Supporting information (Tables S1–S2, Supporting data S1; Fig S1): Granite boulders act as deep-time climate refugia: a Miocene divergent clade of rupicolous Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Mysore Plateau, India, with descriptions of three new species ISHAN AGARWAL, TEJAS THACKERAY, SAUNAK PAL & AKSHAY KHANDEKAR Table S1. Additional sequences used for divergence dating in this study. Museum abbreviations as follows: ABTC, Australian Biological Tissue Collection, South Australian Museum, Adelaide; ADS, Anslem de Silva field series; AMB, Aaron M. Bauer field series; AMS, Australian Museum; BPBM, Bernice P. Bishop Museum; BNHS ,Bombay Natural History Society, Mumbai; CAS, California Academy of Sciences; CD, Charles Daugherty field series; CES G (Karanth lab field series) and CES L (Kartik Shanker lab field series), Centre for Ecological Sciences, Bangalore; CHUNB, Coleção Herpetológica da Universidade de Brasília; CJS, Christopher J. Schneider field series; CUMZ, Chulalongkorn University Museum of Zoology; DB, Don Buden; DJH, D. James Harris; EBG, Eli B. Greenbaum field series; FG/MV, Frank Glaw and Miguel Vences; FGZC, Frank Glaw; FLMNH, Florida Museum of Natural History; FT, frozen tissue collection of Victoria University of Wellington; GVH, Gerald V Haagner; IEBR, Institute of Ecology and Biological Resources (Hanoi); IRSNB, Institute des Sciences Naturelles du Belgique, Brussels; ITB, Institute of Tropical Biology Collection of Zoology; JB, Jon Boone; JEM, John E. Measey; KU, University of Kansas Natural History Museum, Lawrence; LJAMM, Luciano J. Avila and Mariana Morando; LLG, L. Lee Grismer field series; LSHUC, La Sierra University Herpetological Collection, L. Lee Grismer; MCZ, Museum of Comparative Zoology, Harvard University; MTSN, Trento Museum of Natural Sciences; MV, Museum of Victoria; MVZ, Museum of Vertebrate Zoology, Berkeley; MZUSP, Museu de Zoologia da Universidade de São Paulo; NCBS ,National Centre for Biological Sciences, Bangalore; NJNUh, Nanjing Normal University, Jiangsu, China; NMZ, National Museum of Zimbabwe; PEM, Port Elizabeth Museum; PMNH, Pakistan Museum of Natural History; QM, Queensland Museum; RAH, Rod A. Hitchmough; RMB, Rafe M. Brown; ROM, Royal Ontario Museum; SAM, South Australian Museum; SC, Salvador Carranza; SYS, the Museum of Biology, Sun Yat-sen University (SYS), Guangzhou; TG, Tony Gamble; USNM, National Museum of Natural History, Smithsonian Institution; WBJ, W. Bryan Jennings; WDH, Wulf D. Haacke; YPM, Yale Peabody Museum, New Haven; ZCMV, Miguel Vences; ZMKU TM, Zoological Museum, Kasetsart University, Bangkok, Thailand; ZRC, Zoological Reference Collection, Raffles Museum.; ZSM, Zoologische Staatssammlung München. Species Tissue voucher Locality GenBank Accession Aeluroscalabotes felinus JB 16 Cameron Highlands, Malaysia JX041301 Afroedura loveridgei GVH 3969 Mozambique JX041303 Agamura persica FMNH 247474 Gwadar Division, Balochistan, Pakistan JX440515 Alsophylax pipiens CAS 238804 Mongolia, Khovd, 1km N of Bulgam KC151973 Aprasia parapulchella MVD66569 Bendigo Whipstick, Victoria, Australia GU459941 Aristelliger praesignis USNM 337563 Kingston, St. Andrew Parish, Jamaica