Supplemental material for “Live Birth Among Iguanian Lizards Predates Pleistocene-Pliocene Glaciations” by James A. Schulte II and Franck Moreno-Roark
MATERIALS AND METHODS
(a) GenBank accession numbers and reproductive mode states are presented in Table S1 below. Numbers for newly reported sequences will be included upon acceptance of the manuscript.
Table S1. GenBank accession numbers for DNA sequences used for phylogenetic analysis in this study. Reproductive mode assumed for ancestral state reconstruction. (0) denotes oviparity, (1) denotes viviparity.
TAXON / ACCESSION NO. / REPRODUCTIVE MODEElgaria panamitina / U82692 / 0
Varanus griseus / AF407503 / 0
Cnemidophorus tigris / U71332 / 0
Mabuya aurata / U71330 / 0
Acanthosaura capra / AF128498 / 0
Acanthosaura lepidogaster / AF128499 / 0
Agama agama / AF128504 / 0
Agama atra / AF128505 / 0
Agama impalearis / AF128506 / 0
Amphibolurus muricatus / AF128468 / 0
Amphibolurus nobbi / AY132999 / 0
Amphibolurus nobbi coggeri / AY133000 / 0
Amphibolurus norrisi / AY133001 / 0
Amphibolurus temporalis / AY133002 / 0
Anisolepis longicauda / AF528736 / 0
Anolis acutus / AF055926 / 0
Anolis aeneus / AF055950 / 0
Anolis agassizi / AF055952 / 0
Anolis ahli / AY296148 / 0
Anolis alayoni / AY296149 / 0
Anolis alfaroi / AY296150 / 0
Anolis aliniger / AF055959 / 0
Anolis allisoni / AY296151 / 0
Anolis allogus / AY296152 / 0
Anolis altaeKN / AY909735 / 0
Anolis altitudinalis.UW.REG.X / AY654023 / 0
Anolis alumina / AY296153 / 0
Anolis alutaceus / AF055971 / 0
Anolis angusticeps / AF055967 / 0
Anolis annectens1159 / AY909736 / 0
Anolis sp. STRI652 / AY909737 / 0
Anolis aquaticusKN / AY909738 / 0
Anolis argenteolis / AY296154 / 0
Anolis argillaceus.TJ / AY909739 / 0
Anolis armouri / AY263012 / 0
Anolis auratus1163 / AY909740 / 0
Anolis bahorucoensis / AF055932 / 0
Anolis baleatus / AY296155 / 0
Anolis baracoe / AY296156 / 0
Anolis barahonae / AF055972 / 0
Anolis bartschi / AF055960 / 0
Anolis bicaorumKN / AY909741 / 0
Anolis sp. KRL794 / AY909742 / 0
Anolis bimaculatus / AF055930 / 0
Anolis biporcatus / AF294286 / 0
Anolis bitectusKN / AY909743 / 0
Anolis bremeri / AY296157 / 0
Anolis breslini / AY263017 / 0
Anolis brevirostris / AY296158 / 0
Anolis brunneus / AY296159 / 0
Anolis capitoKN / AY909744 / 0
Anolis carolinensis / AF294279 / 0
Anolis carpenteri / AY296160 / 0
Anolis casildaeKN / AY909745 / 0
Anolis caudalis / AY296161 / 0
Anolis centralis / AY296162 / 0
Anolis chlorocyanus / AY296163 / 0
Anolis christophei / AF055957 / 0
Anolis clivicolaCOMP / AY909746 / 0
Anolis coelestinus / AY296164 / 0
Anolis confusus.193863.JJKX / AY909787 / 0
Anolis conspersus / AF294304 / 0
Anolis cooki / AY296165 / 0
Anolis crassulusCOMP / AY909748 / 0
Anolis cristatellus / AF528724 / 0
Anolis cupeyalensis191155KN / AY909749 / 0
Anolis cupreusJMS67 / AY909750 / 0
Anolis cuvieri / AF055973 / 0
Anolis cyanopleurusKN / AY909751 / 0
Anolis cybotes / AF528723 / 0
Anolis darlingtoni / AY367137 / 0
Anolis desachensis / AY296167 / 0
Anolis distichus / AF528725 / 0
Anolis dolichocephalus / AY296169 / 0
Anolis equestris / AF055978 / 0
Anolis ernestwilliamsi / AY296170 / 0
Anolis etheridgei / AF055934 / 0
Anolis eugenegrahami / AY296171 / 0
Anolis evermanni / AY296172 / 0
Anolis ferreus / AY296173 / 0
Anolis fowleri / AY296174 / 0
Anolis frenatusKN / AY909752 / 0
Anolis fuscoauratus / AF337790 / 0
Anolis garmani / AF294289 / 0
Anolis garridoi / AY296175 / 0
Anolis gingivinusKN / AY909753 / 0
Anolis grahami / AF294299 / 0
Anolis griseus / AY296176 / 0
Anolis guafe.2585.JJKX / AY909788 / 0
Anolis guazuma1640 / AY909754 / 0
Anolis gundlachi / AY296177 / 0
Anolis haetianus / AY263042 / 0
Anolis hendersoni / AY296178 / 0
Anolis homolechis / AY296179 / 0
