FROM GENE TO ORGANISMAL PHYLOGENY - RECONCILED TREES AND THE GENE TREE SPECIES TREE PROBLEM

The processes of gene duplication, loss, and lineage sorting can resul t in incongruence between the phylogenies of genes and those of specie s. This incongruence complicates the task of inferring the latter from the former. We describe the use of reconciled trees to reconstruct th e history of a gene tree with respect to a species tree. Reconciled tr ees allow the history of the gene tree to be visualized and also quant ify the relationship between the two trees. The cost of a reconciled t ree is the total number of duplications and gene losses required to re concile a gene tree with its species tree. We describe the use of heur istic searches to find the species tree which yields the reconciled tr ee with the lowest cost. This method can be used to infer species tree s from one or more gene trees. (C) 1997 Academic Press.