<p>1 Appendix S1. Examples of Allopatric Speciation Driven by Glaciation of the Central Southern Alps of New Zealand. Shown are: species </p><p>2 and genetic markers used, timing of splits, number of geographic sites sampled, habitat type, and reference. mtDNA rate calibrations used (per </p><p>3 Ma since divergence): ††2.1% [1], †2.3% [2], *3.54% [3]. Gene marker abbreviations: CO, mitochondrial cytochrome oxidase; A, mitochondrial</p><p>4 ATPase; EF, elongation factor; ND, mitochondrial NADH dehydrogenase; CYB, mitochondrial cytochrome b; 12S, small mitochondrial </p><p>5 ribosomal RNA subunit; CR, mitochondrial control region; bfibint, beta-fibrinogen intron; H, histone cluster.</p><p>Species Markers Dating Si Habitat Refs</p><p> te</p><p> s Maoricicada, cicada COI, COII, A6–8 1.54–2.09 Ma 8 Scrub/grassland <1600 m [4]</p><p>7 Brachaspis, grasshopper COI 1.97 Ma* 9 Subalpine/alpine >1500 m [5] Megalapteryx, moa A/D COIII, ND3–5, CYB, A6–8, 12S 1.98 Ma 1 Subalpine scrub/grassland >900 m [6]</p><p>1 Kikihia, cicada II COI, COII, A6–8, EF–1 2 Ma 9 Scrub/grassland <1500 m [7] Xenicus, rock wren CYB, CR, bfibint7, microsatellites 2 Ma†† 2 Alpine >900 m [8]</p><p>1 Deinacrida, scree weta COI 2.08 Ma* 1 Alpine scree 1200–3600 m [9]</p><p>8 Halticoperla, stonefly COI, H3 2.09 Ma* 1 Alpine [10]</p><p>2 Vesicaperla, flightless stonefly COI, H3 2.2 Ma* 1 Alpine [10]</p><p>1 Paprides, grasshopper COI, 12S 2.2–2.85 9 Subalpine grassland [11] Ma*† Holcoperla, flightless stonefly COI, H3 2.48 Ma* 1 Alpine [10]</p><p>8 Apteryoperla, flightless stonefly COI, H3 2.51 Ma* 1 Alpine [10]</p><p>3 Cristaperla, stonefly COI, H3 2.57 Ma* 1 Alpine [10]</p><p>8 Alpinacris, grasshopper 12S 2.6 Ma† 5 Subalpine/alpine grassland [11] 6</p><p>7</p><p>2 8 References</p><p>9 1. Weir, J.T. and Schluter, D. (2008) Calibrating the avian molecular clock. Mol. Ecol. 17, 2321-2328</p><p>10 2. Brower, A.V.Z. (1994) Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from </p><p>11 patterns of mitochondrial DNA evolution. Proc. Natl. Acad. Sci. U.S.A. 91, 6491-6495</p><p>12 3. Papadopoulou, A., et al. (2010) Revisiting the insect mitochondrial molecular clock: the mid-Aegean Trench calibration. Mol. Biol. Evol.</p><p>13 27, 1659-1672</p><p>14 4. Hill, K.B.R., et al. (2009) Surviving glacial ages within the Biotic Gap: phylogeography of the New Zealand cicada Maoricicada </p><p>15 campbelli. J. Biogeogr. 36, 675-692</p><p>16 5. Trewick, S.A. (2001) Identity of an endangered grasshopper (Acrididae: Brachaspis): taxonomy, molecules and conservation. Conserv. </p><p>17 Genet. 2, 233-243</p><p>18 6. Bunce, M., et al. (2009) The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proc. Natl. Acad. </p><p>19 Sci. U.S.A. 106, 20646-20651</p><p>3 20 7. Marshall, D.C., et al. (2008) Steady Plio-Pleistocene diversification and a 2-million-year sympatry threshold in a New Zealand cicada. </p><p>21 Mol. Phylogenet. Evol. 48, 1054-1066</p><p>22 8. Weston, K.A. and Robertson, B.C. (2015) Population structure within an alpine archipelago: strong signature of past climate change in </p><p>23 the New Zealand rock wren (Xenicus gilviventris). Mol. Ecol. 24, 4778-4794</p><p>24 9. Trewick, S.A., et al. (2000) Phylogeographical pattern correlates with Pliocene mountain building in the alpine scree weta (Orthoptera, </p><p>25 Anostostomatidae). Mol. Ecol. 9, 657-666</p><p>26 10. McCulloch, G.A., et al. (2010) Onset of glaciation drove simultaneous vicariant isolation of alpine insects in New Zealand. Evolution 64,</p><p>27 2033-2043</p><p>28 11. Trewick, S.A. and Wallis, G.P. (2001) Bridging the "beech-gap": New Zealand invertebrate phylogeography implicates Pleistocene </p><p>29 glaciation and Pliocene isolation. Evolution 55, 2170-2180</p><p>30</p><p>4</p>