Supporting information

Gamble et al.

“Coming to America: Multiple Origins of New World Geckos”

Figure Legends

Supplementary Figure 1. Maximum likelihood tree of gekkotan taxa from the

RAxML analysis. Black circles indicate nodes with bootstrap support > 70.

Supplementary Figure 2. Results of fossil cross-validation showing the effect of removing individual calibrations on the difference between fossil age and estimated molecular age. Dark circles are calibrations used in the final analyses. Calibrations are numbered as in the supplementary text. Calibration 8 from the text is not shown as it was used in all cross-validation analyses.

Supplementary Figure 3. A. Time-calibrated phylogeny of geckos based on the

Bayesian uncorrelated relaxed clock analyses of the concatenated data conducted in

BEAST. Red node bars indicate 95% credibility intervals of the posterior divergence time estimates. Calibration nodes are colored green. B. Joint prior divergence time estimates for the Bayesian tree topology. Blue node bars indicate 95% credibility intervals. Calibration nodes are colored green.

Supplementary Figure 4. Ancestral area reconstruction using parsimony and distributions are coded as binary characters.

– 1 – Supplementary Figure 5. Ancestral area reconstruction using maximum likelihood with distributions coded as a binary character.

Supplementary Figure 6. Ancestral area reconstruction using maximum likelihood with distributions coded as one of five biogeographic regions.

Supplementary Figure 7. The number of biogeographical transitions between the Old

World and New World calculated for 5000 Bayesian trees using parsimony.

Distributions are coded as binary characters. Old World to New World transitions are shown in black. New World to Old World transition shown in gray.

– 2 – Supplemetary Table 1. Details of material examined. Family names abbreviated: E, Eublepharidae, D, Diplodactylidae, C, Carphodactylidae, Py,

Pygopodidae, S, Sphaerodactylidae, Ph, Phyllodactylidae, and G, Gekkonidae. Localities marked by an asterisk (*) reflect the collecting locality of sequences new to this study only and not to sequences gathered for that species from Genbank. Sequences for Anolis carolinensis were assembled from multiple, aligned contigs from the Anolis Genome Sequencing Project. We used the following abbreviations: AMB, Aaron M.

Bauer; AMCC, Ambrose Monell Cryo Collection, American Museum of Natural History; AMS, Australian Museum, Sydney; BPN, Brice P.

Noonan; CAS, California Academy of Sciences; CHUNB, Coleção Herpetológica da Universidade de Brasília; ENS, Eric N. Smith; FG/MV,

Frank Glaw and Miguel Vences; FGZC, Frank Glaw; FK, Fred Kraus; FLMNH, Florida Museum of Natural History; JAC, Jonathan Campbell;

JB, Jon Boone; JBLSC, Anolis Genome Sequencing Project; JFBM, James Ford Bell Museum of Natural History; DJH, D. James Harris; JEM,

John E. Measey; JS, Jay Sommers; JV, Jens Vindum; KU, University of Kansas Museum of Natural History; LJAMM, Luciano J. Avila and

Mariana Morando; LLG, L. Lee Grismer; LSUMZ, Louisiana State University Museum of Zoology; MF, Mike Forstner; MHNSM, Museo de

Historia Natural, Universidad Nacional Mayor de San Marcos; MVZ, Museum of Vertebrate Zoology, Berkeley; MZUSP, Universidade de São

Paulo, Museu de Zoologia; QM, Queensland Museum; ROM, Royal Ontario Museum; SAM, South Australian Museum; SC, Salvador Carranza;

TG, Tony Gamble; WBJ, W. Bryan Jennings; UNIBAN, Universidade Bandeirantes de São Paulo; USNM, National Museum of Natural

History, Smithsonian Institution; YPM, Yale Peabody Museum; ZCMV, Miguel Vences; ZFMK, Zoologisches Forschunginstitut und Museum

Alexander Koenig.

– 3 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID CHUNB – Amphisbaena alba Distrito Federal, Brasil* AY662619 DQ119633 AY444016 HQ426422 HQ426249 38770 – Anolis carolinensis JBLSC1 South Carolina, USA n/a n/a n/a n/a n/a – Aspidoscelis tigris TG 00069 Maricopa County, Arizona, USA* AY662620 HQ426512 AF039481 HQ426423 HQ426250 ROM – Dibamus bouretti Quang Thanh, Cao Bang, Vietnam* AY662645 HQ426513 AY662574 HQ426424 HQ426251 36056 – Elgaria kingii TG 00065 Navajo County, Arizona, USA* AY662603 HQ426514 AF039479 HQ426425 HQ426252 – Heloderma suspectum TG 00068 Arizona, USA* AY662606 DQ119635 AY662566 HQ426427 HQ426254 – Plestiodon inexpectatus TG 00792 Florida, USA* AY662632 DQ119628 AY217888 HQ426426 HQ426253 – Podarcis sicula TG 00124 Topeka, Kansas, USA* EF632239 DQ119630 EF679329 HQ426428 HQ426255 Ramphotyphlops – No ID Minneapolis, Minnesota, USA* AY662612 HQ426515 AF544717 HQ426429 HQ426256 braminus FLMNH – Rhineura floridana Alachua County, Florida, USA* AY662618 DQ119631 AY487347 EF534899 EU29371 141814 – Sphenodon punctatus No ID New Zealand* AY662576 HQ426516 AF039483 HQ426430 HQ426257 JFBM – Tiliqua rugosa New South Wales, Australia EF534815 EF534983 EF534941 EF534898 EF534856 13685 Los Angeles County, California, – Xantusia vigilis TG 00121 AY662642 DQ119626 AF148703 HQ426431 HQ426258 USA* AMS C Carphodactylus laevis Queensland, Australia EF534781 EF534947 EF534905 EF534862 EF534821 143258 C Nephrurus milii AMB 499 Western Australia, Australia EF534780 EF534946 EF534904 EF534861 EF534820 C Phyllurus platurus AMB 42 Sydney, NSW, Australia HQ426314 HQ426488 HQ426570 HQ426397 HQ426226 D Bavayia cyclura AMB 7683 New Caledonia HQ426264 HQ426437 HQ426521 HQ426344 HQ426176 Diplodactylus AMS D Sturt Natl. Park, NSW, Australia HQ426278 HQ426451 HQ426533 HQ426358 HQ426189 conspicillatus 158426 58 km S Alice Springs, NT, D Lucasium damaeum AMB 54 HQ426279 HQ426452 HQ426534 HQ426359 HQ426190 Australia AMS D Oedura marmorata Queensland, Australia EF534779 EF534945 EF534903 EF534860 EF534819 143861 Pseudothecadactylus D AMB 84 Kakadu Natl. Park, NT, Australia HQ426318 HQ426492 HQ426573 HQ426401 HQ426230 lindneri

