A large number of the segmental duplications in mammalian genomes have been cataloged by genome-wide sequence analyses. The molecular mechanisms involved in these duplications mostly remain a matter of speculation. To uncover, test, and further quantify the hypotheses on the mechanisms for the recent duplications in the mammalian genomes, we have performed a series of statistical analyses on the sequences flanking the duplicated segments and proposed a dynamic model for the duplication process. The model, when applied to the human duplication data, indicates that ≈30% of the recent human segmental duplications were caused by a recombination-like mechanism, among which 12% were mediated by the most recently active repeat, Alu. But a significant proportion of the duplications are caused by some mechanism independent of the repeat distribution. A less sure but similar picture is found in the rodent genomes. A further analysis on the physical features of the flanking sequences suggests that one of the uncharacterized duplication mechanisms shared by the mammalian genomes is surprisingly well correlated with the physical instability in the DNA sequences.
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