Hypothetical examples of phylogenetic trees with duplication and gene loss events. The phylogenetic trees were inferred from a gene family including members of all genomes used in the current study (human, HS; mouse, MM; rat, RN; chicken, GG; frog, XT; zebrafish, DR; Tetraodon, TN; Ciona, CI). All nodes are assumed to be supported by >70% in bootstrap analysis. Gene duplication can be recognized if at least two gene copies are present for the same species. (a) The duplication event (represented by a pink diamond) was inferred to have occurred early in vertebrate evolution because both land vertebrates and fishes have two copies of the gene. This is the most likely explanation, since the alternative assumption, where all lineages have undergone separate gene duplication events, is much less parsimonious. Subsequently, a gene loss event can be inferred for Tetraodon, since gene2 is missing (dotted line). The general conclusion of this hypothetical tree is thus one gene loss event of a TN duplicate that first had been created in the common ancestor of land vertebrates and fishes. For all other genomes, we count two retained duplicates after this ancient duplication event. (b) This more complex phylogenetic tree contains three duplication events (again indicated by diamonds). The oldest duplication event (pink diamond) is dated early in vertebrate evolution (TP13, similar to the one in (a)). HS, MM, RN and GG lost gene2, which is interpreted as gene loss of a TP13 duplicate in the common ancestor of these organisms (thus at TP7; Figure 2). GG also lost gene1, a gene loss event at TP6 of a duplicate that originated at TP13. The orange diamond indicates a duplication event in the common ancestor of the fishes, not shared with land vertebrates (TP12), resulting in gene1 and gene1' for both DR and TN. Finally, DR gene1 and gene1" are the result of a species-specific duplication event in DR.