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Supplementary Information Supplementary Information Material and methods Data collection. Appendix 1 lists the taxa, localities, and accession numbers of specimens used in the study. DNA extraction was performed as described elsewhere (Winnepenninckx et al. 1993), or with the Nucleospin tissue kit from Biotech, or the DNeasy Tissue Kit from Qiagen. Amplification and sequencing was performed using the following sets of primers: L2408, 5’-TGCACTGTGACATTGGCAA-3’ (Vidal and Hedges, 2004), H2928, 5’-GACTGCYTG GCATTCATTTT-3’ (Vidal and Hedges, 2004) , H2920, 5’-GCCATTCATTTTYCGAA-3’ (Vidal and Hedges, 2004), RAG1F3, 5’-TGCAYTGTGAYATTGGCAATGC-3’ (original), RAG1F4, -5’-TTTGTGADYTAATARAGTGTGA-3’ (original), RAG1R4, 5’-ATTACTTYCACAARACYCTTGCTC-3’ (original) for RAG1; LAM2N, 5’-TAT-CCA-CGT-TAT-GGC-TAT-GAA-CC-3’(Vidal and Hedges, 2005), LAMSQ, 5’-ATGGGAGGATGGATGCACCA-3’ (original), HAM, 5’-CAC-TTC-YTC-YTK-CTT-GGT-YT-3’ (Vidal and Hedges, 2005), HAMSQ, 5’-GGCCATGRTTCAAGAGGYGTAT-3’ (original) for AMEL; BDNF-F, 5’-GAC-CAT-CCT-TTT-CCT-KAC-TAT-GGT-TAT-TTC-ATA-CTT-3’ (Noonan and Chippindale, 2006), BDNF-R, 5’-CTA-TCT-TCC-CCT-TTT-AAT-GGT-CAG-TGT-ACA-AAC-3’ (Noonan and Chippindale, 2006) for BDNF; NT3-F3, 5’-ATA-TTT-CTG-GCT-TTT-CTC-TGT-GGC-3’ (Noonan and Chippindale, 2006), NT3-R4, 5’-GCG-TTT-CAT-AAA-AAT-ATT-GTT-TGA-CCG-G-5’ (Noonan and Chippindale, 2006), NT3F1, 5’-ATGTCCATCTTGTTTTATGTGATATTT-3’ (Townsend et al., 2008), NT3R1, 5’-ACRAGTTTRTTGTTYTCTGAAGTC-3’ (Townsend et al., 2008), NT3r3, 5’-AGCCCRTTGTCTCTGTGGATACAGA-3’ (original), NT3f3, 5’-AGATACAGCTGCTMACAAAAATA-3’ (original), NT3r4, 5’-AGAGCCGRTGGRTCACGGACAA-3’ (original), NT3f4, 5’-AGGAAARAGCCACCGSGGGGAAT-3’ (original) for NT3; BMP2_f6, 5’-CAKCACCGWATTAATATTTATGAAA-3’ (Wiens et al., 2008), BMP2_r3, 5’-ACYTTTTCGTTYTCRTCAAGGTA-3’ (Wiens et al., 2008), BMP2_f9, 5’-AYCAYAAYRCCAGCAAATGGGAA-3’ (original), BMP2_f11, 5’-GAYGGCVTGGGCCRYCCYCTCCA-3’ (original), BMP2_r5, 5’-GTCAATTCWGTGAAYYCCAAAAT-3’ (original) for BMP2. Both strands of the PCR products were sequenced at Pennsylvania State University and Genoscope (http://www.genoscope.fr), or at Genoscreen, a private company (http://www.genoscreen.fr). The two strands obtained for each sequence were combined using the BioEdit Sequence Alignment Editor program (Hall, 1999). Sequence entry and alignment were performed manually with MEGA4 (Tamura et al. 2007). Amino acid translations were used and alignment was straightforward. In all analyses, gaps were treated as missing data. Alignments can be obtained from Nicolas Vidal. Alignments resulted in 630 BDNF sites, 516 RAG1 sites, 591 BMP2 sites, 639 NT3 sites, and 375 AMEL sites (total: 2751 sites). Phylogenetic analysis. We built phylogenies using Maximum Likelihood (ML) and Bayesian methods of inference. We used an anguimorph (genus Varanus), two amerophidians (genera Anilius and Tropidophis) and two afrophidians, a ‘henophidian’ (genus Boa) and a caenophidian (elapid, either Naja or Dendroaspis depending on the gene) as outgroups. ML analyses were performed with RAxML 7.0.4 (Stamatakis 2006; Stamatakis et al. 2008), and Bayesian analyses were performed with MrBayes 3.1 (Ronquist & Huelsenbeck 2003). We treated