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Figure 1 | BMC Evolutionary Biology

Figure 1

From: Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms

Figure 1

Schematic of the tree topology used when simulating DNA sequence triplets for power analyses. The program used to simulate DNA sequences (Seq-Gen) continues to add nucleotide changes until threshold divergence values have been reached. These threshold divergence values were obtained by averaging the estimated sets of branch lengths from actual ITS sequences for 16 annual/perennial/outgroup comparisons (Table 1). These averaged values are given in Phylip format in Table 2. The threshold divergence values for the perennial-like taxon (DIA-perennial) and the outgroup-like taxon (DR-outgroup, DR-IA) were kept constant for each outgroup (closer and further) and each set of nucleotide substitution parameters (ITS1-like, ITS2-like and Combined-ITS-like). To model rate heterogeneity, the threshold divergence value of the annual-like taxon (DIA-annual) for each set of replicate simulations was determined by multiplying the perennial-like taxon divergence threshold (DIA-perennial) by1.5 to 5 in steps of 0.5.

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