Ancestral area reconstruction using the dispersal-extinction-cladogenesis model.

<p>Inset map shows the Madagascar and Indian Ocean Islands biodiversity hotspot (dashed line) and the distribution and number of species of <i>Psiadia</i> (negative values indicate recorded extinctions of putative members of the genus). Contours of smaller islands have been enlarged and highlighted for clarity. Branch colors follow the designated geographic areas on the inset map. Bold node numbers indicate differences in optimal resolution between reconstruction using the dec-model and statistical Dispersal-Vicariance analyses. Asterisks highlight nodes for which multiple equally probable solutions were retrieved using Lagrange and/or S-DIVA. Arrows indicate dispersal events between designated regions. Node numbers refer to per-clade results listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042932#pone.0042932.s004" target="_blank">Table S3</a>. Geographic coverage is indicated by capitals following taxon names. Broken branches lead to nodes with low posterior probabilities (<90) obtained in BEAST.</p

Lineage through time curves (with 95% confidence intervals) for clades A and B.

<p>Black lines: individual empirical curves from the BEAST analysis. Blue (clade A) and red (clade B) lines demarcate 95% confidence intervals generated using a constant rates model. Included rate shifts (*) and 95% HPD intervals shown as described in text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042932#pone-0042932-g003" target="_blank">Figure 3</a>.</p

Results of relaxed Bayesian dating and diversification rate shift analyses for selected nodes.

<p>Notes: Values in Ma. Node numbers refer to symbols used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042932#pone-0042932-g003" target="_blank">Figure 3</a>. Abbreviations: HPD – Highest Posterior Density interval; PP – Posterior Probability; MRCA – Most Recent Common Ancestor; SG – Slowinski-Guyer; RC – Relative Cladogenesis.</p

ERM nodal probabilities obtained in whole-tree tests for diversification rate-variation using SYMMETREE.

<p>Notes: Tests were conducted on the consensus tree obtained with MrBayes and the two separate pruned ingroup clades of clade A and B, and the MCC chronogram obtained with BEAST.</p

Results of birth-death likelihood (BDL) analyses of lineage diversification.

<p>Notes: Analyses were conducted using the ultrametric tree obtained in BEAST. All outgroups and intermittent taxa were pruned to obtain the ingroup clades A and B. Abbreviations: Pb – pure birth; Bd – birth-death; DDX – exponential density dependent; DDL – logistic density dependent; Yule2rate – Yule with 2 rates; Yule3rate – Yule with 3 rates; LH – log-likelihood; r1/r2/r3 – net diversification rates; a – extinction fraction; xp – rate change parameter DDX model; k – carrying capacity parameter DDL model; st1/st2 – timing of rate shift (mya); AIC – Akaike information criterion; ΔAICrc  =  difference between the best rate constant and rate variable models.</p

Chronogram for <i>Psiadia</i> s.l. and results of diversification rate shift analyses.

<p>Broken branches lead to nodes with low posterior probabilities (<90) obtained in BEAST. Arrows indicate rate shifts associated with results obtained using SYMMETREE (rate shift box A, B & C: Δ1, Δ2 and SG) and the Relative Cladogenesis test (RC1 & RC2). Numbered nodes 1–4 indicate calibrated nodes. Numbered Nodes 5–10 refer to key events in the evolutionary history of <i>Psiadia</i>, as discussed in text. Bars: blue, <i>Psiadia</i> clade A & B; grey, other taxa contained with <i>Psiadia</i>-clades; white, outgroup taxa. Abbreviations: Re (Réunion), Mu (Mauritius), Ro (Rodrigues), Md (Madagascar), So (South Africa), Sa (Saudi Arabia), Ta (Tanzania), My (Mayotte), Th (Thailand), Pa (Paraguay), Au (Australia), Ml (Malawi), Co (Congo-Kinshasa), Et (Ethiopia), Ou (Outgroups).</p