Fig. 2

Phylogenomic analyses A maximum likelihood species tree was inferred from a concatenation of 650 single-copy core genes (720,532 nucleotide sites). A The tree was generated using an edge-linked proportional partition model with 1,000 ultra-fast bootstraps, and a subsequent concordance factor analysis was performed. Branch support is reported as ultra-fast bootstrap/gCF/sCF (see text for description of gCF and sCF). The scale bar is representative of substitutions per site. A coalescence-based cladogram was inferred from the 650 genes used in A. B The cladogram branch supports are reported as local posterior probability, major quartet frequency, alternative quartet frequency 1, and alternative quartet frequency 2. Red branch supports indicate alternative quartet frequencies that are significantly unequal (p < 0.001) indicating that incomplete lineage sorting alone does not explain that topology