Anolis humilisKN / AF055944 / 0
Anolis imias / AF294314 / 0
Anolis inexpectatus / AY296180 / 0
Anolis insolitus / AF055933 / 0
Anolis intermediusKN / AY909755 / 0
Anolis isolepis / AY296181 / 0
Anolis isthmicusKN / AY909762 / 0
Anolis jubar / AY296182 / 0
Anolis krugi / AF055928 / 0
Anolis laeviventrisKN / AY909756 / 0
Anolis leachi / AY296183 / 0
Anolis lemurinus / AF337782 / 0
Anolis limifrons / AF337783 / 0
Anolis lineatopus / AF294295 / 0
Anolis lineatus / AF337784 / 0
Anolis lionotusKN / AY909757 / 0
Anolis lividusKN / AY909758 / 0
Anolis longiceps / AY296184 / 0
Anolis longitibialis / AY263010 / 0
Anolis loveridgei / AY909759 / 0
Anolis loysiana / AF055964 / 0
Anolis luciae / AF055951 / 0
Anolis lucius / AF055962 / 0
Anolis luteogularis / AF055977 / 0
Anolis macilentus / AY296185 / 0
Anolis marcanoi / AY263006 / 0
Anolis marmoratus / AY296186 / 0
Anolis marron / AY296187 / 0
Anolis maynardi / AF055969 / 0
Anolis meridionalis / AY909760 / 0
Anolis mestrei / AF337779 / 0
Anolis microtus / AF055947 / 0
Anolis mimusKN / KNunknown / 0
Anolis monensis / AY296188 / 0
Anolis monticola / AY296189 / 0
Anolis nebuloidesKN / AY909763 / 0
Anolis nitens Ecuador / AF337802 / 0
Anolis noblei / AY296190 / 0
Anolis nubilus.1077 / AY909764 / 0
Anolis occultus / AF055976 / 0
Anolis oculatus / AY296191 / 0
Anolis olssoni / AF055945 / 0
Anolis onca1154 / AY909765 / 0
Anolis opalinus / AF294305 / 0
Anolis ophiolepis / AF055942 / 0
Anolis oporinus.KN / AY909766 / 0
Anolis ortonii Para / AF337796 / 0
Anolis oscelloscapularisKN / AY909767 / 0
Anolis oxylophus11853KN / AY909768 / 0
Anolis pachypus175KN / AY909769 / 0
Anolis pandoensis35KN / AY909770 / 0
Anolis paternus / U82679 / 0
Anolis placidus / AY296192 / 0
Anolis poecilopusKN / AY909771 / 0
Anolis pogus / AY296193 / 0
Anolis polylepisKN / AY909772 / 0
Anolis polyrhachis / AY909773 / 0
Anolis poncensis / AY296194 / 0
Anolis porcatus / AY296195 / 0
Anolis pulchellus / AY296196 / 0
Anolis pumilis / AF055963 / 0
Anolis punctatus / AF528726 / 0
Anolis purpurgularisKN / AY909774 / 0
Anolis quadriocellifer / AY296197 / 0
Anolis quercorumKN / AY909775 / 0
Anolis reconditus / AY296198 / 0
Anolis rejectus / AY909761 / 0
Anolis richardi / AF055949 / 0
Anolis ricordii1347.KN / KNunknown / 0
Anolis roquet / AY296199 / 0
Anolis rubribarbus.2719.JJK.X / AY909789 / 0
Anolis sabanusKN / AY909776 / 0
Anolis sagrei / AF528727 / 0
Anolis schwartziKN / AY909777 / 0
Anolis scriptus / AY296200 / 0
Anolis semilineatus / AY296201 / 0
Anolis sericeus7069KN / AY909778 / 0
Anolis sheplani / AF055966 / 0
Anolis shrevei / AY263036 / 0
Anolis singularis / AY296202 / 0
Anolis smallwoodi / AY296203 / 0
Anolis smaragdinus / AF055968 / 0
Anolis sminthusKN / AY909779 / 0
Anolis strahmi / AY263008 / 0
Anolis stratulus / AF055929 / 0
Anolis trachyderma / AF337785 / 0
Anolis tranquillus sp. SBH266328 / AY909780 / 0
Anolis transversalis / AF337769 / 0
Anolis trinitatus / AY296204 / 0
Anolis tropidogasterKN / AY909782 / 0
Anolis tropidonotus11998KN / AY909783 / 0
Anolis uniformisKN / AY909784 / 0
Anolis utilensisKN / AY909785 / 0
Anolis valencienniDBRB / AF294310 / 0
Anolis vanidicus / AF055970 / 0
Anolis vermiculatus / AF055961 / 0
Anolis wattsi / AF055931 / 0
Anolis websteri / AY296205 / 0
Anolis whitemani / AY263024 / 0
Anolis woodi / AF337780 / 0
Anolis zeus13076 / AY909786 / 0
Aphaniotis fuscus / AF128497 / 0
Basiliscus galeritus / AF528714 / 0
Basiliscus plumifrons / U82680 / 0
Basiliscus vittatus / AF528715 / 0
Brachylophus fasciatus / AF528721 / 0
Bradypodion adolfifr / AF448727 / 0
Bradypodion asheorum / DQ335582 / 0
Bradypodion fischeri / U82688 / 0
Bradypodion occidentale / AF448728 / 1
Bradypodion pumilum / AF448729 / 1
Bradypodion tavetanum / AF448730 / 0
