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Figure S1. Raxml Trees for Concatenated Data for 81 Taxa, with Three Different Alignment Treatments for 16S

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Figure S1. Raxml Trees for Concatenated Data for 81 Taxa, with Three Different Alignment Treatments for 16S Title A new subfamily of fossorial colubroid snakes from the Western Ghats of peninsular India Authors DEEPAK, V; Ruane, S; Gower, DJ Description Orcid: 0000-0002-1725-8863 Date Submitted 2019-12-09 Figure S1. RAxML trees for concatenated data for 81 taxa, with three different alignment treatments for 16s. A) ML tree for concatenated data including 16s aligned by ClustalW, with all sites included. Numbers on tree are bootstrap values (based on 1,000 replicates). Scale bar indicates substitutions per site. Mimophis mahfalensis 2 9 2 1 Aparallactus capensis 1 0 Liopholidophis sexlineatus 100 Bothrolycus ater 9 Boaedon fuliginosus Homoroselaps lacteus 1 2 4 3 Pseudaspis cana Ditypophis sp. Bungarus fasciatus 2 9 1 0 100 Naja kaouthia 2 7 Oxyuranus scutellatus 100 Prosymna visseri 3 2 6 Prosymna janii 8 0 Buhoma depressiceps Buhoma procterae 9 9 Micrelaps bicoloratus Cyclocorus lineatus 100 8 5 Cyclocorus nuchalis 9 3 Hologerrhum philippinum Oxyrhabdium leporinum 8 5 Ahaetulla pulverulenta 7 7 4 9 Oligodon arnensis 100 Grayia ornata 4 0 Grayia smythii 2 7 Sibynophis subpunctatus Calamaria pavimentata 100 2 5 9 4 Farancia abacura 8 7 2 5 Contia tenuis Pseudoxenodon karlschmidti 7 4 Aspidura ceylonensis Cantoria violacea 9 8 Azemiops feae 100 Agkistrodon contortrix 9 8 100 Bitis nasicornis Daboia russellii 8 7 Aplopeltura boa 9 8 Pareas carinatus 6 8 Asthenodipsas malaccanus 100 Xylophis captaini 6 4 Xylophis stenorhynchus 6 0 8 7 Xylophis perroteti Xenodermus javanicus 7 4 Acrochordus javanicus Xenophidion schaeferi 7 0 Casarea dussumieri 4 6 Corallus annulatus 4 0 Chilabothrus striatus 9 8 Epicrates cenchria 9 7 Eunectes notaeus 4 3 Boa constrictor 9 8 7 8 Candoia carinata 9 9 Eryx colubrinus 5 6 Eryx conicus 6 8 Ungaliophis continentalis 9 4 Charina bottae 4 3 Calabaria reinhardtii Sanzinia madagascariensis Liasis mackloti 4 0 5 2 5 3 Malayopython reticulatus 9 9 Morelia viridis 100 8 4 Python bivittatus 8 3 Loxocemus bicolor Xenopeltis unicolor 6 1 7 4 Cylindrophis ruffus 8 4 Cylindrophis maculatus Anomochilus leonardi 9 8 Rhinophis drummondhayi 7 7 9 8 Brachyophidium rhodogaster Melanophidium punctatum 9 7 Tropidophis feicki Anilius scytale Indotyphlops braminus 4 4 1 8 Xerotyphlops vermicularis 5 6 Typhlops jamaicensis 8 0 Afrotyphlops punctatus 4 8 Madatyphlops andasibensis 100 Xenotyphlops grandidieri Gerrhophilus mirus 100 Rena humilis 100 9 0 Namibiana occidentalis Liotyphlops albirostris 0.3 B) ML tree for concatenated data including 16s aligned by MUSCLE, with all sites included. Numbers on tree are bootstrap values (based on 1,000 replicates). Scale bar indicates substitutions per site. Bothrolycus ater 9 9 1 2 Boaedon fuliginosus Liopholidophis sexlineatus 1 1 Pseudaspis cana 9 1 3 1 8 Mimophis mahfalensis Homoroselaps lacteus 1 1 Ditypophis sp. Buhoma depressiceps 6 4 2 1 Buhoma procterae Aparallactus capensis 2 9 Oxyuranus scutellatus 9 0 100 Bungarus fasciatus 2 9 1 9 Naja kaouthia Prosymna visseri 100 Prosymna janii 9 9 Micrelaps bicoloratus Cyclocorus nuchalis 100 8 6 Cyclocorus lineatus 9 3 Hologerrhum philippinum Oxyrhabdium leporinum Grayia ornata 9 9 Grayia smythii 6 1 4 7 Ahaetulla pulverulenta 8 2 3 0 Oligodon arnensis 3 1 Calamaria pavimentata Sibynophis subpunctatus 