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Published in final edited form as: Mol Phylogenet Evol. 2018 Apr 4;126:116–128. doi: 10.1016/j.ympev.2018.03.033

(a) The deep filtered phylogenetic reconstruction (left) and the ExaML-TENT phylogenetic reconstruction. 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 ExaML-TENT phylogeny. The points are labeled with the same node labels as in Fig. 6(a) except for: (1) the label muh, which corresponds to the nodes A, B, C, E, H, J, K, L, N, O, CC, and FF as in Fig. 6(a); (2) the label mul2, which corresponds to the nodes AAA and X in Fig. 6(a) (3) the label Neo, which denotes the neoaves node EE in the deep filtered and the ExaML-TENT phylogeny; and (5) Pass, which denotes the Passerea node MM in the deep filtered phylogeney and Z in the ExaML-TENT phylogeny in Fig. 6(a).

(a) The deep filtered phylogenetic reconstruction (left) and the ExaML-TENT phylogenetic reconstruction. 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 ExaML-TENT phylogeny. The points are labeled with the same node labels as in Fig. 6(a) except for: (1) the label muh, which corresponds to the nodes A, B, C, E, H, J, K, L, N, O, CC, and FF as in Fig. 6(a); (2) the label mul2, which corresponds to the nodes AAA and X in Fig. 6(a) (3) the label Neo, which denotes the neoaves node EE in the deep filtered and the ExaML-TENT phylogeny; and (5) Pass, which denotes the Passerea node MM in the deep filtered phylogeney and Z in the ExaML-TENT phylogeny in Fig. 6(a).