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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

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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 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) REFERENCES Ericson P.G.P. Evolution of terrestrial birds in three continents: biogeography and parallel radiations. J Biogeogr, 2012;39:813-824. Ericson P.G.P., Anderson C.L., Britton T., Elzanowski A., Johansson U.S., Kallersjo M., Ohlson J.I., Parsons T.J., Zuccon D., Mayr G. Diversification of Neoaves: integration of molecular sequence data and fossils. Biol Lett, 2006;2:543-547. Fain, M.G., Houde, P. Parallel radiations in the primary clades of birds. Evolution, 2004;58: 2558-2573. Hackett S.J., Kimball R.T., Reddy S., Bowie R.C.K., Braun E.L., Braun M.J., Chojnowski J.L., Cox W.A., Han K.L., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Sheldon F.H., Steadman D.W., Witt C.C., Yuri T. A phylogenomic study of birds reveals their evolutionary history. Science, 2008;320:1763-1768. Kimball R.T., Wang N., Heimer-McGinn V., Ferguson C., Braun E.L. Identifying localized biases in large datasets: A case study using the avian tree of life. Mol Phylogenet Evol, 2013;69:1021-1032. Yuri T., Kimball R.T., Harshman J., Bowie R.C.K., Braun M.J., Chojnowski J.L., Han K.L., Hackett S.J., Huddleston C.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Witt C.C., Braun E.L. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology (Basel), 2013;2:419-444. .
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