– 4 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID D Rhacodactylus ciliatus TG 00080 New Caledonia – EF534944 EF534902 EF534859 – AMS D Rhacodactylus ciliatus Rivière Bleue, New Caledonia EF534778 – – – EF534818 146595 Aeleuroscalabotes E JB 16 Cameron Highlands, Malaysia HQ426259 HQ426432 HQ426517 HQ426338 HQ426171 felinus E Coleonyx brevis TG 00194 Hudspeth County, Texas, USA HQ426271 HQ426444 HQ426528 HQ426351 HQ426182 E Coleonyx mitratus TG 00075 unknown HQ426272 HQ426445 HQ426529 HQ426352 HQ426183 CAS E Coleonyx variegatus California, USA EF534777 EF534943 EF534901 EF534858 EF534817 205334 E Eublepharis macularius TG 00081 Pakistan – EF534942 EF534900 EF534857 – E Eublepharis macularius JS 2 Pakistan EF534776 – – – EF534816 JFBM E Goniurosaurus araneus Vietnam HQ426286 HQ426455 HQ426537 HQ426362 HQ426197 15830 E Goniurosaurus luii TG 00795 China HQ426287 HQ426456 HQ426538 HQ426363 HQ426198 Hemitheconyx E TG 00180 unknown HQ426294 HQ426468 HQ426552 HQ426377 HQ426205 caudicinctus E Hemitheconyx taylori JB 12 Somalia HQ426295 HQ426469 HQ426553 HQ426378 HQ426206 CAS E Holodactylus africanus Kajiado District, Kenya HQ426296 HQ426470 HQ426554 HQ426379 HQ426207 198845 Chondrodactylus G JV1850 30 km N Swakopmund, Namibia EU293645 EU293735 EU293690 EU293667 EU293712 bibronii G Cnemaspis limi LLG 6267 Pulau Tioman, Malaysia EF534809 EF534977 EF534935 EF534892 EF534851 Cyrtodactylus G FK 11689 West Sepik, Papua New Guinea HQ426274 HQ426447 HQ426531 HQ426354 HQ426185 novaeguinea G Cyrtopodion scabrum TG 00109 Egypt HQ426275 HQ426448 HQ426532 HQ426355 HQ426186 ZCMV G Ebenavia inunguis Marojejy, Madagascar HQ426280 HQ426453 HQ426535 HQ426360 HQ426191 2099 G Gekko gecko No ID unknown EF534813 – – – EF534854 G Gekko gecko TG 00079 Indonesia – EF534981 EF534939 EF534896 – MVZ G Hemidactylus angulatus Togo Hills, Nkwanta, Ghana EU268306 – HQ426540 HQ426365 EU268336 245438

– 5 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID Hemidactylus MZUSP Parque Nacional da Serra das G EU268290 HQ426439 HQ426523 HQ426346 EU268320 brasilianus 92493 Confusões, Piauí, Brazil Hemidactylus FMNH G Punjab Province, Pakistan EU268294 HQ426458 HQ426541 HQ426366 EU268324 flavivirdus 245515 G Hemidactylus frenatus TG 00088 Indonesia – EF534982 EF534940 EF534897 – G Hemidactylus frenatus AMB 7411 Pidenipitiya, Sri Lanka EF534814 – – – EF534855 CAS G Hemidactylus greefi Praia da Mutamba, Sao Tome EU268308 HQ426459 HQ426542 HQ426367 EU268338 219044 G Hemidactylus haitianus AMB 4189 Puerto Rico HM559700 – HQ426543 HQ426368 HM559667 Hemidactylus G TG 00568 Pakistan HM559703 HQ426506 HQ426587 HQ426416 HM559670 imbricatus Hemidactylus CAS G Lagoa Azul, Sao Tome HQ426289 HQ426460 HQ426544 HQ426369 HQ426200 longicephalus 218939 CHUNB G Hemidactylus mabouia Caseara, Tocantins, Brazil HQ426290 HQ426461 HQ426545 HQ426370 HQ426201 45337 G Hemidactylus mabouia JEM 1864 Wundanyi, Kenya HQ426291 HQ426462 HQ426546 HQ426371 HQ426202 Hemidactylus CAS Bari Region, Puntland State, G HQ426292 HQ426463 HQ426547 HQ426372 HQ426203 macropholis 227520 Somalia Hemidactylus LSUMZ G Roraima, Brazil EU268307 HQ426464 HQ426548 HQ426373 EU268337 palaichthus H–12421 JFBM G Hemidactylus platyurus unknown HQ426273 HQ426446 HQ426530 HQ426353 HQ426184 15815 FMNH Makran District, Baluchistan G Hemidactylus robustus EU054271 HQ426465 HQ426549 HQ426374 EU054255 245519 Province, Pakistan G Hemidactylus triedrus JB 09 India HM559715 HQ426466 HQ426550 HQ426375 HM559682 Gainesville, Alachua County, G Hemidactylus turcicus TG 00567 HQ426293 HQ426467 HQ426551 HQ426376 HQ426204 Florida, USA G Lepidodactylus lugubris AMB 4111 Kirimati, Kiribati EF534812 EF534980 EF534938 EF534895 EF534853 63.5 km W Kamanjab, Kunene G Lygodactylus bradfieldi AMB 7628 HQ426301 HQ426474 HQ426558 HQ426383 HQ426212 Region, Namibia G Lygodactylus klugei No ID Santo Inácio, Bahia, Brazil HQ426298 HQ426471 HQ426555 HQ426380 HQ426209

– 6 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID G Lygodactylus miops FGZC 205 Andohahela, Madagascar HQ426299 HQ426472 HQ426556 HQ426381 HQ426210 FG/MV G Lygodactylus miribilis Madagascar HQ426300 HQ426473 HQ426557 HQ426382 HQ426211 2000.B3 FG/MV G Lygodactylus tolampyae Ankarafantsika, Madagascar HQ426302 HQ426475 HQ426559 HQ426384 HQ426213 2001.C14 G Narudasia festiva AMB 3243 Narudas, Namibia EF534808 EF534976 EF534934 EF534891 EF534850 Pachydactylus Farm Celine, Limpopo Prov., South G AMB 8311 EU293646 – – – EU293713 punctatus Africa Pachydactylus Farm Celine, Limpopo Prov., South G AMB 8312 – EU293736 EU293691 EU293668 – punctatus Africa JFBM G Paroedura masobe Madagascar EF536145 HQ426478 HQ426560 HQ426387 EF536169 15832 FG/MV G Paroedura picta Berenty, Madagascar EF536149 EU293737 EU293692 EU293669 EF536173 2002.B1 G Phelsuma borbonica JB 95 Reunion HQ426305 HQ426479 HQ426561 HQ426388 HQ426216 Phelsuma FG/MV G Manongarivo, Madagascar EF534811 EF534979 EF534937 EF534894 AB081507 madagascariensis 2002.797 G Phelsuma modesta FGZC 56 Ambovombe, Madagascar HQ426307 HQ426481 HQ426563 HQ426390 HQ426218 22 km E Sendelingsdrif, G Phelsuma ocellata AMB 3860 Richtersveld National Park, HQ426308 HQ426482 HQ426564 HQ426391 HQ426219 Northern Cape, South Africa G Phelsuma rosagularis JB 109 Mauritius HQ426306 HQ426480 HQ426562 HQ426389 HQ426217 CAS G Rhoptropus boultoni Twyfelfontein, Namibia EF534810 EF534978 EF534936 EF534893 EF534852 214713 FG/MV G Uroplatus henkeli Nosy Be, Madagascar EF490743 – – – EF490716 2000.C1 JFBM G Uroplatus henkeli Madagascar – HQ426510 HQ426591 HQ426420 – 15833 FG/MV G Uroplatus phantasticus Ranomafana, Madagascar EF490746 HQ426511 HQ426592 HQ426421 EF490719 2002.64

