Fig. 4

Short successive internal branches and gene tree topology distribution indicate presence of an empirical anomaly zone. a ASTRAL and MP-EST species tree topologies for intron-set and exon-set are shown with internal branch lengths in coalescent units. Terminal branch lengths are uninformative and are drawn as a constant value across taxa. Coalescent branch lengths for all pairs of branches (x and y) are given below, with a(x) calculated as described in Ref. [12]. Anomaly zone are expected when y < a(x). Clades fulfilling this anomaly zone criterion are marked (red arrows). b Gene concordance factors (gCFs, blue bars) for the nodes (1–7) that support the species tree (upper) and the two most common alternative topologies (gDF1 and gDF2, orange and yellow bars, respectively). The gray bars (gDFp) are the relative frequencies of all other topologies. The nodes showing lower concordance factors (5, 6, and 7) represent the lineages that fall into anomaly zone, with a remarkable number of alternative topologies. c Topology distribution of the four lineages consisting of the subclade of Prunella falling into anomaly zone. The most common topology (topology 1 indicated by green) occurring only in 16% of 50-kb windows. The topology recovered by the intron-set based phylogeny (topology 4 indicated by blue), the MP-EST species tree (topology 13 indicated by dark green) and the ASTRAL species tree (topology 14 indicated by olive green) inferred from the exon-set are the fourth (12% of 50-kb windows), thirteenth (2.5% of 50-kb windows), and fourteenth (2.1% of 50-kb windows) most commonly observed topologies (marked by red stars), respectively