Appendix S2 Empirical divergence dates and literature references for Fig. 5. Taxon Estimated age of diversification (Ma) Reference Remarks Sphenodon (tuatara) 0.008 Hay et al. (2010) Estimated divergence of tuatara populations, considered one species by Hay et al. (2010) Paulfreemania (midges) 4.15 Krosch et al. (2011) Median age inferred by BEAST Dinornithiformes (moas) 21 Haddrath & Baker (2012) Median age inferred by BEAST Apteryx (kiwis) 6.3 Haddrath & Baker (2012) Median age inferred by BEAST Acanthisitta (wrens)1 16 Worthy et al. (2010) Based on fossil data only Deinacrida (weta) 17 Trewick & Morgan-Richards (2005) Assumed strict molecular clock Cyclodina + Oligosoma (skinks) 18.3 Chapple et al. (2009) Median age inferred by BEAST Hoplodactylus (geckos) 24.4 Nielsen et al. (2011) Median age inferred by BEAST Eukieffieriella (midges) 26.27 Krosch et al. (2011) Median age inferred by BEAST Anzacladius (midges) 29.01 Krosch et al. (2011) Median age inferred by BEAST Pirara (midges) 31.29 Krosch et al. (2011) Median age inferred by BEAST Naonella (midges) 33.48 Krosch et al. (2011) Median age inferred by BEAST Leiopelma (frogs)2 48 Roelants et al. (2007) Age inferred by penalized likelihood Aoraki (harvestmen) 90 Giribet et al. (2012) Median age inferred by BEAST Rakaia (harvestmen) 91 Giribet et al. (2012) Median age inferred by BEAST 1 Acanthisitiid species driven extinct by humans are counted as extant. time estimate does not include species that went extinct in the Holocene. 3 Nestorinae parrots are not included here due to ambiguous divergence time calibration (Wright et al., 2008). 2 Divergence REFERENCES Chapple, D.G., Ritchie, P.A. & Daugherty, C.H. (2009) Origin, diversification, and systematics of the New Zealand skink fauna (Reptilia: Scincidae). Molecular Phylogenetics and Evolution, 52, 470–487. Giribet, G., Sharma, P.P., Benavides, L.R., Boyer, S.L., Clouse, R.M., de Bivort, B.L., Dimitrov, D., Kawauchi, G.Y., Murienne, J. & Schwendinger, P.J. (2012) Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement. Biological Journal of the Linnean Society, 105, 92–130. Haddrath, O., Baker, A.J. (2012) Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds. Proceedings of the Royal Society B: Biological Sciences, 279, 4617-4625. Hay, J.M., Sarre, S.D., Lambert, D.M., Allendorf, F.W., Daugherty, C.H. (2010) Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia). Conservtion Genetics, 11, 1063–1081. Krosch, M.N., Baker, A.M., Mather, P.B. & Cranston, P.S. (2011) Systematics and biogeography of the Gondwanan Orthocladiinae (Diptera: Chironomidae). Molecular Phylogenetics and Evolution, 59, 458–468. Roelants, K., Gower, D.J., Wilkinson, M., Loader, S.P., Guillaume, K., Moriau, L. & Bossuyt, F. (2007) Global patterns of diversification in the history of modern amphibians. Proceedings of the National Academy of Sciences USA, 104, 887–892. Trewick, S.A. & Morgan-Richards, M. (2005) After the deluge: mitochondrial DNA indicates Miocene radiation and Pliocene adaptation of tree and giant weta (Orthoptera: Anostostomatidae). Journal of Biogeography, 32, 295–309. Worthy, T.H., Hand, S.J., Nguyen, J.M.T., Tennyson, A.J.D., Worthy, J.P., Scofield, R.P., Boles, W.E., Archer, M. (2010) Biogeographical and phylogenetic implications of an early Miocene wren (Aves: Passeriformes: Acanthisittidae) from New Zealand. Journal of Vertebrate Paleontology, 30, 479–498. Wright, T.F., Schirtzinger, E.E., Matsumoto, T., Eberhard, J.R., Graves, G.R., Sanchez, J.J., Müller, H., Scharpegge, J. Chambers, G.K., Fleischer, R.C. (2008). A multilocus molecular phylogeny of the parrots (Psittaciformes): support for a Gondwanan origin during the Cretaceous. Molecular Biology and Evolution, 25, 2141-2156.