– 7 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID CAS Ph Asaccus platyrhynchus Wilayat Nazwa, Oman EU293625 EU293715 EU293670 EU293647 EU293693 227605 Ph Asaccus sp. JB 15 Mirbat, Oman EU293626 EU293716 EU293671 EU293648 EU293694 CHUNB Ph Bogertia lutzae Mata de São João, Bahia, Brazil HQ426265 HQ426438 HQ426522 HQ426345 HQ426177 50462 Ph Garthia gaudichaudii SC 1 Chile HQ426281 HQ426454 HQ426536 HQ426361 HQ426192 CHUNB Ph Gymnodactylus amarali Cocalzinho, Goiás, Brazil HQ426288 HQ426457 HQ426539 HQ426364 HQ426199 38646 Ph Haemodracon riebeckii JB 11 Socotra Island, Yemen EU293627 EU293717 EU293672 EU293649 EU293695 LJAMM Puerto Deseado, Santa Cruz, Ph Homonota darwinii EU293628 EU293718 EU293673 EU293650 EU293696 4601 Argentina Ph Homonota fasciata TG 00085 Paraguay EU293629 EU293719 EU293674 EU293651 EU293697 AMCC Ph Phyllodactylus boardi Oaxaca, Mexico HQ426309 HQ426483 HQ426565 HQ426392 HQ426220 118242 Phyllodactylus ROM Isla Santa Catalina, Baja California Ph EU293631 EU293721 EU293676 EU293653 EU293699 bugastrolepis 38489 Sur, Mexico Phyllodactylus Ph JAC 21928 Guerrero, Mexico HQ426310 HQ426484 HQ426566 HQ426393 HQ426221 delcampoi Phyllodactylus ROM La Paz, Baja California Sur, Ph HQ426311 HQ426485 HQ426567 HQ426394 HQ426222 nocticolus 39005 Mexico Ph Phyllodactylus reissii JB 39 Peru EU293632 EU293722 EU293677 EU293654 EU293700 Phyllodactylus PN El Imposible, Ahuachapán, El Ph KU 289758 EU293630 EU293720 EU293675 EU293652 EU293698 tuberculosus Salvador ROM La Paz, Baja California Sur, Ph Phyllodactylus unctus HQ426312 HQ426486 HQ426568 HQ426395 HQ426223 39002 Mexico ROM Ph Phyllodactylus xanti Baja California Sur, Mexico EF534807 EF534975 EF534933 EF534890 EF534849 38490 Phyllopezus ZFMK Ph Balsas, Amazonas, Peru EU293633 EU293723 EU293678 EU293655 EU293701 maranjonensis 84995

– 8 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID Phyllopezus pollicaris CHUNB Ph São Domingos, Goiás, Brazil HQ426313 HQ426487 HQ426569 HQ426396 HQ426224 pollicaris 43850 Phyllopezus pollicaris MZUSP Parque Nacional da Serra das Ph EU293635 EU293725 EU293680 EU293657 EU293702 pollicaris 92491 Confusões, Piauí, Brazil Phyllopezus pollicaris Ph TG 00105 Paraguay – EU293724 EU293679 EU293656 HQ426225 przewalskii Phyllopezus pollicaris YPM Ph Paraguay EU293634 – – – – przewalskii 13683 Ph Ptyodactylus guttatus TG 00072 Egypt EU293636 EU293726 EU293681 EU293658 EU293703 Ptyodactylus YPM Ph Egypt EU293637 EU293727 EU293682 EU293659 EU293704 hasselquistii 13609 MVZ 13 km E of Pilon, Granma Ph Tarentola americana HQ426332 HQ426503 HQ426584 HQ426413 HQ426243 241223 Province, Cuba Ph Tarentola chazaliae TG 00130 Morocco EU293638 EU293728 EU293683 EU293660 EU293705 Ph Tarentola delalandii JB 43 Canary Islands EU293639 EU293729 EU293684 EU293661 EU293706 Ph Tarentola deserti JB 44 unknown HQ426333 HQ426504 HQ426585 HQ426414 HQ426244 Ph Tarentola fascicularus JB 29 unknown HQ426334 HQ426505 HQ426586 HQ426415 HQ426245 Ph Tarentola gigas JB 45 Cape Verde Islands EU293640 EU293730 EU293685 EU293662 EU293707 Ph Tarentola mauritanica TG 00129 Egypt EU293641 EU293731 EU293686 EU293663 EU293708 Thecadactylus USNM Ph St. Croix, U.S. Virgin Islands EU293643 EU293733 EU293688 EU293665 EU293710 rapicauda 561446 Thecadactylus Ph ENS 7108 Izabal, Guatemala EU293642 EU293732 EU293687 EU293664 EU293709 rapicauda Thecadactylus MHNSM Cuzco Amazonico, Madre de Dios, Ph HQ426337 HQ426509 HQ426590 HQ426419 HQ426248 solimoensis 14716 Peru Thecadactylus Cuzco Amazonico, Madre de Dios, Ph KU 214929 EU293644 EU293734 EU293689 EU293666 EU293711 solimoensis Peru MV– Bendigo Whipstick, Victoria, Py Aprasia parapulchella HQ426260 HQ426433 AY134539 HQ426339 HQ426172 D66569 Australia Py Delma butleri SAM– Coonbah, New South Wales, HQ426276 HQ426449 AY134548 HQ426356 HQ426187

– 9 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID R36144 Australia AMS Py Delma tincta Sturt Natl. Pk., NSW, Australia HQ426277 HQ426450 AY172926 HQ426357 HQ426188 151607 Py Lialis burtonis TG 00078 Provinsi Papua, Indonesia EF534782 EF534948 EF534906 EF534863 EF534822 Ophidiocephalus SAM– Todmorden Station, South Py HQ426303 HQ426476 AY134565 HQ426385 HQ426214 taeniatus R44653 Australia, Australia QM– 20 km N Capella, Queensland, Py Paradelma orientalis HQ426304 HQ426477 AY134569 HQ426386 HQ426215 J56089 Australia Lesueur National Park, Western Py Pletholax gracilis WBJ–2483 HQ426315 HQ426489 AY134566 HQ426398 HQ426227 Australia, Australia Lesueur National Park, Western Py Pygopus lepidopodus WBJ–1206 HQ426319 HQ426493 AY134567 HQ426402 HQ426231 Australia, Australia Py Pygopus nigriceps AMB 53 Northern Territory, Australia EF534783 EF534949 EF534907 EF534864 EF534823 S Aristelliger georgensis JB 101 unknown HQ426261 HQ426434 HQ426518 HQ426340 HQ426173 S Aristelliger lar JB 01 Dominican Republic EF534805 EF534973 EF534931 EF534888 EF534847 USNM Kingston, St. Andrew Parish, S Aristelliger praesignis HQ426262 HQ426435 HQ426519 HQ426342 HQ426174 337563 Jamaica USNM Negril, Westmoreland Parish, S Aristelliger praesignis HQ426263 HQ426436 HQ426520 HQ426343 HQ426175 337565 Jamaica Coleodactylus LSUMZ S Santarém, Pará, Brazil HQ426267 HQ426440 HQ426524 HQ426347 HQ426178 amazonicus H–14233 Coleodactylus LSUMZ S Manaus, Amazonas, Brazil HQ426268 HQ426441 HQ426525 HQ426348 HQ426179 amazonicus H–16400 Coleodactylus LSUMZ S Rio Ituxi, Amazonas, Brazil HQ426269 HQ426442 HQ426526 HQ426349 HQ426180 amazonicus H–14050 Coleodactylus MZUSP S Piauí, Brazil EF534792 EF534959 EF534917 EF534874 EF534833 brachystoma 92569 Coleodactylus cf. CHUNB S São Domingos, Goiás, Brazil HQ426270 HQ426443 HQ426527 HQ426350 HQ426181 brachystoma 43901

