Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees

摘要

Phylogenetic tree reconciliation is a widely used approach for analyzing the inconsistencies between the evolutionary histories of genes, and the species through which they have evolved. An important aspect of tree reconciliation are the cost functions involved that are the minimum number of evolutionary events explaining such inconsistencies. Mean values for these functions are fundamental when analyzing tree reconciliations. Here we describe mean value formulas when a history of genes is fixed for the cost functions for the events gene duplication, gene loss and gene duplication-loss, under the uniform model of species trees. We show that these formulas can be efficiently computed, and finally analyze the mean values using empirical and simulated data.