Bradypodion tenue / AM422796 / 0
Bradypodion transvaalense / AF448731 / 1
Bradypodion ventralae / AF448732 / 1
Bradypodion xenorhinum / DQ335581 / 0
Bronchocela cristatellus / AF128495 / 0
Brookesia antoetrae / AF448773 / 0
Brookesia brygooi / AF448774 / 0
Brookesia nasus / AF448775 / 0
Brookesia perarmata / AF448776 / 0
Brookesia peyrierasi / AF448777 / 0
Brookesia superciliaris / AF448778 / 0
Brookesia theili / AF448780 / 0
Brookesia therezieni / AF448779 / 0
Brookesia tuberculata / AF448781 / 0
Bufoniceps laungwalensis / DQ008214 / 0
Caimanops amphiboluroides / AF128472 / 0
Callisaurus draconoides / AY297492 / 0
Calotes calotes / AF128482 / 0
Calotes ceylonensis / AF128483 / 0
Calotes chincollium215505SAG / DQ289459 / 0
Calotes emma / AF128487 / 0
Calotes htunwiniShwe1 / DQ289463 / 0
Calotes irawadiMandalay / DQ289467 / 0
Calotes jerdoni219992 / GQ502783 / 0
Calotes kakhienensis / GQ502784 / 0
Calotes liocephalus / AF128484 / 0
Calotes liolepis / AF128485 / 0
Calotes mystaceus Mand-checkGB## / AF128488 / 0
Calotes mystaceusViet / AF128487 / 0
Calotes nigrilabris / AF128486 / 0
Calotes versicolor / AF128489 / 0
Calotes versicolor / DQ289476 / 0
Calumma boettgeri / AF448733 / 0
Calumma brevicornis / AF448734 / 0
Calumma cucullata / AF448735 / 0
Calumma furcifer / AF448736 / 0
Calumma gastrotaenia / AF448737 / 0
Calumma globifer2 / AF448738 / 0
Calumma hilleniusi / AF448739 / 0
Calumma nasuta / AF448740 / 0
Calumma oshaughnessyi / AF448741 / 0
Calumma parsonii / AF448742 / 0
Ceratophora aspera / AF128491 / 0
Ceratophora erdeleni / AF128522 / 0
Ceratophora karu / AF128520 / 0
Ceratophora stoddartii / AF128492 / 0
Ceratophora tennentii / AF128521 / 0
Chalarodon madagascarensis / AF528722 / 0
Chamaeleo africanus / AF448743 / 0
Chamaeleo arabicus / EF222194 / 0
Chamaeleo calcaricarens / EF222195 / 0
Chamaeleo calyptratus / AF448744 / 0
Chamaeleo chamaeleon / AF448745 / 0
Chamaeleo cristatus / AF448746 / 0
Chamaeleo deremensis / AF448747 / 0
Chamaeleo dilepis / AF128460 / 0
Chamaeleo ellioti / AF448748 / 1
Chamaeleo feae / AF448749 / 0
Chamaeleo fuelleborni / AF448750 / 1
Chamaeleo gracilis / AF448751 / 0
Chamaeleo hoehneli / AF448752 / 1
Chamaeleo jacksonii1 / AF448753 / 1
Chamaeleo johnstoni / AF448754 / 0
Chamaeleo melleri / AF448755 / 0
Chamaeleo monachus / EF222190 / 0
Chamaeleo montium / AF448756 / 0
Chamaeleo namaquensis / AF448757 / 0
Chamaeleo pfefferi / AF448758 / 0
Chamaeleo quadricornis / AF448759 / 0
Chamaeleo quilensis / AF448760 / 0
Chamaeleo rudis / AF448761 / 1
Chamaeleo sternfeldi / AF448762 / 1
Chamaeleo wiedersheimi / AF448763 / 0
Chamaeleo zeylanicus / EF222191 / 0
Chamaeleolis barbatus / AY296146 / 0
Chamaeleolis barbouri / AF055946 / 0
Chamaeleolis chamaeleonides / AF055975 / 0
Chamaeleolis guamuhaya / AF055974 / 0
Chamaeleolis porcus / AY296147 / 0
Chelosania brunneus / AF128465 / 0
Chlamydosaurus kingii / AF128469 / 0
Cnemidophorus tigris / U71332 / 0
Cophosaurus texana / AY297489 / 0
Cophotis ceylanica / AF128493 / 1
Cophotis dumbara / GQ502785 / 1
Corytophanes cristatus / AF528717 / 0
Corytophanes percarinatus / AF528718 / 1
Crotaphytus antiquus JLE12615 / EU038469 / 0
Crotaphytus bicinctoresMVZ137454 / EU038710 / 0
Crotaphytus bicinctores5PC / EU038698 / 0
Crotaphytus collarisE / U82681 / 0
Crotaphytus collarisW JAS300 / EU038619 / 0
Crotaphytus dickersonae ROM15051 / EU038721 / 0
Crotaphytus insularis ROM34013 / EU038732 / 0
Crotaphytus nebrius H5519 / EU038761 / 0
Crotaphytus reticulatus p1 / EU038786 / 0
Crotaphytus vestigiumS ROM13573 / EU038796 / 0
Crotaphytus vestigiumN MtSprgs / EU038788 / 0
Ctenoblepharys adspersa / AF305784 / 0
Ctenophorus caudicinctus / AF375623 / 0
Ctenophorus clayi / AF375620 / 0
Ctenophorus cristatus / AF375622 / 0
