Suppl. Table S1 Source information for genome assemblies used in phylogenomic analyses Common name Scientific name Reference Little bush moa Anomalopteryx didiformis 1 North Island brown kiwi Apteryx mantelli 2 Okarito brown kiwi Apteryx rowi 3 Great spotted kiwi Apteryx haastii 3 Little spotted kiwi Apteryx owenii 3 Emu Dromaius novaehollandiae 3 Southern cassowary Casuarius casuarius 3 Greater rhea Rhea americana 3 Lesser rhea Rhea pennata 3 Chilean tinamou Nothoprocta perdicaria 3 Elegant crested tinamou Eudromia elegans 3 Thicket tinamou Crypturellus cinnamomeus 3 White -throated tinamou Tinamus guttatus 4 Ostrich Struthio camelus 4 Chicken (galGal4) Gallus gallus 5 [1] Cloutier, A., Sackton, T.B., Grayson, P., Edwards, S.V., Baker, A.J. 2018. First nuclear genome assembly of an extinct moa species, the little bush moa ( Anomalopteryx didiformis ). bioRxiv doi: https://doi.org/10.1101/262816. [2] Le Duc, D., Renaud, G., Krishnan, A. 2015. Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biol. 16:147. [3] Sackton, T.B., Grayson, P., Cloutier, A., Hu, Z., Liu, J., Wheeler, N., Gardner, P., Clarke, J., Baker, A.J., Clamp, M., Edwards, S.V. 2018. Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds. bioRxiv doi: https://doi.org/10.1101/262584. [4] Zhang, G., Li, B., Li, C., Gilbert, M.T.P., Jarvis, E.D., Wang, J. 2014. Comparative genomic data of the Avian Phylogenomics Project. GigaScience 3:26. [5] International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695716. Suppl. Table S2 Source information and attributions for images used in Fig. 4 Page URL Attribution Great spotted kiwi https://commons.wikimedia.org/wiki/File% John Gerrard Keulemans [Public domain], 3AApteryxHaastiiKeulemans.jpg via Wikimedia Commons Little spotted kiwi https://commons.wikimedia.org/wiki/File% By G.D. Rowley [Public domain], via 3AApteryx_owenii_0.jpg Wikimedia Commons Emu https://commons.wikimedia.org/wiki/File% GFDL [CC BY -SA 3.0 3AEmu_RWD2_white_background.jpg (http://creativecommons.org/licenses/by- sa/3.0)], via Wikimedia Commons Southern cassowary https://commons.wikimedia.org/wiki/File% By Kirby, W. F.; Schuber t, Gotthilf Heinrich 3ANatural_history_of_the_animal_kingdom von; Society for Promoting Christian _for_the_use_of_young_people_(Plate_XXI Knowledge (Great Britain). [CC BY 2.0 V)_(5974393563).jpg (http://creativecommons.org/licenses/by/2 .0) or Public domain], via Wikimedia Commons Greater rhea https://commons.wikimedia.org/wiki/File% By Chubb, Charles.; Grönvold, Henrik; 3AThe_birds_of_South_America_(Pl._1)_(7 Knatchbull-Hugessen, Wyndham 822907530).jpg Wentworth; Swann, H. Kirke [CC BY 2.0 (http://creativecommons.org/licenses/by/2 .0) or Public domain], via Wikimedia Commons Chilean tinamou https://commons.wikimedia.org/wiki/File% John Gerrard Keulemans [Public domain], 3ANothoproctaCoquimbicaKeulemans.jpg via Wikimedia Commons Thicket tinamou https://commons.wikimedia.org/wiki/File% John Gerrard Keulemans [Public domain], 3ACrypturellus_cinnamomeus_mexicanus_ via Wikimedia Commons 1902.jpg Ostrich https://commons.wikimedia.org/wiki/File% By Kirby, W. F.; Schubert, Gotthilf Heinrich 3ANatural_history_of_the_animal_kingdom von; Society for Promoting Christian _for_the_use_of_young_people_(Plate_XXI Knowledge (Great Britain). [CC BY 2.0 V)_(5974393563).jpg (http://creativecommons.org/licenses/by/2 .0) or Public domain], via Wikimedia Commons .