– 10 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID Coleodactylus LSUMZ S Roraima, Brazil EF534791 EF534958 EF534916 EF534873 EF534832 septentrionalis H–12351 S Euleptes europaea No ID Liguria, Italy EF534806 EF534974 EF534932 EF534889 EF534848 MVZ S Gonatodes albogularis Limon, Costa Rica EF534797 – – – EF534839 204073 S Gonatodes albogularis KU 289808 San Salvador, El Salvador – EF534965 EF534923 EF534880 – ROM S Gonatodes annularis Guyana – EF534961 EF534919 EF534876 – 22961 S Gonatodes annularis No ID French Guiana EF534794 – – – EF534835 Gonatodes S KU 218359 Limon, Ecuador EF534795 EF534962 EF534920 EF534877 EF534836 caudiscutatus S Gonatodes ceciliae TG 00039 Trinidad - EF564114 EF564088 EF564062 HQ426193 LSUMZ S Gonatodes concinnatus Sucumbios, Ecuador HQ426282 EF564096 EF564070 EF564044 HQ426194 H–12688 S Gonatodes daudini JB 38 Union, St. Vincent and Grenadines EF534793 EF534960 EF534918 EF534875 EF534834 CHUNB S Gonatodes eladioi Pará, Brazil HQ426283 EF564107 EF564081 EF564055 HQ426195 40097 UNIBAN S Gonatodes hasemani Rondônia, Brazil – EF534963 EF534921 EF534878 EF534837 1649 S Gonatodes humeralis MF 19492 Ecuador EF534796 EF534964 EF534922 EF534879 EF534838 S Gonatodes ocellatus TG 00038 Tobago HQ426284 EF564098 EF564072 EF564046 HQ426196 Gonatodes S BPN 1303 Imbaimadai, Guyana EF534798 EF534966 EF534924 EF534881 EF534840 alexandermendesi S Gonatodes vittatus TG 00040 Trinidad HQ426285 EF564112 EF564086 EF564060 - LSUMZ S Lepidoblepharis festae Sucumbios, Ecuador HQ426297 EF564094 EF564068 EF564042 HQ426208 H–12704 S Lepidoblepharis sp. KU 218367 Manabi, Ecuador EF534789 EF534956 EF534914 EF534871 EF534830 S Lepidoblepharis MVZ Limon, Costa Rica EF534790 EF534957 EF534915 EF534872 EF534831

– 11 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID xanthostigma 171438 S Pristurus carteri TG 00083 Yemen EF534803 EF534971 EF534929 EF534886 EF534845 Pseudogonatodes AMCC S Berbice River, Guyana HQ426316 HQ426490 HQ426571 HQ426399 HQ426228 guianensis 106916 Pseudogonatodes LSUMZ S Rio Jurura, Acre, Brazil HQ426317 HQ426491 HQ426572 HQ426400 HQ426229 guianensis H–13583 Pseudogonatodes S KU 222142 Loreto, Peru EF534784 EF534950 EF534908 EF534865 EF534824 guianensis S Quedenfeldtia moerens JB 77 Moroccco HQ426320 HQ426494 HQ426574 HQ426403 HQ426232 Quedenfeldtia MVZ S Oukaimeden, Morocco EF534804 EF534972 EF534930 EF534887 EF534846 trachyblephara 178121 DJH – El S Saurodactylus brosseti El Jadida, Morocco HQ426321 HQ426406 HQ426575 HQ426404 HQ426233 95 S Saurodactylus brosseti TG 00082 Morocco EF534802 EF534970 EF534928 EF534885 EF534844 DJH – S Saurodactylus fasciatus Zumi, Morocco HQ426322 HQ426495 HQ426576 HQ426405 HQ426234 M616 Saurodactylus DJH – S NW of Ain Benimather, Morocco HQ426323 HQ426496 HQ426577 HQ426406 HQ426235 mauritainicus Sm61 Sphaeodactylus FLMNH S Long Island, Bahamas HQ426329 EF534953 EF534911 EF534868 EF534827 nigropunctatus 144010 S Sphaerodactylus argus TG 00125 Key West, Florida, USA HQ426324 HQ426497 HQ426578 HQ426407 HQ426236 Sphaerodactylus YPM S Monroe County, Florida, USA EF534787 EF534954 EF534912 EF534869 EF534828 elegans 14795 Sphaerodactylus S JAC 24229 Oaxaca, Mexico HQ426325 HQ426498 HQ426579 HQ426408 HQ426237 glaucus Sphaerodactylus S macrolepis TG 00099 Puerto Rico HQ426326 HQ426499 HQ426580 HQ426409 HQ426238 grandisquamis Sphaerodactylus S TG 00089 Puerto Rico HQ426327 HQ426500 HQ426581 HQ426410 HQ426239 klauberi

– 12 – Specimen Family Species Locality RAG1 RAG2 C-MOS ACM4 PDC ID Sphaerodactylus S TG 00211 Bahia de la Ballena, Puerto Rico HQ426328 HQ426501 HQ426582 HQ426411 HQ426240 nicholsi Sphaerodactylus FLMNH S Miami–Dade County, Florida, USA HQ426330 EF564093 EF564067 EF564041 HQ426241 notatus 132440 Sphaerodactylus CAS S Bahia de la Ballena, Puerto Rico EF534785 EF534951 EF534909 EF534866 EF534825 roosevelti 198428 S Sphaerodactylus torrei JB 34 Cuba EF534788 EF534955 EF534913 EF534870 EF534829 Sphaerodactylus S TG 00210 Puerto Rico HQ426331 HQ426502 HQ426583 HQ426412 HQ426242 townsendi Teratoscincus CAS S Yazd Province, Iran EF534801 HQ426508 HQ426589 HQ426418 EF534843 keyserlingii 228808 Teratoscincus S TG 00074 Pakistan EF534800 EF534968 EF534926 EF534883 EF534842 microlepis Teratoscincus JFBM S China HQ426335 HQ426507 HQ426588 HQ426417 HQ426246 przewalskii 15828 Teratoscincus S TG 00070 China EF534799 EF534967 EF534925 EF534882 EF534841 roborowskii JFBM S Teratoscincus scincus Turkmenistan HQ426336 EF534969 EF534927 EF534884 HQ426247 14252

