetic polymorphism in population samples. The first is to identify polymorphisms that have important phenotypic ef-fects. The pattern of polymorphism is important when search-ing for alleles that are statistically associated with phenotypi