Fig. 3

Topological discordance between phylogenies estimated using different methods. Most broadly, the different methods included concatenation, a summary MSC approach (ASTRAL) and the full MSC (StarBEAST2). We also performed analyses using different maximum likelihood implementations (RAxML, R; IQTREE, Q), partitioning (Q_P), and analyses that excluded third codon positions (Q₁₂) (see Additional file 2: Figure S1). In this matrix, the colour of each cell indicates the Robinson-Foulds distance between trees estimated using two different methods, or in the case of the StarBEAST2 trees, between one of the nine replicate analyses