A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data
Figure 5
Partitioned RAD analysis: loci favoring or disfavoring globally suboptimal topologies.
Each plus sign represents one of 200 phylogenetic trees in which the topology has been modified from the globally optimal tree using 1 or 2 steps of nearest neighbor interchange (NNI). The red filled circle indicates the globally optimal tree. Loci were included in this analysis only if the total range in log-likelihood across all trees was 4.0 or more and at least 20 unique phylogenies remained after pruning taxa not present in the locus. Each locus was counted as favoring trees that fell within 2 log-likelihood points of the best-supported tree for that locus, and disfavoring trees that fell within 2 log-likelihood points of the most poorly supported tree for that locus. A. All 201 trees, with y-axis indicating number of loci favoring each tree. B. Only trees supported at log-likelihood > -1.35E06, with y-axis indicating number of loci favoring each tree; dashed lines enclose the 95% prediction interval. C. All 201 trees, with y-axis indicating number of loci disfavoring each tree.