Figure 1.
Chronogram from the BEAST uncorrelated log normal relaxed clock analysis.
The outgroup, corbiculate apids, have been removed and the four Xylocopinae tribes are colour coded. The root node was set at 107Ceratina unimaculata (Ceratinini), Allodapula rozeni (Allodapini), Manuelia gayi (Manueliini) and Xylocopa sp. (Xylocopini).
Table 1.
Age estimates of Xylocopinae root age and tribal crown ages obtained from an uncorrelated log normal relaxed clock model from BEAST as well a penalized likelihood transformation of a Bayesian phylogram from MrBayes (in parentheses).
Figure 2.
Log lineage through time (LTT) plots for Xylocopinae.
Top panel gives results for an uncorrelated log normal relaxed clock (RC) model and the bottom panel gives results for a penalized likelihood (PL) transformation of MrBayes phylograms. The red lines indicate the maximum credibility tree for the RC analysis in the top panel and the PL-transformed consensus phylogram for the MrBayes/r8s analysis. Black lines indicate LTT plots for 200 post-burnin trees from each analysis. The blue line represents the K-T boundary.
Figure 3.
LTT plots for TreeSim simulations of a massive extinction event and three scenarios involving a 3-phase process where birth/death (λ/μ) values vary over time.
Simulations specified 1000 actual extant taxa, pruned to 200 taxa to represent incomplete taxon sampling. (a) A massive extinction event at 65 Mya where λ = 0.2, μ = 0.1, and 92% of lineages go extinct at 65 Mya. (b) A 3-phase Yule process where λ = 0.2, μ = 0.1 prior to 65 Mya, λ = 0.0, μ = 0.0 between 90 and 65 Mya and where λ = 0.2, μ = 0.1 after 65 Mya. (c) A 3-phase Yule process where λ = 0.2, μ = 0.1 prior to 65 Mya, λ = 0.02, μ = 0.01 between 90 and 65 Mya and where λ = 0.2, μ = 0.1 after 65 Mya. (d) A 3-phase Yule process where λ = 0.2, μ = 0.1 prior to 65 Mya, λ = 0.002, μ = 0.001 between 90 and 65 Mya and where λ = 0.2, μ = 0.1 after 65 Mya. The red lines show the empirical LTT plots from Figure 2 based on the maximum credibility BEAST tree.