My results are similar to those of Oaks et al. [ 7] in that I find msBayes will often infer strong support for clustered divergences when divergences are random over quite broad timescales.
Clades H and I are strongly supported in the species tree and concatenation analyses; clade H is inferred, with strong support, in two and clade I in one of the single-locus analyses.
Within Strepsirrhines, the inferred phylogenetic relationships received strong support under both methodological frameworks.
However, the tree inferred using PhyloBayes provided strong support for this clade (Fig. 5).> The monophyly of Ovalentaria and the clade containing cichlids and Pholidichthys were supported with 100%% bootstrap support (Figs. 2, 3, 4, 5 and 6, Additional file 3: Table S3, Additional file 4: Figure S1, and Additional file 5: Figure S2).
The new method, dpp-msBayes, has greater power to detect random temporal variation in divergences, is less prone to spurious inference of clustered divergence models, and much less likely to incorrectly infer such models with strong support.
For all replicates in the Felsenstein zone, BI incorrectly infers the AC/BD tree with very strong support when the AB/CD tree is true, and it infers AB/CD when AC/BD is true.
The novel result inferred from these data is the strong support of sister relationships of Caryophyllales (including buckwheat) and asterids.
The phylogeny inferred using PhyloBayes (Fig. 5) provided strong support for the clades listed above, and also resolved a monophyletic Pseudochromidae.
In the A1 and A2 matrices, Copernicia and Washingtonia together are inferred to be the sister group to Pritchardia with strong support (100% JK; Figures 2 and 3).