– 13 – Rhacodactylus ciliatus Bavayia cyclura Pseudothecadactylus lindneri Oedura marmorata Lucasium damaeum Diplodactylus conspicillatus S1 Phyllurus platurus Carphodactylus laevis Nephrurus milii Delma butleri Delma tincta Lialis burtonis Ophidiocephalus taeniatus Pletholax gracilis Aprasia parapulchella Paradelma orientalis Pygopus lepidopodus Pygopus nigriceps Aeleuroscalabotes felinus Coleonyx mitratus Coleonyx brevis Coleonyx variegatus Goniurosaurus araneus Goniurosaurus luii Eublepharis macularius Holodactylus africanus Hemitheconyx taylori Hemitheconyx caudicinctus Pristurus carteri Euleptes europaea Teratoscincus microlepis Teratoscincus roborowskii Teratoscincus przewalskii Teratoscincus scincus Teratoscincus keyserlingii Quedenfeldtia moerens Quedenfeldtia trachyblephara Aristelliger lar Aristelliger georgensis Aristelliger praesignis St.Andrew Aristelliger praesignis Westmoreland Saurodactylus fasciatus Saurodactylus mauritainicus Saurodactylus brosseti El Jadida Saurodactylus brosseti JFBM Coleodactylus amazonicus Santarém Coleodactylus amazonicus Rio Ituxi Coleodactylus amazonicus Manaus Lepidoblepharis xanthostigma Lepidoblepharis festae Lepidoblepharis sp. Gonatodes eladioi Gonatodes caudiscutatus Gonatodes hasemani Gonatodes alexandermendesi Gonatodes annularis Gonatodes daudini Gonatodes albogularis Gonatodes vittatus Gonatodes concinnatus Gonatodes humeralis Gonatodes ceciliae Gonatodes ocellatus Pseudogonatodes guianensis Guyana Pseudogonatodes guianensis Peru Pseudogonatodes guianensis Brazil Coleodactylus septentrionalis Coleodactylus cf. brachystoma Coleodactylus brachystoma Sphaerodactylus glaucus Sphaerodactylus torrei Sphaerodactylus nigropunctatus Sphaerodactylus.elegans Sphaerodactylus notatus Sphaerodactylus roosevelti Sphaerodactylus argus Sphaerodactylus macrolepis Sphaerodactylus townsendi Sphaerodactylus nicholsi Sphaerodactylus klauberi Haemodracon riebeckii Asaccus platyrhynchus Asaccus sp. Ptyodactylus hasselquistii Ptyodactylus guttatus Thecadactylus solimoensis Thecadactylus solimoensis Thecadactylus rapicauda St. Croix Thecadactylus rapicauda Guatemala Tarentola chazaliae Tarentola gigas Tarentola delalandii Tarentola americana Tarentola mauritanica Tarentola fascicularus Tarentola deserti Gymnodactylus amarali Bogertia lutzae Phyllopezus maranjonensis Phyllopezus p. przewalskii Paraguay Phyllopezus p. pollicaris Paiui Phyllopezus p. pollicaris Goiás Garthia gaudichaudii Homonota fasciata Homonota darwinii Phyllodactylus reissii Phyllodactylus tuberculosus Phyllodactylus boardi Phyllodactylus delcampoi Phyllodactylus nocticolus Phyllodactylus bugastrolepis Phyllodactylus xanti Phyllodactylus unctus Uroplatus phantasticus Uroplatus henkeli Narudasia festiva Ebenavia inunguis Paroedura picta Paroedura masobe Rhoptropus boultoni Pachydactylus punctatus Chondrodactylus bibronii Phelsuma ocellata Phelsuma madagascariensis Phelsuma modesta Phelsuma rosagularis Phelsuma borbonica Lygodactylus miops Lygodactylus tolampyae Lygodactylus miribilis Lygodactylus klugei Lygodactylus bradfieldi Cnemaspis limi Gekko gecko Lepidodactylus lugubris Cyrtopodion scabrum Cyrtodactylus novaeguinea Hemidactylus angulatus Hemidactylus haitianus Hemidactylus triedrus Hemidactylus flavivirdis Hemidactylus imbricatus Hemidactylus frenatus Hemidactylus robustus Hemidactylus macropholis Hemidactylus turcicus Hemidactylus platyurus 0.01 substitutions/site Hemidactylus.mabouia Brazil Hemidactylus.mabouia Kenya Hemidactylus palaichthus Hemidactylus longicephalus Hemidactylus brasilianus Hemidactylus greefi S2