Ctenophorus decresii / AF128470 / 0
Ctenophorus femoralis / AF375627 / 0
Ctenophorus fionni / AF375638 / 0
Ctenophorus fordi / AF375626 / 0
Ctenophorus gibba / AF375625 / 0
Ctenophorus isolepis / AF375629 / 0
Ctenophorus maculatus / AF375628 / 0
Ctenophorus maculosus / AF375621 / 0
Ctenophorus mckenziei / AF375631 / 0
Ctenophorus nguyarna / DQ683736 / 0
Ctenophorus nuchalis / AF375633 / 0
Ctenophorus ornatus / AF375624 / 0
Ctenophorus pictus / AF375635 / 0
Ctenophorus reticulatus / AF375634 / 0
Ctenophorus rubens / AF375630 / 0
Ctenophorus rufescens / AF375636 / 0
Ctenophorus salinarum / AF375640 / 0
Ctenophorus scutulatus / AF375632 / 0
Ctenophorus tjantjalka / AF375637 / 0
Ctenophorus vadnappa / AF375639 / 0
Ctenosaura palearis162073 / GQ502763 / 0
Diplolaemus altopatagonica / AF528728 / 0
Diplolaemus darwinii / AF528729 / 0
Diporiphora albilabris / AY133003 / 0
Diporiphora arhemenica / AY133004 / 0
Diporiphora australis / AY133005 / 0
Diporiphora bennentii / AY133006 / 0
Diporiphora bilineata / AF128473 / 0
Diporiphora lalliae / AY133007 / 0
Diporiphora linga / AY133008 / 0
Diporiphora magna / AY133009 / 0
Diporiphora pindan / AY133010 / 0
Diporiphora reginae / AY133011 / 0
Diporiphora winneckei / AY133012 / 0
Dipsosaurus dorsalis / AF049857 / 0
Draco beccarii / AF288276 / 0
Draco biaro / AF288277 / 0
Draco bimaculatus / AF288241 / 0
Draco blanfordii / AF288242 / 0
Draco boschmai Flores / AF288269 / 0
Draco boschmai Lembata / AF288271 / 0
Draco boschmai Sumba / AF288270 / 0
Draco boschmai Sumbawa / AF288273 / 0
Draco bourouniensis / AF288279 / 0
Draco caerhulians / AF288281 / 0
Draco cornutus / AF288244 / 0
Draco cristatellus Sarawak / AF288255 / 0
Draco cyanopterus Mindanao / AF288245 / 0
Draco fimbriatus Java / AF288257 / 0
Draco fimbriatus MP / AF288256 / 0
Draco fimbriatus Poring / AF288254 / 0
Draco formosus / AF288263 / 0
Draco guentheri / AF288260 / 0
Draco haematopogon / AF288259 / 0
Draco indochinensis / AF128477 / 0
Draco Luwuk / AF288283 / 0
Draco maculatus / AF288248 / 0
Draco maximus / AF288231 / 0
Draco melanopogon / AF288258 / 0
Draco mindanensis / AF288249 / 0
Draco obscurus / AF288250 / 0
Draco ornatus Bohol / AF288253 / 0
Draco ornatus Samar / AF288252 / 0
Draco palawanensis / AF288262 / 0
Draco quadrasi Mindoro / AF288261 / 0
Draco quadrasi Sibuyan / AF288268 / 0
Draco quinquefasciatus / AF288232 / 0
Draco reticulatus Bohol / AF288247 / 0
Draco reticulatus Samar / AF288246 / 0
Draco rhytisma / AF288280 / 0
Draco spilonotus / AF288282 / 0
Draco spilopterus Bicol / AF288233 / 0
Draco spilopterus Cebu / AF288239 / 0
Draco spilopterus Isarog / AF288234 / 0
Draco spilopterus Maragondon / AF288235 / 0
Draco spilopterus Negros / AF288237 / 0
Draco spilopterus Panay / AF288238 / 0
Draco spilopterus Polillo / AF288236 / 0
Draco spilopterus Siquijor / AF288240 / 0
Draco sumatranus Borneo / AF288264 / 0
Draco sumatranus Malay Pen / AF288265 / 0
Draco sumatranus Sumatra / AF288266 / 0
Draco taeniopterus / AF288251 / 0
Draco timoriensis Timor / AF288275 / 0
Draco volans Java / AF288267 / 0
Elgaria panamitina / U82692 / 0
Enyalioides heterolepis1 / EU586744 / 0
Enyalioides laticeps / AF528719 / 0
Enyalioides microlepis / EU586750 / 0
Enyalioides oshaughnessyi1 / EU586751 / 0
Enyalioides palpebralis / EU586754 / 0
Enyalioides praestabilis2 / EU786755 / 0
Enyalius leechii / AF528733 / 0
Furcifer balteatus / AF448764 / 0
Furcifer belalandaensis / AF448765 / 0
Furcifer campani / AF448766 / 0
Furcifer labordi / AF448767 / 0
Furcifer lateralis / AF448768 / 0
Furcifer oustaleti / AF448769 / 0
Furcifer verrucosus / AF448770 / 0
Gambelia copei161173 / GQ502765 / 0
Gambelia sila / EU038400 / 0
Gambelia wislizenii / U82682 / 0
Gonocephalus grandis / AF128496 / 0