each of the three codon positions of the genes as a separate partition, so our combined dataset is partitioned into three partitions. Bayesian analyses were performed by running 5,000,000 generations in four chains, saving the current tree every 100 generations, with a GTR model as inferred by Modeltest using the AIC criterion (Posada & Crandall 1998) applied to each of the three partitions. The last 48,000 trees were used to construct a 50% majority rule consensus tree. For the ML analysis, we used the same three partitions and performed 1000 bootstrap replicates. Typhlops agoralionis Typhlops sylleptor Typhlops jamaicensis Typhlops capitulatus Typhlops sulcatus Typhlops rostellatus Typhlops lumbricalis Typhlops schwartzi Typhlops eperopeus Typhlops syntherus Typhlops catapontus Typhlops naugus Typhlops richardii Typhlops platycephalus Typhlops hypomethes Typhlops granti Typhlops geotomus Typhlops monastus Typhlops dominicanus Typhlops notorachius Typhlops anousius Typhlops anchaurus Typhlops contorhinus Typhlops arator Typhlops caymanensis Typhlops brongersmianus Typhlops reticulatus Typhlops punctatus Typhlops congestus Typhlops lineolatus Typhlops fornasinii Typhlops bibronii Rhinotyphlops mucruso Rhinotyphlops schlegelii Typhlops angolensis Typhlops elegans Typhlops sp Typh obtusus Rhinotyphlops feae Rhinotyphlops newtonii Rhinotyphlops lalandei Rhinotyphlops unitaeniatus Typhlops sp Typhlops arenarius Typhlops andasibensis Ramphotyphlops ligatus Ramphotyphlops ganei Ramphotyphlops kimberleyensis Ramphotyphlops troglodytes Ramphotyphlops unguirostris Ramphotyphlops guentheri Ramphotyphlops howi Ramphotyphlops diversus Ramphotyphlops bituberculatus Ramphotyphlops longissimus Ramphotyphlops grypus Ramphotyphlops endoterus Ramphotyphlops hamatus Ramphotyphlops australis Ramphotyphlops pilbarensis Ramphotyphlops waitii Ramphotyphlops pinguis Ramphotyphlops splendidus Ramphotyphlops bicolor Ramphotyphlops, polygrammicus Acutotyphlops subocularis Acutotyphlops kunuaensis Acutotyphlops sp Ramphotyphlops acuticaudus Ramphotyphlops sp Ramphotyphlops lineatus Ramphotyphlops braminus Typhlops pammeces Ramphotyphlops albiceps Typhlops luzonensis Typhlops vermicularis Xenotyphlops sp Xenotyphlops grandidieri Typhlops hedraeus Typhlops mirus Mitophis asbolepis Mitophis leptepileptus Mitophis pyrites Siagonodon septemstriatus Epictia columbi Rena dulcis Rhinoleptus koniagui Guinea bicolor Myriopholis adleri Myriopholis algeriensis Myriopholis longicauda Leptotyphlops nigroterminus Leptotyphlops conjunctus Namibiana occidentalis Liotyphlops albirostris Typhlophis squamosus Boa constrictor Elapidae Tropidophis sp Anilius scytale Varanus sp 10 ML phylogram 100 80 Typhlops agoralionis 47 Typhlops sylleptor 37 Typhlops jamaicensis 41 Typhlops capitulatus Typhlops sulcatus Typhlops rostellatus 98 84 92 Typhlops lumbricalis 38 Typhlops schwartzi Typhlops eperopeus Typhlops syntherus 97 Typhlops catapontus 48 98 55 Typhlops naugus 73 Typhlops richardii 100 Typhlops platycephalus Typhlops hypomethes 100 Typhlops granti 100 100 Typhlops geotomus 100 Typhlops monastus Typhlops dominicanus 43 50 Typhlops notorachius 89 Typhlops anousius 100 Typhlops anchaurus 93 100 Typhlops contorhinus Typhlops arator