Figure 2 in Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)

Figure 2. Description of hypothesis-testing procedures. Models were constructed in MESQUITE v. 2.74 and simulations of 1000 gene trees were generated for each of the 13 loci for each of the eight models (step 1). We then compared the simulated trees for each locus against the corresponding model in order to obtain an approximation of a probability distribution of expected deep coalescence events (step 2). Finally, we counted the number of deep coalescences of the real gene tree within the model and obtained the probability of observing that value given the model (step 3). If the empirical data fell outside the 95% confidence interval, then the hypothesized number of deep coalescence events for that gene tree (real data) is not expected under the specified model, thus rejecting that hypothesis.