Lupinus.online.FigureS3.04.26.11

SUPPLEMENTARY FIGURE S3. Net diversification rates (r = lineages/million years) in Lupinus estimated under the MEDUSA birth–death likelihood model, including relative extinction (ε = birth/death) as a free parameter. 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. Surface plots show the frequency (ƒ) of estimates from replicate MEDUSA likelihood runs, including the joint relationship between r and ε: a) background rates in Lupinus; b) eastern South America; c) western North America; d) Mexico/Andes. Estimates of net diversification were generally similar to estimates obtained under a pure–birth MEDUSA model, with the primary differences including lower r and high ε in the eastern South American clade (Fig. S3b), and a bimodal distribution of ε in the Mexican/Andean clade (Fig. S3d). However, ΔAIC scores shown in Figure S2a indicate that the pure–birth model was strongly favored over the birth–death results shown here. We obtained similar results for pure–birth and birth–death MEDUSA analyses based on the posterior distribution of trees from birth–death Bayesian MCMC tree searches in BEAST (results not shown), indicating that the MEDUSA analyses were robust to the choice of tree prior used for phylogenetic inference. Note that estimates of ε for eastern South America should be considered unreliable, since unresolved terminal clades do not contain sufficient information to infer this parameter (Rabosky et al. 2007; Alfaro et al. 2009).