Figure 4

Evolution of the AGAMOUS gene lineage. (A) Potential AGAMOUS (AG) gene copy histories within the Zingiberales. Scenario 1 assumes one single duplication event at the base of the Zingiberales order, leading to two distinct orthologous AG lineages (ZinAG-1 and ZinAG-2). Scenarios 2 and 3 depict alternative histories of duplications and losses of the AG copies, particularly in the Zingiberaceae lineage. In both cases, orthologous relationships would be complicated by the existence of subsequent duplication events, unique to the Zingiberaceae lineage, leading to the evolution of yet another copy of AG, ZinAG-3. (B) Shimodaira-Hasewaga test (Shimodaira & Hasewaga [37]), SH test) was performed using PAUP* on a constrained topology, where the two first paraphyletic lineages were forced to form a monophyletic clade. The likelihood score for the constrained topology was compared to the likelihood score of the unconstrained gene tree, as obtained on Bayesian and maximum likelihood phylogenetic analysis (Figure 3). The constrained topology shows a better likelihood score than the one calculated for the gene tree topology presented here (although not significantly different), supporting the idea that the first two paraphyletic lineages are actually derived from a single duplication event. This result supports the evolutionary history depicted by Scenario 1, in which ZinAG-1 and ZinAG-2 are orthologous lineages.