Figure 3

Results of the (a) RAxML and (b) STEAC analyses of all 1650 loci selected by our transcriptome mining (TM) analysis and the 415 anchored enriched (AHE) loci with taxa pruned the 10 ingroup and one outgroup taxa present in the TM data set. Numbers above the nodes in the RAxML tree indicate bootstrap proportions from 1000 pseudoreplicates. Clade support was identical between the TM and pruned AHE analyses, with the exception of the Lampropholis + Saproscincus clade that was supported by a bootstrap proportion of 100 and 96, respectively. We used PHYML maximum likelihood analyses to infer trees from 1000 bootstrap pseudoreplicates per locus. We used 1000 bootstrapped trees per locus (1,650,000 total trees) as input trees for the STEAC analysis, and numbers above or below the nodes indicate the proportion of times STEAC inferred that clade. Clade support was identical between the TM and pruned AHE analyses. Outgroup not shown.