Reconciliation of Gene and Species Trees With Polytomies

Motivation: Millions of genes in the modern species belong to only thousands of gene families. Genes duplicate and are lost during evolution. A gene family includes instances of the same gene in different species and duplicate genes in the same species. Two genes in different species are ortholog if their common ancestor lies in the most recent common ancestor of the species. Because of complex gene evolutionary history, ortholog identification is a basic but difficult task in comparative genomics. A key method for the task is to use an explicit model of the evolutionary history of the genes being studied, called the gene (family) tree. It compares the gene tree with the evolutionary history of the species in which the genes reside, called the species tree, using the procedure known as tree reconciliation. Reconciling binary gene and specific trees is simple. However, tree reconciliation presents challenging problems when species trees are not binary in practice. Here, arbitrary gene and species tree reconciliation is studied in a binary refinement model. Results: The problem of reconciling gene and species trees is proved NP-hard when species tree is not binary even for the duplication cost. We then present the first efficient method for reconciling a nonbinary gene tree and a non-binary species tree. It attempts to find a binary refinement of the given gene and species trees that minimizes the given reconciliation cost if they are not binary. Our algorithms have been implemented into a software to support quick automated analysis of large data sets. Availability: The program, together with the source code, is available at its online server http://phylotoo.appspot.com. Contact: yu [email protected] or [email protected]