Summary of bootstrap percentages (BPs) from coalescent and concatenation analyses using different gene subsampling and rate partitions.

<p>(A) BPs from coalescent and concatenation analyses using different gene subsampling. The 305 nuclear genes were subsampled for four different gene size categories (i.e., 25, 47, 100, or 200 genes; 10 replicates each), and the 47 plastid genes were subsampled for 25 genes (10 replicates). Cells with hatching indicate that support for the placement of <i>Ginkgo biloba</i> from all replicates is below 80 BP; colored cells indicate relationships that received bootstrap support ≥80 BP from at least one replicate (pink = cycads plus <i>Ginkgo</i> as sister to all remaining extant gymnosperms, yellow = <i>Ginkgo</i> alone as sister to conifers and gnetophytes within extant gymnosperms; see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080870#pone-0080870-g001" target="_blank">Figure 1D</a>). (B) BPs from coalescent and concatenation analyses across different nucleotide rate partitions. Parsimony informative sites in concatenated matrices were sorted based on estimated evolutionary rates, and subsequently divided into two equal partitions. The index of substitution saturation (<i>I</i>_SS) was used to measure nucleotide substitution saturation for sites within each rate partition. The two critical <i>I</i>_SS values, i.e., <i>I</i>_SS.C1 and <i>I</i>_SS.C2, were estimated using an asymmetrical and symmetrical topology, respectively (for data including more than 32 species, only values estimated from 32 terminals are shown here).