Holbrookia elegans / EU543797 / 0
Holbrookia lacerata / EU543795 / 0
Holbrookia maculata / AY297490 / 0
Holbrookia propinqua / AY297491 / 0
Holbrookia thermophila / EU543798 / 0
Hoplocercus spinosus / U82683 / 0
Hydrosaurus sp / AF128476 / 0
Hypsilurus boydii / AY133013 / 0
Hypsilurus bruijnii / AY133014 / 0
Hypsilurus dilophus / AF128466 / 0
Hypsilurus modestus / AY133015 / 0
Hypsilurus nigrigularis / AY133016 / 0
Hypsilurus papuensis / AY133017 / 0
Hypsilurus spinipes / AY133018 / 0
Japalura flaviceps / AF128500 / 0
Japalura splendida / AF128501 / 0
Japalura tricarinata / AF128478 / 0
Japalura variegata / AF128479 / 0
Laemanctus longipes / AF528716 / 0
Laudakia caucasia / AF028683 / 0
Laudakia erythrogastra / AF028680 / 0
Laudakia himalayana / AF028676 / 0
Laudakia lehmanni / AF028677 / 0
Laudakia microlepis / AF028678 / 0
Laudakia nupta / AF128513 / 0
Laudakia sacra / AF128515 / 0
Laudakia stellio / AF128516 / 0
Laudakia stoliczkana / AF128519 / 0
Laudakia tuberculata / AF128514 / 0
Leiocephalus barahonensis / EF591774 / 0
Leiocephalus carinatus / AF049864 / 0
Leiocephalus personatus / AF528754 / 0
Leiocephalus schreibersi / AF528753 / 0
Leiocephalus raviceps / GQ502767 / 0
Leiolepis belliana / U82689 / 0
Leiolepis guentherpetersi / AF128461 / 0
Leiosaurus bellii / AF528730 / 0
Leiosaurus catamarcensis / AF528731 / 0
Liolaemus abaucan / AF099263 / 0
Liolaemus albiceps / AF099267 / 1
Liolaemus andinus1 / AF099251 / 1
Liolaemus andinus2 / AF099245 / 1
Liolaemus archeforus / AY661901 / 1
Liolaemus atacamensis / AF305787 / 0
Liolaemus audituvelatus / AF305792 / 1
Liolaemus austromendocinus / AF099239 / 1
Liolaemus aymararum / AF305788 / 1
Liolaemus baguali / AY661905 / 1
Liolaemus bellii / AF099223 / 1
Liolaemus bibronii / AF099221 / 0
Liolaemus bitaeniatus / AF099219 / 0
Liolaemus boulengeri / AF099275 / 0
Liolaemus buergeri / AF099236 / 1
Liolaemus canqueli / AY297536 / 0
Liolaemus capillitas / AF099234 / 1
Liolaemus ceii / AF099237 / 1
Liolaemus cf. poecilochromus / DQ002485 / 1
Liolaemus cf. rothioldmelanops / AF099261 / 0
Liolaemus cf. silvanae / AY661900 / 1
Liolaemus chacoensis / AF099270 / 0
Liolaemus chaltin / AF099218 / 0
Liolaemus chiliensis / AF099224 / 0
Liolaemus orientalis chlorostictus / AF099247 / 1
Liolaemus coeruleus / AF099217 / 0
Liolaemus curis / GQ502779 / 1
Liolaemus cuyanus / AF099252 / 0
Liolaemus darwiniiLaRioja / AF099274 / 0
Liolaemus dorbignyi / AF099248 / 1
Liolaemus elongatus / AF099240 / 1
Liolaemus escarchardosi / unknown / 1
Liolaemus fabiani / AF305793 / 1
Liolaemus famatinae / AF099246 / 1
Liolaemus fitzingerii / AF099253 / 0
Liolaemus fuscus / AF099232 / 0
Liolaemus gallardoi / AY661902 / 1
Liolaemus gracilis / AF099222 / 0
Liolaemus gravenhorsti / AY297527 / 1
Liolaemus grosseorum / AF099272 / 0
Liolaemus hatcheri / AY661904 / 1
Liolaemus huacahuasicus / AY297533 / 1
Liolaemus incaicus alticolorTif51471DO / GQ502778 / 0
Liolaemus irregularis / AF099268 / 1
Liolaemus isabelae / GQ502776 / 1
Liolaemus josephorum / GQ502777 / 0
Liolaemus kingii / GQ502782 / 1
Liolaemus koslowskyi / AF099264 / 0
Liolaemus kriegi / AY297530 / 1
Liolaemus laurenti / AF099273 / 0
Liolaemus lemniscatus / AF099229 / 0
Liolaemus leopardinus / AF099235 / 1
Liolaemus lineomaculatus / AF099241 / 1
Liolaemus lutzae / AF099255 / 0
Liolaemus magellanicus / AF099243 / 1
Liolaemus molinai / AF305915 / 1
Liolaemus monticola / AF099230 / 0
Liolaemus multicolor / AF099250 / 1
Liolaemus multimaculatus / AF099257 / 0
Liolaemus nigroviridis / AF099233 / 1
Liolaemus nigroviridis ampanae[LNC22 / GQ502774 / 1
Liolaemus nitidus / AF099231 / 0
Liolaemus occipitalis / AF099256 / 0
Liolaemus olongasta / AF099271 / 0
Liolaemus ornatus / AF099266 / 1
Liolaemus paulinae / AY297531 / 1