JX041312 Asaccus platyrhynchus CAS 227605 Wilayat Nazwa, Oman JX041313 Calodactylodes illingworthorum AMB7415 Sri Lanka, Pitakumbura JX041318 Carphodactylus laevis AMS 143258 Lamb Range, Queensland, Australia GU459943 Chondrodactylus fitzsimonsi MCZ R185712 Namibia, Gai-as spring JN393945 Christinus marmoratus AMS 135338 Wirralie, Ladysmith, New South Wales, JX041322 Australia Cnemaspis africana CAS 168872 Amani, Tanga, Tanzania JX041323 Cnemaspis dickersonae MTSN 8604 Uzungwa Scarp, Tanzania JX041324 Cnemaspis kendalii LSHUC6562 Selangor, Malaysia JX041326 Cnemaspis limi LSHUC 6267 Pulau Tioman, Malaysia JX041327 Cnemaspis siamensis USNM 594370 Myanmar, Tanintharyi Region, MN104945 Coleodactylus cf. brachystoma CHUNB 43901 São Domingos, Goiás, Brazil JX041331 Coleonyx brevis TG 00194 Hudspeth County, Texas, USA JX041333 Colopus wahlbergii NMZ 16974 Kalamba Station, Kazungula Dist., JX041337 Zambia Crenadactylus ocellatus AMS R162089 Trephina Gorge, Northern Territory, JX024364 Australia Cyrtodactylus albofasciatus CES09/1109 Karnataka, Chikmagalur District, KM878626 Kudremukh Cyrtodactylus angularis FMNH 265815 Thailand, Sa Kaeo, Muang Sa Kaeo JX440523 Cyrtodactylus ayeyarwadyensis CAS 216459 Myanmar, Rakhine State, Than Dawe JX440526 District Cyrtodactylus battalensis PMNH 2301 Pakistan, NWFP, Battagram City KC151983 Cyrtodactylus collegalensis CES09/1444 Karnataka, Chamarajanagar District, KM878627 base of MM Hills Cyrtodactylus deccanensis CES09/1243 Maharashtra, Thane District, Malshej KM878614 Ghat Cyrtodactylus jeyporensis CES09/1356 Andhra Pradesh, Visakhapatnam KM878616 District, Arakku Valley Cyrtodactylus nebulosus CES09/1205 Orissa, Koraput District, Gupteswar KM878621 Cyrtodactylus triedra AdS 35 Sri Lanka, Yakkunehela JX440522 Cyrtodactylus varadgirii CES09/1381 Gujarat, Navsari District, Chikli KM878612 Cyrtopodion' kohsulaimanai PMNH 2388 Sakhi Sarwar, Pakistan KC151965 Delma butleri SAM R36144 Coonbah, New South Wales, Australia AY134584 Diplodactylus tesselatus AMS 143855 Stonehenge area, Queensland, JQ173631 Australia Dixonius vietnamensis FMNH 263003 Cambodia, Mondolkiri Province, Keo EU054297 Seima district Ebenavia inunguis ZCMV 2099 Cambonia Marojejy, Madagascar JX041348 Elasmodactylus tetensis PEM 5551 Niassa Game Reserve, Mozambique JX041349 Eublepharis macularius TG00081 Pakistan JX041350 Euleptes europaea No ID Liguria, Italy JN393941 Garthia gaudichaudii SC 1 Chile JX041351 Geckolepis maculata FGZC 463 Montagne d'Ambre, Madagascar EU054235 Gehyra dubia AMS 152245 Daydawn, New South Wales, Australia JN393911 Gehyra mutilata AMS 139934 Australia, Western Australia, El Questro JN019081 Gehyra oceanica USNM 559790 Palau: Ngkesill Island JN393924 Gehyra robusta AMS NR2429 Australia: Queensland, 17.7KM N JN393928 Barkly Hwy via Kajabbi Rd Gehyra variegata AMS136026 Australia: Northern Territory, vic. 8-mile JN393916 bore Gehyra xenopus AMS140173 Australia: Western Australia, Mitchell JN393932 Plateau Gekko badenii JB 13 Vietnam JN019065 Gekko chinensis LSHUC 4209 Wuzhi Shan, Hainan Id., China JN019058 Gekko monarchus LLG 4824 West Malaysia, Selangor, Kepong, JN019078 FRIM Gekko smithi LLG 7648 West Malaysia, Johor, Endau-Rompin, JN019056 