Fig. 6

Constrained analyses reveal support for alternative clades. a On the avian genomics dataset [33], we estimated ASTRAL-III trees with no constraints (right) using 2022 binned (super)gene trees. The tree did not include the Passerea vs. Columbea division that most other analyses of this dataset reveal. Constraining the ASTRAL tree to include Passerea as a clade resulted in a tree (left) with two new branches and 0.97 localPP support for Columbea. LocalPP support values below 1.0 are shown on branches (red: change in support across the two trees). b Similar to (a), constrained analyses are performed to find support for five other clades found in the TENT (†) and (in some cases) in MP-EST* (‡) but not found in the unconstrained analyses. For each clade, we show localPP support for branches that differ between the constrained and unconstrained trees (one to three branches change in constrained searches). We also show the reduction in the quartet score in the constrained analyses as an abosulte number and percentage