Liolaemus petrophilus / AF099238 / 1
Liolaemus pictus cyanogaster / AF099225 / 1
Liolaemus pictus neuquen / AF099226 / 1
Liolaemus platei / AY297528 / 0
Liolaemus poecilochromis / AF099249 / 1
Liolaemus polychromus / GQ502780 / 1
Liolaemus pseudoanomalus / AF099254 / 0
Liolaemus puna walkeri / AF305790 / 1
Liolaemus quilmes / AF099265 / 0
Liolaemus reichei / AF305794 / 1
Liolaemus riojanus / AY297534 / 0
Liolaemus robertmertensi / AF099220 / 0
Liolaemus rothi / AF099262 / 0
Liolaemus ruibali / AF099244 / 1
Liolaemus salinicola / AF099259 / 0
Liolaemus sarmientoi / AY661907 / 1
Liolaemus scapularis / AF099258 / 0
Liolaemus schroederi / AF305791 / 1
Liolaemus somuncurae / AF099242 / 1
Liolaemus sp nigromaculatus / AY297526 / 0
Liolaemus stolzmanni / AY297532 / 1
Liolaemus tari / AY661906 / 1
Liolaemus tenuis / AF099228 / 0
Liolaemus tenuispunct / GQ502775 / 0
Liolaemus torresi / GQ502781 / 1
Liolaemus uspallatensis / AF099269 / 0
Liolaemus wiegmannii / AF099260 / 0
Liolaemus xanthoviridisFBC2 / AY297535 / 0
Liolaemus zapallarensis / AF099227 / 0
Liolaemus zullyi / AY661903 / 1
Lophognathus gilberti / AY133019 / 0
Lophognathus longirostris / AF128462 / 0
Lyriocephalus scutatus / AF128494 / 0
Mabuya aurata / U71330 / 0
Mantheyus phuwuanensis / AY555836 / 0
Microlophus albemarlensisG11 / AY625179 / 0
Microlophus albemarlensisG261 / AY625184 / 0
Microlophus albemarlensisG280B / AY625173 / 0
Microlophus atacamensis / AF528752 / 0
Microlophus bivittatusG43 / AY625163 / 0
Microlophus delanonisG104 / AY625167 / 0
Microlophus grayiiG132 / AY625170 / 0
Microlophus habeliiG205 / AY625166 / 0
Microlophus occipitalisG4 78 / AY625162 / 0
Microlophus pacificusG192 / AY625171 / 0
Microlophus peruvianusG4 91 / AY625158 / 0
Microlophus stolzmanniP6 258 / AY625161 / 0
Microlophus theresiaeP6 389 / AY625155 / 0
Microlophus tigrisP6 84 / AY625156 / 0
Moloch horridus / AF128467 / 0
Morunasaurus annularis / EU586758 / 0
Morunasaurus peruvianus / AF528720 / 0
Oplurus cuvieri / U82685 / 0
Otocryptis wiegmanni / AF128480 / 0
Petrosaurus mearnsi / L40444; L41450 / 0
Petrosaurus mearnsi161164DO / GQ502768 / 0
Petrosaurus thalassinus / AF049858 / 0
Phenacosaurus heteroderma TJ / AY296144 / 0
Phenacosaurus inderanae TJ / AY296145 / 0
Phenacosaurus nicefori LP REG01 / AF337768 / 0
Phrynocephalus interscapularis / AF128517 / 0
Phrynocephalus mystaceus / AF128518 / 0
Phrynocephalus raddei / U82691 / 0
Phrynosoma asio / GQ502772 / 0
Phrynosoma blainvillii / DQ385346 / 0
Phrynosoma cerroense / DQ385347 / 0
Phrynosoma cornutum / AY297487 / 0
Phrynosoma coronatum / AY297485 / 0
Phrynosoma ditmarsi / GQ502771 / 1
Phrynosoma douglassi / EU543778 / 1
Phrynosoma goodei / DQ385345 / 0
Phrynosoma hernandesi / U82686 / 1
Phrynosoma mcallii / AY297486 / 0
Phrynosoma modestum / AY297484 / 0
Phrynosoma orbicularae / GQ502770 / 1
Phrynosoma platyrhinos / AY297488 / 0
Phrynosoma solare / AF528739 / 0
Phrynosoma taurus / GQ502769 / 1
Phrynosoma wigginsi / DQ385348 / 0
Phymaturus antofogasta / AY661892 / 1
Phymaturus indistinctus / AY661893 / 1
Phymaturus mallimaccii / AF305785 / 1
Phymaturus palluma / AF099216 / 1
Phymaturus patagonicus / AY661894 / 1
Phymaturus punae / AF305786 / 1
Phymaturus somuncurensis / AF049865 / 1
Phymaturus zapalensis / GQ502773 / 1
Physignathus cocincinus / U82690 / 0
Physignathus lesueurii / AF128463 / 0
Pogona barbata / AF128474 / 0
Pogona brevis / AY133020 / 0
Pogona henrylawsoni / AY133021 / 0
Pogona minimus / AY133022 / 0
Pogona minor / AY133023 / 0
Pogona mitchelli / AY133024 / 0
Pogona nullarbor / AY133025 / 0
Pogona vitticeps / AY133026 / 0
Polychrus acutirostris / AF528737 / 0
Polychrus marmoratus / AF528738 / 0
Pristidactylus scapulatus / AF528732 / 0
