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= endemic EX = extinct or assumed extinct

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Tropicagama temporalis
Northern Water Dragon | 
Karin, Stubbs, Arifin, Bloch, Ramadhan, Iskandar, Arida, Reilly, Kusnadi & Mcguire 2018
Karin, Stubbs, Arifin, Iskandar, Arida, Austin & McGuire 2020
Rooij 1915
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Genus
Gehyra (Four-clawed Geckos) |
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Lepidodactylus pantai
Kai Islands Scaly-toed Gecko | 
Karin, Oliver, Stubbs, Arifin, Iskandar, Arida, Oong, McGuire, Kraus, Fujita, Ineich, Ota, Hathaway & Fisher 2021
Karin, Stubbs, Arifin, Bloch, Ramadhan, Iskandar, Arida, Reilly, Kusnadi & Mcguire 2018
Stubbs, Karin, Arifin, Iskandar, Arida, Reilly, Bloch, Kusnadi & McGuire 2017
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Genus
Nactus (Hook-toed Geckos) |
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Genus
Carlia (Australian-Pacific Rainbow Skinks) |
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Emoia reimschisseli
Morotai Slender Skink | 
How, Durrant, Smith & Saleh 1998
Karin, Stubbs, Arifin, Bloch, Ramadhan, Iskandar, Arida, Reilly, Kusnadi & Mcguire 2018
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Lamprolepis smaragdina
Emerald Tree Skink | 
Karin, Stubbs, Arifin, Bloch, Ramadhan, Iskandar, Arida, Reilly, Kusnadi & Mcguire 2018
Mertens 1929
Rooij 1915
Schmitt, How, Hisheh, Goldberg & Maryanto 2000
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Genus
Tiliqua (Blue-tongued Skinks) |
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Varanus indicus
Pacific Monitor | 
Boehme, Horn & Ziegler 1994
Dryden & Ziegler in Pianka, King & King (eds.) 2004
Karin, Stubbs, Arifin, Bloch, Ramadhan, Iskandar, Arida, Reilly, Kusnadi & Mcguire 2018 [as "V. cf. indicus"]
Weijola, Kraus, Vahtera, Lindqvist & Donnellan 2017
Ziegler, Schmitz, Koch & Boehme 2007
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