Locating Multiple Gene Duplications through Reconciled Trees

We introduce the first exact and efficient algorithm for Guigó et al.’s problem that, given a collection of rooted, binary gene trees and a rooted, binary species tree, determines a minimum number of locations for gene duplication events from the gene trees on the species tree. We examined the performance of our algorithm using a set of 85 gene trees that contain genes from a total of 136 plant taxa. There was evidence of large-scale gene duplication events in Populus, Gossypium, Poaceae, Asteraceae, Brassicaceae, Solanaceae, Fabaceae, and near the root of the eudicot clade. However, error in gene trees can produce erroneous evidence of large-scale duplication events, especially near the root of the species tree. Our algorithm can provide hypotheses for precise locations of large-scale gene duplication events with data from relatively few gene trees and can complement other genomic approaches to provide a more comprehensive view of ancient large-scale gene duplication events.