Figure 1. A typical error made by gain-loss methods is avoided with reconciliation.

A gene family with a history of parallel losses illustrates the increased accuracy associated with explicit use of a gene tree by phylogenetic reconciliation. (a) A hypothetical gene family, based on the real enzyme family in Figure 2, possesses one gene in arabidopsis, shark, amphibians, and fish, and two genes in each amniote species. (b) A gain-loss method, Wagner parsimony, incorrectly infers a single gene family member in the common ancestral species and a recent gain on the lineage leading to chicken and human. This scenario implies that all chicken and human genes are equally related to g_S and g_F, an inference that is not supported by the true tree. (c) Gene tree-species tree reconciliation correctly infers an earlier duplication, followed by parallel losses in the shark and fish lineages, and shows that g1_H and g1_C are more closely related to g_S in shark and g_F in fish, than to g2_H and g2_C.