Pseudocalotes brevipes / AF128502 / 0
Pseudocalotes larutensis / AF128503 / 0
Pseudotrapelus sinaitus / AF128507 / 0
Ptyctolaemus collicristatus / AY555837 / 0
Ptyctolaemus gularis / AY555838 / 0
Rankinia adelaidensis / AF128471 / 0
Rankinia diemensis / AF375619 / 0
Rhamphol brevicaudatusB / AF448771 / 0
Rhampholeon spectrum / AF448772 / 0
Salea horsfieldii / AF128490 / 0
Sator angustus / AF049859 / 0
Sauromalus australis / GQ502764 / 0
Sauromalus obesus / U82687 / 0
Sceloporus adleri / AY297519 / 1
Sceloporus carinatus / AY297496 / 0
Sceloporus cautus / AY297522 / 0
Sceloporus clarki / AY297511 / 0
Sceloporus cyanogenys / AY297524 / 1
Sceloporus formosus / AY297498 / 1
Sceloporus graciosus / AF049860 / 0
Sceloporus grammicus / AY297509 / 1
Sceloporus hunsakeri / AY297506 / 0
Sceloporus jalapae / AY297504 / 0
Sceloporus jarrovii / AY297512 / 1
Sceloporus lundelli / AY297499 / 0
Sceloporus maculosus / AY297501 / 0
Sceloporus magister / AF528741 / 0
Sceloporus malachiticus / AY297518 / 1
Sceloporus merriami / AY297520 / 0
Sceloporus mucronatus / AY297497 / 1
Sceloporus occidentalis / AY297515 / 0
Sceloporus ochoterenae / AF528743 / 0
Sceloporus olivaceous / AY297521 / 0
Sceloporus orcutti / AY297508 / 0
Sceloporus ornatus / AY297523 / 1
Sceloporus pictus / AY297500 / 0
Sceloporus poinsettii / AY297510 / 1
Sceloporus pyrocephalus / AY297502 / 0
Sceloporus scalaris / AF528742 / 0
Sceloporus siniferus / AY297494 / 0
Sceloporus smaragdinus / AY297517 / 1
Sceloporus spinosus / AY297525 / 0
Sceloporus squamosus / AY297495 / 0
Sceloporus teapensis / AY297505 / 0
Sceloporus undulatus NewMex / AY297514 / 0
Sceloporus utiformis / AF528740 / 0
Sceloporus variabilis / AY297507 / 0
Sceloporus virgatus / AY297516 / 0
Sceloporus woodi / AY297513 / 0
Sceloporus zosteromus / AY297503 / 0
Sitana ponticeriana / AF128481 / 0
Stenocercus angel / DQ080212 / 0
Stenocercus angulifer / EF565142 / 0
Stenocercus apurimacus / DQ080213 / 0
Stenocercus azureus / DQ080214 / 0
Stenocercus boettgeri / DQ080215 / 0
Stenocercus caducus / DQ080216 / 0
Stenocercus chota / DQ080217 / 0
Stenocercus chrysopygus / EF565141 / 0
Stenocercus crassicaudatus / AF049866 / 0
Stenocercus cupreus / DQ080218 / 0
Stenocercus doellojuradoi / AF528744 / 0
Stenocercus empetrus / DQ080219 / 0
Stenocercus eunetopsis / DQ080220 / 0
Stenocercus festae / DQ080221 / 0
Stenocercus formosus / DQ080238 / 0
Stenocercus guentheri / DQ080223 / 0
Stenocercus humeralis / DQ080224 / 0
Stenocercus imitator / DQ080225 / 0
Stenocercus iridescens / DQ080226 / 0
Stenocercus latebrosus / DQ080227 / 0
Stenocercus limitaris / DQ080228 / 0
Stenocercus marmoratus / EF565143 / 0
Stenocercus melanopygus / DQ080229 / 0
Stenocercus ochoai / AF528746 / 0
Stenocercus orientalis / DQ080230 / 0
Stenocercus ornatissimus / DQ080240 / 0
Stenocercus ornatus / DQ080231 / 0
Stenocercus percultus / DQ080232 / 0
Stenocercus puyango / DQ080233 / 0
Stenocercus rhodomelas / DQ080234 / 0
Stenocercus roseiventris / DQ080235 / 0
Stenocercus scapularis / DQ080222 / 0
Stenocercus stigmosus / DQ080236 / 0
Stenocercus torquatus / DQ080239 / 0
Stenocercus varius / DQ080237 / 0
Trapelus agilis / AF128509 / 0
Trapelus persicus / AF128510 / 0
Trapelus ruderatus / AF128508 / 0
Trapelus sanguinolentus / AF128511 / 0
Trapelus savignii / AF128512 / 0
Tropidurus etheridgei / AF528750 / 0
Tropidurus etheridgeiTC 921 / AY625152 / 0
Tropidurus hispidus4 76 / AY625154 / 0
Tropidurus koepkeorum / GQ502766 / 0
Tropidurus plica / AF528748 / 0
Tropidurus spinulosus / AF528751 / 0
Tympano centralis / AY133030 / 0
Tympano cephalus / AY133027 / 0
Tympano houstoni / AY133028 / 0
Tympano intima / AY133029 / 0
Tympano lineata / AF128475 / 0
Tympano pinguicolla / AY133031 / 0
Tympano tetrapophora / AY133032 / 0