1600

1400

1200

1000

s 800

600

400

200

0 all 1 2 3 4 5 6 7 Fossil Calibration Node Removed Dibamus bouretti Xantusia vigilis Eumeces inexpectatus Tiliqua rugosus Ramphotyphlops braminus Anolis carolinensis Elgaria kingii Heloderma suspectum S3a Aspidoscelis tigris Podarcis sicula Rhineura floridana Amphisbaena alba Bavayia cyclura Rhacodactylus ciliatus Pseudothecadactylus linderi Oedura marmorata Lucasium damaeum Diplodactylus conspicillatus Phyllurus platurus Carphodactylus laevis Nephrurus milii Delma butleri Delma tincta Lialis burtonis Pletholax gracilis Ophidiocephalus taeniatus Aprasia parapulchella Paradelma orientalis Pygopus lepidopodus Pygopus nigriceps Aeleuroscalabotes felinus Coleonyx mitratus Coleonyx brevis Coleonyx variegatus Goniurosaurus araneus Goniurosaurus luii Eublepharis macularius Holodactylus africanus Hemitheconyx caudicinctus Hemitheconyx taylori Pristurus carteri Euleptes europaea Teratoscincus microlepis Teratoscincus scincus Teratoscincus keyserlingii Teratoscincus roborowskii Teratoscincus przewalskii Quedenfeldtia moerens Quedenfeldtia trachyblephara Aristelliger lar Aristelliger georgensis Aristelliger praesignis Westmoreland Aristelliger praesignis St. Andrew Saurodactylus fasciatus Saurodactylus mauritainicus Saurodactylus brosseti JFBM Saurodactylus brosseti El Jadida Coleodactylus amazonicus Pará Coleodactylus amazonicus Manaus Coleodactylus amazonicus Rio Ituxi Lepidoblepharis xanthostigma Lepidoblepharis sp. Lepidoblepharis festae Gonatodes caudiscutatus Gonatodes eladioi Gonatodes alexandermendesi Gonatodes annularis Gonatodes hasemani Gonatodes albogularis Gonatodes vittatus Gonatodes daudini Gonatodes humeralis Gonatodes concinnatus Gonatodes ceciliae Gonatodes ocellatus Coleodactylus septentrionalis Coleodactylus brachystoma Coleodactylus cf. brachystoma Pseudogonatodes guianensis Guyana Pseudogonatodes guianensis Brazil Pseudogonatodes guianensis Peru Sphaerodactylus glaucus Sphaerodactylus nigropunctatus Sphaerodactylus torrei Sphaerodactylus elegans Sphaerodactylus notatus Sphaerodactylus klauberi Sphaerodactylus nicholsi Sphaerodactylus townsendi Sphaerodactylus argus Sphaerodactylus grandisquamis Sphaerodactylus roosevelti Haemodracon reibeckii Asaccus platyrhynchus Asaccus sp. Ptyodactylus guttatus Ptyodactylus hasselquistii Thecadactylus solimoensis Thecadactylus rapicauda Guatemala Thecadactylus rapicauda St. Croix Tarentola chazaliae Tarentola delandii Tarentola gigas Tarentola americana Tarentola mauritanica Tarentola fascicularus Tarentola deserti Gymnodactylus amarali Bogertia lutzae Phyllopezus maranjonensis Phyllopezus pollicaris Paraguay Phyllopezus pollicaris Goias Phyllopezus pollicaris Piaui Garthia gaudichaudii Homonota darwinii Homonota fasciata Phyllodactylus reissii Phyllodactylus tuberculosus Phyllodactylus boardi Phyllodactylus delcampoi Phyllodactylus bugastrolepis Phyllodactylus nocticolus Phyllodactylus xanti Phyllodactylus unctus Gekko gecko Lepidodactylus lugubris Cyrtopodion scaber Cyrtodactylus novaeguinea Hemidactylus angulatus Hemidactylus haitianus Hemidactylus triedrus Hemidactylus flavivirdus Hemidactylus frenatus Hemidactylus imbricatus Hemidactylus robustus Hemidactylus macropholis Hemidactylus turcicus Hemidactylus platyurus Hemidactylus mabouia Brazil Hemidactylus mabouia Kenya Hemidactylus palaichthus Hemidactylus longicephalus Hemidactylus greefi Hemidactylus brasilianus Cnemaspis limi Uroplatus henkeli Uroplatus phantasticus Narudasia festiva Ebenavia inunguis Paroedura masobe Paroedura picta Rhoptropus boultoni Chondrodactylus bibronii Pachydactylus punctatus Lygodactylus miops Lygodactylus tolampyae Lygodactylus miribilis Lygodactylus bradfieldi Lygodactylus klugei Phelsuma ocellata Phelsuma modesta Phelsuma madagascariensis Phelsuma borbonica Phelsuma rosagularis

250 0 200 0 150 0 100 0 50 0 0 0 Dibamus bouretti Xantusia vigilis Eumeces inexpectatus Tiliqua rugosus Ramphotyphlops braminus Anolis carolinensis Elgaria kingii Heloderma suspectum Aspidoscelis tigris Podarcis sicula Rhineura floridana Amphisbaena alba Bavayia cyclura Rhacodactylus ciliatus S3b Pseudothecadactylus linderi Oedura marmorata Lucasium damaeum Diplodactylus conspicillatus Phyllurus platurus Carphodactylus laevis Nephrurus milii Delma butleri Delma tincta Lialis burtonis Pletholax gracilis Ophidiocephalus taeniatus Aprasia parapulchella Paradelma orientalis Pygopus lepidopodus Pygopus nigriceps Aeleuroscalabotes felinus Coleonyx mitratus Coleonyx brevis Coleonyx variegatus Goniurosaurus araneus Goniurosaurus luii Eublepharis macularius Holodactylus africanus Hemitheconyx caudicinctus Hemitheconyx taylori Pristurus carteri Euleptes europaea Teratoscincus microlepis Teratoscincus scincus Teratoscincus keyserlingii Teratoscincus roborowskii Teratoscincus przewalskii Quedenfeldtia moerens Quedenfeldtia trachyblephara Aristelliger lar Aristelliger georgensis Aristelliger praesignis Westmoreland Aristelliger praesignis St. Andrew Saurodactylus fasciatus Saurodactylus mauritainicus Saurodactylus brosseti JFBM Saurodactylus brosseti El Jadida Coleodactylus amazonicus Pará Coleodactylus amazonicus Manaus Coleodactylus amazonicus Rio Ituxi Lepidoblepharis xanthostigma Lepidoblepharis sp. Lepidoblepharis festae Gonatodes caudiscutatus Gonatodes eladioi Gonatodes albogularis Gonatodes vittatus Gonatodes daudini Gonatodes hasemani Gonatodes alexandermendesi Gonatodes annularis Gonatodes humeralis Gonatodes concinnatus Gonatodes ceciliae Gonatodes ocellatus Coleodactylus septentrionalis Coleodactylus brachystoma Coleodactylus cf. brachystoma Pseudogonatodes guianensis Guyana Pseudogonatodes guianensis Brazil Pseudogonatodes guianensis Peru Sphaerodactylus glaucus Sphaerodactylus nigropunctatus Sphaerodactylus torrei Sphaerodactylus elegans Sphaerodactylus notatus Sphaerodactylus klauberi Sphaerodactylus nicholsi Sphaerodactylus townsendi Sphaerodactylus argus Sphaerodactylus grandisquamis Sphaerodactylus roosevelti Haemodracon reibeckii Asaccus platyrhynchus Asaccus sp. Ptyodactylus guttatus Ptyodactylus hasselquisti Thecadactylus solimoensis Thecadactylus rapicauda Guatemala Thecadactylus rapicauda St. Croix Tarentola chazaliae Tarentola delalandii Tarentola gigas Tarentola americana Tarentola mauritanica Tarentola fascicularus Tarentola deserti Gymnodactylus amarali Bogertia lutzae Phyllopezus maranjonensis Phyllopezus pollicaris Paraguay Phyllopezus pollicaris Goias Phyllopezus pollicaris Piaui Garthia gaudichaudii Homonota darwinii Homonota fasciata Phyllodactylus reissii Phyllodactylus tuberculosus Phyllodactylus boardi Phyllodactylus delcampoi Phyllodactylus bugastrolepis Phyllodactylus nocticolus Phyllodactylus xanti Phyllodactylus unctus Cnemaspis limi Gekko gecko Lepidodactylus lugubris Cyrtopodion scaber Cyrtodactylus novaeguinea Hemidactylus angulatus Hemidactylus haitianus Hemidactylus triedrus Hemidactylus flavivirdus Hemidactylus frenatus Hemidactylus imbricatus Hemidactylus platyurus Hemidactylus robustus Hemidactylus macropholis Hemidactylus turcicus Hemidactylus mabouia Brazil Hemidactylus mabouia Kenya Hemidactylus palaichthus Hemidactylus longicephalus Hemidactylus brasiliensis Hemidactylus greefi Narudasia festiva Ebenavia inunguis Paroedura masobe Paroedura picta Uroplatus henkeli Uroplatus phantasticus Rhoptropus boultoni Chondrodactylus bibronii Pachydactylus punctatus Lygodactylus miops Lygodactylus tolampyae Lygodactylus miribilis Lygodactylus bradfieldi Lygodactylus klugei Phelsuma ocellata Phelsuma modesta Phelsuma madagascariensis Phelsuma borbonica Phelsuma rosagularis

