Lupinus.online.FigureS2.04.26.11

SUPPLEMENTARY FIGURE S2. Net diversification rates (r = lineages/million years) in Lupinus estimated under the MEDUSA birth–death likelihood model. MEDUSA analyses were conducted using 1000 trees randomly selected from the posterior distribution of constrained pure–birth Bayesian MCMC tree searches in BEAST, pruned to the infrageneric skeleton topology in Figure 3 of the main text. Histograms show the frequency (ƒ) of estimates from replicate MEDUSA likelihood runs: a) ΔAIC scores for pure–birth versus birth–death models; b) background rates of net diversification in Lupinus; c) ΔAIC scores for a rate shift in eastern South America; d) net diversification rates in eastern South America; e) ΔAIC scores for a rate shift in western North America; f) net diversification rates in western North America; g) ΔAIC scores for a rate shift in Mexico/Andes; h) net diversification rates in Mexico/Andes. ΔAIC scores indicated that a pure–birth model was strongly favored over a model incorporating extinction (Fig. S2a). The strongest support for a primary rate shift was recovered in western North America (Fig. S2e), although the fastest rates were estimated in the Mexican/Andean clade (Fig. S2h).