Tympanocryptis lineata / AF128475 / 0
Uma exsul / EU543779 / 0
Uma inornata / EU543785 / 0
Uma notata / EU543784 / 0
Uma paraphygas / EU543780 / 0
Uma rufopunctata / EU543783 / 0
Uma scoparia / AF049861 / 0
Uracentron flaviceps / AF528747 / 0
Uranoscodon superciliosa / AF528749 / 0
Uromastyx acanthinurus / U71325 / 0
Uromastyx aegyptia / AB113806 / 0
Uromastyx benti / AB113821 / 0
Uromastyx dispar / AB113818 / 0
Uromastyx geyri / AB113809 / 0
Uromastyx hardwickii / AB113803 / 0
Uromastyx macfadyeni / AB113814 / 0
Uromastyx ocellata / AB113812 / 0
Uromastyx ornata / AB113824 / 0
Urosaurus graciosus / AF049862 / 0
Urosaurus ornatus / AY297493 / 0
Urostrophus gallardoi / AF528735 / 0
Urostrophus vautieri / AF528734 / 0
Uta stansburiana / AF049863 / 0
Varanus griseus / AF407503 / 0
Xenagama taylori / DQ008215 / 0
Table S1. Squamate fossils and approximate dates used as calibration points
Date (MYA) / Fossil taxon/Geological Event / Node assigned age / Reference218-144 / ROOT (maximum-minimum) / This age range was chosen to include the estimated divergence dates from several recent analyses of squamate and iguanian relationships as well as recent fossils of possible iguanian crown or stem origin, such as Tikiguania, Bharatagama, and Parviraptor. See arguments made by authors in associated references. / Wiens et al. 2006; Okajima & Kumazawa 2009; Hugall et al. 2007; Evans et al. 2002; Sues & Olson 1990; Datta & Ray 2006
1. / 50 / Anquingosaurus brevicephalus / Stratigraphic age corresponding to the end of Lower Eocene designating the common ancestor of clade containing all Chameleonidae species / Hou 1976; Estes 1983
2. / 13.8 / Chamaeleo caroliquarti / Midpoint stratigraphic age (11.6-16 mya) of common ancestor of all species in Cham. chameleo clade and sister group / Moody & Rocek 1980; Estes 1983
3. / 33.5 / Uromastyx europaeus / Stratigraphic age corresponding to the beginning of Lower Oligocene designating the common ancestor of Uromastyx and Leiolepis / Auge 1988
4. / 21 / Physignathus sp. cf. lesueurii / Stratigraphic age estimate assigned to common ancestor of Physignathus leusuerii and its amphibolurine sister group / Covacevich et al. 1990
5. / 33.5 / Crotaphytus oligocenicus / Stratigraphic age corresponding to the beginning of Lower Oligocene placed at common ancestor of Crotaphytus and Gambelia / Holman 1972 (but see Estes 1983)
6. / 20 / Dipsosaurus sp. / Stratigraphic age corresponding to approximate midpoint (16-23) of Lower Miocene placed at common ancestor of Dipsosaurus and its sister group / Estes 1983
7. / 2.7 / Sceloporus undulatus clade / Approximate midpoint stratigraphic age of Pliocene (1.8-3.6) placed at common ancestor of taxa referred to as members of Sceloporus undulatus clade and their sister group / Estes 1983
8. / 14.5 / Sceloporus / Stratigraphic age of fossil horizon (12-17 mya) placed at common ancestor of Sceloporus and its sister group / Robinson & Van Devender 1973; Estes 1983
9. / 31 / Paraphrynosoma greeni / Midpoint stratigraphic age (28-33 mya) of fossil horizon placed at common ancestor of Phrynosoma and the sand lizard clade / Holman 1987
10. / 13.5 / Holbrookia antigua / Midpoint stratigraphic age (11-16 mya) of fossil horizon placed at common ancestor of Holbrookia and Cophosaurus / Yatkola 1976
11. / 21.5 / Anolis dominicanus / Midpoint stratigraphic age (15-24 mya) of fossil horizon placed at common ancestor of Anolis chlorocyanus group and its sister group / Rieppel 1980; Polcyn et al. 2002
12. / 33.7 / Polychrus charisticus / Midpoint stratigraphic age (30.5-36.5 mya) of fossil horizon placed at common ancestor of Polychrus and its sister group / Smith 2006
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