Peta Gekko vittatus AMS 138865 Vanuatu, Gaua Island JN019072 Goggia lineata AMB4762 Park, Northern Cape Prov., South JX041353 Africa Hemidactylus angulatus EBG 746 Guinea, Daniah village at Koulete River HM559620 Hemidactylus mabouia AMB 8301 South Africa, Limpopo Prov., nr. HM559638 Huntleigh Hemidactylus macropholis CAS 227520 Bari Region, JX041369 Puntland State, Somalia Hemidactylus prashadi JB 30 India (captive specimen) HM559644 Hemiphyllodactylus arakuensis BNHS 2275 Araku, Visakhapatnam District, Andhra MK570109 Pradesh Hemiphyllodactylus dushanensis n/a Guizhou, China FJ971016 Hemiphyllodactylus harterti LSUHC 10384 Bukit Larut, Malaysia KF219761 Hemiphyllodactylus jnana CES G174 India, Karnataka, Bangalore, IISc MK570112 Holodactylus africanus CAS 198845 Kajiado District, Kenya JX041372 Homonota darwinii LJAMM 4601 Puerto Deseado, Santa Cruz, Argentina JX041373 Homopholis walbergii AMB 8410 n/a EU054244 Hoplodactylus duvaucelii FT(VUW) 174 Mercury Island, New Caledonia GU459843 Hoplodactylus pacificus CD853 Pupuha, New Caledonia GU459787 Kolekanos plumicaudus WDH 1 Parque Nacional do Iona, Cunene JX041304 Prov., Angola Lepidodactylus lugubris ZRC 24847 Singapore JN393944 Lepidodactylus orientalis BPBM 19794 Papua New Guinea: Sudest Island JN019080 Lialis jicari n/a Australia AY369025 Lucasium stenodactylum AMS 139897 Western Australia, Australia JQ173630 Luperosaurus cumingii RMB 3546 Philippines, Cumiagi JX515623 Lygodactylus miops ZSM 116/2004 Andohahela, Madagascar KM034118 Matoatoa brevipes FG/MV Tulear area, Madagascar EF490777 2002.2237 Mediodactylus brachykolon PMNH 2165 Pakistan, NWFP, Battagram City KC151981 Mediodactylus russowii JEM 863 Kazakhstan, Ili River JX440517 Nactus vankampeni BPBM 23365 Papua New Guinea, East Sepik EU054295 Province, Wewak Naultinus elegans No ID Whangarei, New Zealand GU459757 Nephrurus levis AMS 140561 Western Australia, Australia AY369018 Oedodera marmorata CAS 230936 Paagoumène, New Caledonia GU459947 Oedura marmorata AMS 143861 Australia, Queensland GU459951 Pachydactylus gaiasensis AMB 7596 Gai-As, Namibia JX041391 Paradelma orientalis QM J56089 20 km N Capella, Queensland, AY134605 Australia Paragehyra gabriellae FGZC 2366 Grotte Ampasy, Madagascar JX041399 Paroedura picta FG/MV 2002.B1 Berenty, Madagascar EF536197 Perochirus ateles DB Dmale Dehpelhi Id., Pohnpei, Federated JN393938 States of Micronesia Phelsuma astriata - - EU423286 Phelsuma borbonica JB 95 Réunion JX041400 Phelsuma inexpectata JB 56 Réunion (captive) JN393939 Phelsuma ornata - - EU423282 Phelsuma rosagularis n/a Mauritius EU423292 Phyllodactylus xanti ROM 38490 Mexico, Baja California Sur JN393940 Phyllopezus pollicaris MZUSP 92491 das Confusões, Piauí, Brazil JX041417 Pseudogekko smaragdina KU 303995 Philippines: Quezon JX515626 Pseudogonatodes guianensis KU 222142 Loreto, Peru JX041421 Pseudothecadactylus lindneri MVZ 99544 Kakadu Natl. Park, NT, Australia GU459946 Ptyodactylus guttatus TG 00072 Egypt (captive) JX041426 Pygopus lepidopodus WBJ 1206 Western Australia, Australia AY134603 Pygopus nigriceps MVZ 197233 Australia, Northern Territory JX440518 Quedenfeldtia trachyblepharus MVZ 178121 Oukaimeden,