Typhlops caymanensis 99 Typhlops brongersmianus Typhlops reticulatus 81 Typhlops punctatus 100 Typhlops congestus 49 92 Typhloplineolatus 100 Typhlops fornasinii 85 Typhlops bibronii 100 Rhinotyphlops mucruso 63 Rhinotyphlops schlegelii 100 98 Typhlops angolensis 100 30 Typhlops elegans 100 Typhlops sp Typhlops obtusus 100 Rhinotyphlops feae 73 Rhinotyphlops newtoni i 55 Rhinotyphlops lalandei Rhinotyphlops unitaeniatus 100 100 Typhlops sp Typhlops arenarius Typhlops andasibensis 99 Ramphotyphlops ligatus 100 Ramphotyphlops ganei 100 99 Ramphotyphlops kimberleyensis Ramphotyphlops troglodytes Ramphotyphlops unguirostris 93 90 87 Ramphotyphlops guentheri Ramphotyphlops howi 52 87 Ramphotyphlops diversus Ramphotyphlops bituberculatus 100 100 Ramphotyphlops longissimus Ramphotyphlops grypus 100 76 59 Ramphotyphlops endoterus Ramphotyphlops hamatus 99 Ramphotyphlops australis 65 100 Ramphotyphlops pilbarensis 95 Ramphotyphlops waitii 100 Ramphotyphlops pinguis 100 Ramphotyphlops splendidus 55 Ramphotyphlops bicolor Ramphotyphlops polygrammicus 63 91 84 Acutotyphlops subocularis 100 Acutotyphlops kunuaensis Acutotyphlops sp 93 Ramphotyphlops acuticaudus 93 79 Ramphotyphlops sp Ramphotyphlops lineatus 100 100 100 Ramphotyphlops braminus 86 Typhlops pammeces 92 Ramphotyphlops albiceps Typhlops luzonensis Typhlops vermicularis 100 Xenotyphlops sp Xenotyphlops grandidieri 76 Typhlops hedraeus 76 Typhlops mirus 78 Mitophis asbolepis 100 Mitophis leptepileptus 39 71 Mitophis pyrites 64 Siagonodon septemstriatus Epictia columbi 87 Rena dulcis 68 Rhinoleptus koniagui Guinea bicolor 100 92 100 Myriopholis adleri Myriopholis algeriensis 100 Myriopholis longicauda 100 100 Leptotyphlops nigroterminus Leptotyphlops conjunctus Namibiana occidentalis 99 Boa constrictor 100 Elapidae 46 97 Tropidophis sp Anilius scytale 100 Liotyphlops albirostris Typhlophis squamosus Varanus sp ML bootstrap majority-rule consensus tree (1000 replicates) 100 100 Typhlops agoralionis 75 Typhlops sylleptor 94 Typhlops jamaicensis 82 Typhlops capitulatus Typhlops sulcatus Typhlops rostellatus 100 100 Typhlops lumbricalis 100 Typhlops schwartzi 81 Typhlops eperopeus Typhlops syntherus 40 Typhlops catapontus 53 100 70 Typhlops naugus 96 Typhlops richardii Typhlops platycephalus 100 Typhlops hypomethes 100 Typhlops granti 100 100 Typhlops geotomus 100 Typhlops monastus Typhlops dominicanus 21 27 Typhlops anchaurus 99 Typhlops anousius 100 Typhlops notorachius 100 100 Typhlops contorhinus Typhlops arator Typhlops caymanensis 100 Typhlops brongersmianus Typhlops reticulatus 74 Typhlops punctatus 100 Typhlops congestus 38 100 Typhloplineolatus 100 100 Typhlops fornasinii Typhlops bibronii 100 92 Rhinotyphlops mucruso Rhinotyphlops schlegelii 100 100 Typhlops angolensis 100 Typhlops elegans Typhlops sp 100 Typh obtusus 100 46 Rhinotyphlops feae 99 Rhinotyphlops newtonii Rhinotyphlops unitaeniatus Rhinotyphlops lalandei 100 Ramphotyphlops ligatus 100 Ramphotyphlops ganei 100 100 Ramphotyphlops kimberleyensis Ramphotyphlops troglodytes 100 Ramphotyphlops unguirostris 100 98 Ramphotyphlops guentheri 79 100 Ramphotyphlops howi Ramphotyphlops diversus 100 Ramphotyphlops bituberculatus 100
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