Simulation setup D. 61-taxon setup used for simulation of nucleotide and amino acid gene partitions. Alignment lengths of single gene partitions were set to 500, 1000, 1500, 2000, and 2500 character state positions. To simulate different substitution rates, internal and terminal branches were stepwise increased for each gene partition length (highlighted red), ranging from 0.1 to 1.3 (B L 2 = 0.1,0.5,0.9,1.3). Internal branches in close vicinity to elongated branches are kept very short (B L 1 = 0.01). All remaining branches are kept equally long (R B = 0.1).