5.

(a) The phylogenetic reconstruction based on nucleotide UCE positions which had phylogenetic signal within in the top 20th percent of the UCE′s adjusted phylogenetic signal score for species divergences between 60-62MYA (deep filtered, left) and the phylogenetic reconstruction using all nucleotide positions (unfiltered, right). Bootstrap support values less than 100% are shown for each internal node. (b) Scatter plot of percent bootstrap support (BS) when the same clade is supported in the deep filtered UCE phylogeny and the unfiltered UCE phylogeny. The points are labeled with the same node labels as in Fig. 5a except for: (1) the label mul, which corresponds to the nodes A, B, C, E, I, K, L, N, O, AA, CC, FF, and II in Fig. 5(a); (2) the label Afro, which denotes the afroaves node H in the deep filtered UCE phylogeny and in the unfiltered UCE phylogeny; (3) the label Neo, which denotes the neoaves nodes EE in the deep filtered phylogeny and OO in the unfiltered UCE phylogeny; and (4) Pass, which denotes the Passerea node MM in Fig. 5(a).