Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree

Taoyang Wu, Louxin Zhang

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)


A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events might occur. Hence, it is of great challenge to infer the containing species tree from a set of gene trees. One common approach to this inference problem is through gene tree and species tree reconciliation.

In this paper, we generalize the traditional least common ancestor (LCA) reconciliation to define a reconciliation between a gene tree and species tree under the tree homomorphism framework. We then study the structural properties of the space of all reconciliations between a gene tree and a species tree in terms of the gene duplication, gene loss or deep coalescence costs. As application, we show that the LCA reconciliation is the unique one that has the minimum deep coalescence cost, provide a novel characterization of the reconciliations with the optimal duplication cost, and present efficient algorithms for enumerating (nearly-)optimal reconciliations with respect to each cost.

This work provides a new graph-theoretic framework for studying gene tree and species tree reconciliations.
Original languageEnglish
Article numberS7
Number of pages10
JournalBMC Bioinformatics
Issue numberSuppl 9
Publication statusPublished - 5 Oct 2011

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