A Fain and Houde (2004) (FGB only) B Ericson (2012) (5 genes) ‘Metaves’ Hoatzin (clades iii, v, vi, vii, and hoatzin) Hoatzin identical to Fain and Houde)
Oilbird Tropicbirds ‘Metaves’ (circumscription Potoos Mesites Frogmouths Grebes
Doves sensu Flamingos Nightjars Sunbittern Flamingos Sandgrouse
Tropicbirds Fain and Houde Doves Hummingbirds Nightjars Swifts Potoos Mesites Oilbird Owlet-nightjars Frogmouths Sunbittern Owlet-nightjars Sandgrouse Hummingbirds Grebes Swifts (all other Neoaves) (all other Neoaves) ‘Coronaves’ ‘Coronaves’
C Hackett et al. (2008) (19 genes) D Yuri et al. (2008) (indels from 19 genes)
Grebes ‘Metaves’ Flamingos Other ‘Coronaves’ Tropicbirds (clades iii, v, vi, and vii) (clades iii, v, vi, and hoatzin)
Sandgrouse Hoatzin ‘Metaves’ Mesites Doves sensu Doves Sandgrouse Sunbittern Mesites Hackett
Oilbird Tropicbirds sensu Potoos Sunbittern Frogmouths Oilbird
Nightjars Potoos Yuri et a Owlet-nightjars Frogmouths et a Hummingbirds l. Nightjars Swifts Owlet-nightjars l.
‘Coronaves’ Hummingbirds Swifts Most ‘Coronaves’ plus hoatzin sensu plus clade vii Fain and Houde
FIGURE S2. The EB2 noJAR J2-contradicting clade is similar to ‘Metaves.’ Various studies have recovered Metaves, a clade comprising most or all members of clades iii, v, vi, and vii as well as the hoatzin. All of those studies included FGB. Specifically, the studies that recovered Metaves were (A) Fain and Houde (2004) (partially dashed lineages indicate use of a partial oilbird sequence and absence of a potoo in this study); (B) Ericson et al. (2006) and Ericson (2012); (C) Hackett et al. (2008); and (D) Yuri et al. (2013). The Metaves-like clade in the Yuri et al. (2013) indel tree is nested within ‘Coronaves.’ The ‘J2-contradicting clade’ in the EB2 noJAR tree (E; next page) includes many ‘metavian’ taxa (clades v, vi, and vii). The basis for the strong signal in FGB that supports Metaves is unclear (Kimball et al. 2013); the simplest explanation is gene tree-species tree discordance. The EB2 noJAR and EB2 noJAR/noFGB trees are available in Nexus format as Supplementary File S9. E Early Bird II data (no Jarvis overlap) Otidiphaps nobilis 9 6 Treron vernans Columbina passerina (vi) * 7 9 Geotrygon montana
Columba livia ‘Metaves-like clade’ (contradicts J2) * Podiceps cristatus 9 4 Podiceps auritus J1 * Phoenicopterus chilensis (vii) Phoenicopterus ruber 3 7 * Monias benschi * Mesitornis unicolor 7 8 7 1 Pterocles namaqua (vi) Pterocles gutturalis * Syrrhaptes paradoxus * Steatornis caripensis Nyctibius bracteatus Nyctibius grandis * * Eurostopodus mystacalis Lyncornis macrotis 3 9 * Systellura longirostris * * Antrostomus carolinensis 5 4 Podargus strigoides Batrachostomus septimus (v) 1 9 * Aegotheles insignis 8 1 Aegotheles cristatus * Hemiprocne mystacea Streptoprocne zonaris * * Chaetura pelagica * Aerodramus vanikorensis * Colibri coruscans * Calypte anna * Phaethornis griseogularis * 8 6 Topaza pella Shorebirds Hoatzin 2 2 2 1 Bustards (clade iv)
7 6 Cuckoos (clade iv) Turacos (clade iv) 3 0 3 2 Gruiformes 2 8 Waterbirds (clade ii) Sunbittern + Kagu (clade iii) J3 8 6 Tropicbirds (clade iii) N 6 9 Landbirds (clade i)
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