250 0 200 0 150 0 100 0 50 0 0 0 Pletholax gracilis Ophidiocephalus taeniatus Pygopus nigriceps Pygopodidae Pygopus lepidopodus Paradelma orientalis Aprasia parapulchella S4 Lialis burtonis Delma butleri Delma tincta Carphodactylus laevis Nephrurus milii Carphodactylidae Phyllurus platurus Pseudothecadactylus linderi Oedura marmorata Lucasium damaeum Diplodactylus conspicillatus Diplodactylidae Bavayia cyclura Rhacodactylus ciliatus Coleonyx brevis Coleonyx variegatus Coleonyx mitratus Aeleuroscalabotes felinus Eublepharidae Hemitheconyx caudicinctus Hemitheconyx taylori Holodactylus africanus Eublepharis macularius Goniurosaurus araneus Goniurosaurus luii Saurodactylus brosseti JFBM Saurodactylus brosseti El Jadida Saurodactylus mauritainicus Saurodactylus fasciatus Coleodactylus amazonicus Para Coleodactylus amazonicus Manaus Coleodactylus amazonicus Rio Ituxi Gonatodes caudiscutatus Gonatodes eladioi Gonatodes alexandermendesi Gonatodes annularis Gonatodes hasemani Gonatodes daudini Gonatodes albogularis Gonatodes vittatus Gonatodes humeralis Gonatodes concinnatus Gonatodes ceciliae Gonatodes ocellatus Lepidoblepharis sp. Lepidoblepharis festae Lepidoblepharis xanthostigma Sphaerodactylus nigropunctatus Sphaero- Sphaerodactylus torrei dactylidae Sphaerodactylus klauberi Sphaerodactylus nicholsi Sphaerodactylus townsendi Sphaerodactylus macrolepis Sphaerodactylus roosevelti Sphaerodactylus argus Sphaerodactylus notatus Sphaerodactylus elegans Sphaerodactylus glaucus Coleodactylus brachystoma Coleodactylus cf. brachystoma Coleodactylus septentrionalis Pseudogonatodes guianensis Guyana Pseudogonatodes guianensis Brazil Pseudogonatodes guianensis Peru Aristelliger praesignis Westmoreland Aristelliger praesignis St. Andrew Aristelliger georgensis Aristelliger lar Quedenfeldtia moerens Quedenfeldtia trachyblephara Teratoscincus microlepis Teratoscincus scincus Teratoscincus keyserlingii Teratoscincus roborowskii Teratoscincus przewalskii Euleptes europaea Pristurus carteri Ptyodactylus guttatus Ptyodactylus hasselquistii Thecadactylus rapicauda Guatemala Thecadactylus rapicauda St. Croix Thecadactylus solimoensis Tarentola chazaliae Tarentola delandii Tarentola gigas Tarentola mauritanica Tarentola fascicularis Tarentola deserti Tarentola americana Bogertia lutzae Phyllo- Phyllopezus maranjonensis dactylidae Phyllopezus pollicaris Goias Phyllopezus pollicaris Paiui Phyllopezus pollicaris Paraguay Gymnodactylus amarali Homonota darwinii Homonota fasciata Phyllodactylus tuberculosus Phyllodactylus bugastrolepis Phyllodactylus nocticolus Phyllodactylus xanti Phyllodactylus unctus Phyllodactylus delcampoi Phyllodactylus boardi Phyllodactylus reissii Garthia gaudichaudii Asaccus platyrhynchus Asaccus sp. Haemodracon reibeckii Cyrtopodion scabrum Hemidactylus greefi Hemidactylus brasilianus Hemidactylus longicephalus Hemidactylus palaichthus Hemidactylus mabouia Brazil Hemidactylus mabouia Kenya Hemidactylus platyurus Hemidactylus robustus Hemidactylus macropholis Hemidactylus turcicus Hemidactylus triedrus Hemidactylus flavivirdus Hemidactylus frenatus Hemidactylus imbricatus Hemidactylus angulatus Hemidactylus haitiensis Cyrtodactylus novaeguinea Gekko gecko Lepidodactylus lugubris Uroplatus henkeli Gekkonidae Uroplatus phantasticus Chondrodactylus bibronii Pachydactylus punctatus Rhoptropus boultoni Lygodactylus miribilis Lygodactylus bradfieldi Lygodactylus klugei Distribution Lygodactylus tolampyae Lygodactylus miops Phelsuma modesta Old World Phelsuma madagascariensis Phelsuma borbonica New World Phelsuma rosagularis Phelsuma ocellata Node Absent Ebenavia inunguis Paroedura masobe Equivocal Paroedura picta Narudasia festiva Cnemaspis limi Cretaceous Paleogene Neogene 150 125 100 75 50 25 0 Ma S5 Pletholax gracilis Ophidiocephalus taeniatus Pygopus nigriceps Pygopodidae Pygopus lepidopodus Paradelma orientalis Aprasia parapulchella Lialis burtonis Delma butleri Delma tincta Carphodactylus laevis Nephrurus milii Carphodactylidae Phyllurus platurus Pseudothecadactylus linderi Oedura marmorata Lucasium damaeum Diplodactylus conspicillatus Diplodactylidae Bavayia cyclura Rhacodactylus ciliatus Coleonyx brevis Coleonyx variegatus Coleonyx mitratus Aeleuroscalabotes felinus Eublepharidae Hemitheconyx caudicinctus Hemitheconyx taylori Holodactylus africanus Eublepharis macularius Goniurosaurus araneus Goniurosaurus luii Saurodactylus brosseti JFBM Saurodactylus brosseti El Jadida Saurodactylus mauritainicus Saurodactylus fasciatus Coleodactylus amazonicus Para Coleodactylus amazonicus Manaus Coleodactylus amazonicus Rio Ituxi Gonatodes caudiscutatus Gonatodes eladioi Gonatodes alexandermendesi Gonatodes annularis Gonatodes hasemani Gonatodes daudini Gonatodes albogularis Gonatodes vittatus Gonatodes humeralis Gonatodes concinnatus Gonatodes ceciliae Gonatodes ocellatus Lepidoblepharis sp. Lepidoblepharis festae Lepidoblepharis xanthostigma Sphaerodactylus nigropunctatus Sphaero- Sphaerodactylus torrei Sphaerodactylus klauberi dactylidae Sphaerodactylus nicholsi Sphaerodactylus townsendi Sphaerodactylus macrolepis Sphaerodactylus roosevelti Sphaerodactylus argus Sphaerodactylus notatus Sphaerodactylus elegans Sphaerodactylus glaucus Coleodactylus brachystoma Coleodactylus cf. brachystoma Coleodactylus septentrionalis Pseudogonatodes guianensis Guyana Pseudogonatodes guianensis Brazil Pseudogonatodes guianensis Peru Aristelliger praesignis Westmoreland Aristelliger praesignis St. Andrew Aristelliger georgensis Aristelliger lar Quedenfeldtia moerens Quedenfeldtia trachyblephara Teratoscincus microlepis Teratoscincus scincus Teratoscincus keyserlingii Teratoscincus roborowskii Teratoscincus przewalskii Euleptes europaea Pristurus carteri Ptyodactylus guttatus Ptyodactylus hasselquistii Thecadactylus rapicauda Guatemala Thecadactylus rapicauda St. Croix Thecadactylus solimoensis Tarentola chazaliae Tarentola delandii Tarentola gigas Tarentola mauritanica Tarentola fascicularis Tarentola deserti Tarentola americana Bogertia lutzae Phyllo- Phyllopezus maranjonensis dactylidae Phyllopezus pollicaris Goias Phyllopezus pollicaris Paiui Phyllopezus pollicaris Paraguay Gymnodactylus amarali Homonota darwinii Homonota fasciata Phyllodactylus tuberculosus Phyllodactylus bugastrolepis Phyllodactylus nocticolus Phyllodactylus xanti Phyllodactylus unctus Phyllodactylus delcampoi Phyllodactylus boardi Phyllodactylus reissii Garthia gaudichaudii Asaccus platyrhynchus Asaccus sp. Haemodracon reibeckii Cyrtopodion scabrum Hemidactylus greefi Hemidactylus brasilianus Hemidactylus longicephalus Hemidactylus palaichthus Hemidactylus mabouia Brazil Hemidactylus mabouia Kenya Hemidactylus platyurus Hemidactylus robustus Hemidactylus macropholis Hemidactylus turcicus Hemidactylus triedrus Hemidactylus flavivirdus Hemidactylus frenatus Hemidactylus imbricatus Hemidactylus angulatus Hemidactylus haitiensis Cyrtodactylus novaeguinea Gekko gecko Lepidodactylus lugubris Uroplatus henkeli Gekkonidae Uroplatus phantasticus Chondrodactylus bibronii Pachydactylus punctatus Rhoptropus boultoni Lygodactylus miribilis Lygodactylus bradfieldi Distribution Lygodactylus klugei Lygodactylus tolampyae Lygodactylus miops Old World Phelsuma modesta Phelsuma madagascariensis New World Phelsuma borbonica Phelsuma rosagularis Node Absent Phelsuma ocellata Ebenavia inunguis Equivocal Paroedura masobe Paroedura picta Narudasia festiva Cnemaspis limi