100 3 2 Farancia abacura 9 5 8 2 2 5 Contia tenuis Pseudoxenodon karlschmidti 6 2 Aspidura ceylonensis Cantoria violacea Bitis nasicornis 100 Daboia russellii 100 Azemiops feae 9 5 9 5 Agkistrodon contortrix Aplopeltura boa 8 5 9 9 Pareas carinatus 6 8 Asthenodipsas malaccanus 100 Xylophis captaini 7 3 8 4 Xylophis stenorhynchus 5 8 Xylophis perroteti Xenodermus javanicus 7 6 Acrochordus javanicus 7 1 Xenophidion schaeferi Casarea dussumieri Brachyophidium rhodogaster 7 6 9 6 Rhinophis drummondhayi 1 0 Melanophidium punctatum Cylindrophis ruffus 9 8 5 6 Cylindrophis maculatus 9 9 Anomochilus leonardi Malayopython reticulatus 4 6 6 5 6 3 Liasis mackloti 9 9 Morelia viridis 8 0 Python bivittatus 8 7 Loxocemus bicolor Xenopeltis unicolor Corallus annulatus 4 6 3 9 Chilabothrus striatus 5 2 9 9 Epicrates cenchria 100 9 7 Eunectes notaeus 4 2 Boa constrictor 7 8 Candoia carinata Eryx colubrinus 100 6 1 Eryx conicus 8 4 Ungaliophis continentalis 9 4 Charina bottae Calabaria reinhardtii 4 6 Sanzinia madagascariensis Tropidophis feicki 9 7 Anilius scytale Indotyphlops braminus 4 2 Xerotyphlops vermicularis 5 9 Afrotyphlops punctatus 8 09 Typhlops jamaicensis 3 8 Madatyphlops andasibensis 100 Gerrhophilus mirus Xenotyphlops grandidieri 100 Namibiana occidentalis 9 9 8 7 Rena humilis Liotyphlops albirostris 0.4 C) ML tree for concatenated data including 16s aligned by ClustalW, with ambiguously aligned sites removed under ‘less stringent’ option in Gblocks. Numbers on tree are bootstrap values (based on 1,000 replicates). Scale bar indicates substitutions per site. Mimophis mahfalensis 1 2 1 4 Homoroselaps lacteus 7 Pseudaspis cana 9 Liopholidophis sexlineatus Bothrolycus ater 1 0 9 7 Boaedon fuliginosus Ditypophis sp. 4 Bungarus fasciatus 9 5 100 Oxyuranus scutellatus Naja kaouthia Cyclocorus lineatus 100 1 9 7 7 Cyclocorus nuchalis 9 1 Hologerrhum philippinum Oxyrhabdium leporinum 6 Buhoma depressiceps 9 8 4 6 5 3 0 Buhoma procterae Aparallactus capensis Micrelaps bicoloratus Prosymna janii 100 Prosymna visseri 9 9 Grayia ornata 7 2 4 6 Grayia smythii 8 9 Ahaetulla pulverulenta 3 9 Oligodon arnensis 2 9 Calamaria pavimentata Sibynophis subpunctatus 100 3 7 Farancia abacura 9 3 7 4 4 9 Contia tenuis Pseudoxenodon karlschmidti 6 3 Aspidura ceylonensis Cantoria violacea 9 4 Agkistrodon contortrix 100 Azemiops feae 9 8 Bitis nasicornis 100 Daboia russellii 5 4 Aplopeltura boa 9 8 Pareas carinatus 7 3 Asthenodipsas malaccanus 100 Xylophis captaini 4 9 7 5 Xylophis stenorhynchus 6 7 Xylophis perroteti Xenodermus javanicus 8 2 Acrochordus javanicus Xenophidion schaeferi 8 3 Casarea dussumieri Corallus annulatus 5 9 4 7 Chilabothrus striatus 9 9 Epicrates cenchria 9 9 Eunectes notaeus Boa constrictor 6 7 9 8 9 8 Eryx colubrinus 4 8 Eryx conicus 5 1 Candoia carinata Ungaliophis continentalis 8 3 6 9 Charina bottae Calabaria reinhardtii 4 6 Sanzinia madagascariensis Rhinophis drummondhayi 7 3 Brachyophidium rhodogaster 6 1 8 7 1 5 Melanophidium punctatum 100 8 7 Anomochilus leonardi Cylindrophis maculatus 7 6 Cylindrophis ruffus Malayopython reticulatus 7 0 3 6 4 Liasis mackloti 9 9 Python bivittatus 8 4 Morelia viridis 7 9 Loxocemus bicolor Xenopeltis unicolor 9 4 Tropidophis feicki Anilius scytale Indotyphlops braminus 7 4 Afrotyphlops punctatus 5 1 Xerotyphlops vermicularis 6 6 4 6 Typhlops jamaicensis 4 6 Madatyphlops andasibensis 100 Gerrhophilus mirus Xenotyphlops grandidieri 100 100 Rena humilis 8 4 Namibiana occidentalis Liotyphlops albirostris 0.3 .
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