Scatter plots from gene discordance analysis. The graphs show the relationships between PP (gene tree analysis [GTA]), BS (GTA), BS (concatenated analysis [CA]), polytomy test [PT] (GTA), PT (PA), gene concordance factor (gCF), site concordance factor (sCF), gene discordance factors (gDF1, gDF2), gene discordance factor (P stands for paraphyly) (gDFP) and site discordance factors (sDF1, sDF2). The strength and direction of correlations (r) between variables are described as follows: r = -1, perfect negative relationship; -1 < r ≤ -0.70, strong negative relationship; -0.70 < r ≤ -0.50, moderate negative relationship; -0.50 < r ≤ -0.30, weak negative relationship; -0.30 < r < 0.30, no relationship; 0.30≥ r < 0.50, weak positive relationship; 0.50 ≥ r < 0.70, moderate positive relationship; 0.70 ≥ r < 1, strong positive relationship; r = 1, perfect positive relationship.