A parsimony approach to analysis of human segmental duplications

Segmental duplications are abundant in the human genome, but their evolutionary history is not well-understood. The mystery surrounding them is due in part to their complex organization; many segmental duplications are mosaic patterns of smaller repeated segments, or duplicons. A two-step model of duplication has been proposed to explain these mosaic patterns. In this model, duplicons are copied and aggregated into primary duplication blocks that subsequently seed secondary duplications. Here, we formalize the problem of computing a duplication scenario that is consistent with the two-step model. We first describe a dynamic programming algorithm to compute the duplication distance between two strings. We then use this distance as the cost function in an integer linear program to obtain the most parsimonious duplication scenario. We apply our method to derive putative ancestral relationships between segmental duplications in the human genome.