Cretaceous Paleogene Neogene 150 125 100 75 50 25 0 Ma Pletholax gracilis Ophidiocephalus taeniatus Pygopus nigriceps Pygopodidae Pygopus lepidopodus Paradelma orientalis S6 Aprasia parapulchella Lialis burtonis Delma butleri Delma tincta Carphodactylus laevis Nephrurus milii Carphodactylidae Phyllurus platurus Pseudothecadactylus linderi Oedura marmorata Lucasium damaeum Diplodactylus conspicillatus Diplodactylidae Bavayia cyclura Rhacodactylus ciliatus Coleonyx brevis Coleonyx variegatus Coleonyx mitratus Aeleuroscalabotes felinus Eublepharidae Hemitheconyx caudicinctus Hemitheconyx taylori Holodactylus africanus Eublepharis macularius Goniurosaurus araneus Goniurosaurus luii Saurodactylus brosseti JFBM Saurodactylus brosseti El Jadida Saurodactylus mauritainicus Saurodactylus fasciatus Coleodactylus amazonicus Para Coleodactylus amazonicus Manaus Coleodactylus amazonicus Rio Ituxi Gonatodes caudiscutatus Gonatodes eladioi Gonatodes alexandermendesi Gonatodes annularis Gonatodes hasemani Gonatodes daudini Gonatodes albogularis Gonatodes vittatus Gonatodes humeralis Gonatodes concinnatus Gonatodes ceciliae Gonatodes ocellatus Lepidoblepharis sp. Lepidoblepharis festae Lepidoblepharis xanthostigma Sphaerodactylus nigropunctatus Sphaero- Sphaerodactylus torrei dactylidae Sphaerodactylus klauberi Sphaerodactylus nicholsi Sphaerodactylus townsendi Sphaerodactylus macrolepis Sphaerodactylus roosevelti Sphaerodactylus argus Sphaerodactylus notatus Sphaerodactylus elegans Sphaerodactylus glaucus Coleodactylus brachystoma Coleodactylus cf. brachystoma Coleodactylus septentrionalis Pseudogonatodes guianensis Guyana Pseudogonatodes guianensis Brazil Pseudogonatodes guianensis Peru Aristelliger praesignis Westmoreland Aristelliger praesignis St. Andrew Aristelliger georgensis Aristelliger lar Quedenfeldtia moerens Quedenfeldtia trachyblephara Teratoscincus microlepis Teratoscincus scincus Teratoscincus keyserlingii Teratoscincus roborowskii Teratoscincus przewalskii Euleptes europaea Pristurus carteri Ptyodactylus guttatus Ptyodactylus hasselquistii Thecadactylus rapicauda Guatemala Thecadactylus rapicauda St. Croix Thecadactylus solimoensis Tarentola chazaliae Tarentola delandii Tarentola gigas Tarentola mauritanica Tarentola fascicularis Tarentola deserti Tarentola americana Bogertia lutzae Phyllo- Phyllopezus maranjonensis dactylidae Phyllopezus pollicaris Goias Phyllopezus pollicaris Paiui Phyllopezus pollicaris Paraguay Gymnodactylus amarali Homonota darwinii Homonota fasciata Phyllodactylus tuberculosus Phyllodactylus bugastrolepis Phyllodactylus nocticolus Phyllodactylus xanti Phyllodactylus unctus Phyllodactylus delcampoi Phyllodactylus boardi Phyllodactylus reissii Garthia gaudichaudii Asaccus platyrhynchus Asaccus sp. Haemodracon reibeckii Cyrtopodion scabrum Hemidactylus greefi Hemidactylus brasilianus Hemidactylus longicephalus Hemidactylus palaichthus Hemidactylus mabouia Brazil Hemidactylus mabouia Kenya Hemidactylus platyurus Hemidactylus robustus Hemidactylus macropholis Hemidactylus turcicus Hemidactylus triedrus Hemidactylus flavivirdus Hemidactylus frenatus Hemidactylus imbricatus Hemidactylus angulatus Hemidactylus haitiensis Cyrtodactylus novaeguinea Gekko gecko Lepidodactylus lugubris Uroplatus henkeli Gekkonidae Uroplatus phantasticus Chondrodactylus bibronii Pachydactylus punctatus Rhoptropus boultoni Lygodactylus miribilis Distribution Lygodactylus bradfieldi Lygodactylus klugei Australia/Pacific Lygodactylus tolampyae Asia Lygodactylus miops Phelsuma modesta Africa Phelsuma madagascariensis North America Phelsuma borbonica Phelsuma rosagularis South America/Caribbean Phelsuma ocellata Node Absent Ebenavia inunguis Paroedura masobe Equivocal Paroedura picta Narudasia festiva Cnemaspis limi

Cretaceous Paleogene Neogene 150 125 100 75 50 25 0 Ma S7

1 Old World -> New World 0.9 0.8 New World -> Old World 0.7 0.6 0.5 0.4

% of trees 0.3 0.2 0.1 0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 No. of changes