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The genera Lichanura and Charina are currently classified as erycines [1], but are strongly supported as the sister group to Ungaliophiinae, as in previous studies [20,36,47,166]. We expand Ungaliophiinae to include these two genera (Figure 21), rather than erect a new subfamily for these taxa. The subfamily Ungaliophiinae is placed as the sister group to a well-supported clade (SHL = 87) containing the rest of the traditionally recognized Erycinae and Boinae. We restrict Erycinae to the Old World genus Eryx. The genus Candoia (Boinae) from Oceania and New Guinea [1], is placed as the sister taxon to a moderately supported clade (SHL = 83) consisting of Erycinae (Eryx) and the remaining genera of Boinae (Boa, Corallus, Epicrates, and Eunectes). To solve the non-monophyly of Boinae with respect to Erycinae (due to Candoia), we place Candoia in a new subfamily (Candoiinae, subfam. nov.; see Appendix I). Boinae then comprises the four Neotropical genera that have traditionally been classified in this group (Boa, Corallus, Epicrates, and Eunectes). We acknowledge that non-monophyly of Boinae could be resolved in other ways (e.g. expanding it to include Erycinae). However, our taxonomy maintains the traditionally used subfamilies Boinae, Erycinae, and Ungaliophiinae, modifies them to reflect the phylogeny, and recognizes the phylogenetically distinct boine clades as separate subfamilies (Candoiinae, Sanziniinae). Within Boinae, Eunectes renders Epicrates paraphyletic, but this is not strongly supported see also ([48]). Our results for advanced snakes (Caenophidia) are generally similar to those of other recent studies [41,42,169], and will only be briefly described. However, in contrast to most recent studies [20,36,41,42,81,159,160], Acrochordidae is here strongly placed (SHL = 95) as the sister group to Xenodermatidae. This clade is then the sister group to the remaining Colubroidea, which form a strongly supported clade (SHL = 100; Figures 1, 22). This relationship has been found in some previous studies [169,170], and was hypothesized by early authors [171]. Further evidence will be required to resolve this conclusively. Analyses based on concatenation of 20–44 loci do not support this grouping [20,36], though preliminary species-tree analyses of >400 loci do (Pyron et al., in prep.). Relationships in Pareatidae are similar to recent studies [172], and the group is strongly placed as the sister taxon to colubroids excluding xenodermatids (SHL = 100; Figures 1 , 22), as in most recent analyses (e.g. [41,43,44]). The family Viperidae is the sister group to all colubroids excluding xenodermatids and pareatids (Figure 1), as in other recent studies. The family Viperidae is strongly supported (Figure 22), as is the subfamily Viperinae, and the sister-group relationship between Azemiopinae and Crotalinae (SHL = 100). Our results generally support the existing genericlevel taxonomy within Viperinae (Figure 22). However, we recover a strongly supported clade within Viperinae consisting of Daboia russelii, D. palaestinae, Macrovipera mauritanica, and M. deserti (Figure 22), as in previous studies [173]. We corroborate previous suggestions that these taxa be included in Daboia [174], though this has not been widely adopted [1]. The other Macrovipera species (including the type species) remain in that genus (Figure 22). Within Crotalinae (Figure 22), a number of genera appear to be non-monophyletic. The species Trimeresurus gracilis is strongly supported as the sister taxon to Ovophis okinavensis and distantly related to other Trimeresurus, whereas the other Ovophis are strongly placed as the sister group to Protobothrops. A well-supported clade (SHL = 90) containing Atropoides picadoi, Cerrophidion, and Porthidium renders Atropoides paraphyletic (see also [175]). The species Bothrops pictus, considered incertae sedis in previous studies [176], is here strongly
supported as the sister taxon to a clade containing Rhinocerophis, Bothropoides, Bothriopsis, and Bothrops (Figure 22). Most of these relationships are strongly supported. Viperidae is strongly placed (SHL = 95) as the sister taxon to a well-supported clade (SHL = 100) containing Colubridae, Elapidae, Homalopsidae, and Lamprophiidae (Figure 1). Monophyly of Homalopsidae is also strongly supported (Figure 23). Within Homalopsidae, the non-monophyly of the genus Enhydris is strongly supported (Figure 23), and should likely be split into multiple genera. Homalopsidae is weakly supported (SHL = 58) as the sister group of Elapidae + Lamprophiidae (Figure 1). This same relationship was also weakly supported by previous analyses [41,44], but other studies have found strong support for placing Homalopsidae as the sister group of a strongly supported clade including Elapidae, Lamprophiidae, and Colubridae [20,36], including data from >400 loci (Pyron et al., in prep.). Support for the monophyly of Lamprophiidae is strong (but excluding Micrelaps; see below), and most of its subfamilies are well-supported [40,41,177,178] including Atractaspidinae, Aparallactinae, Lamprophiinae, Prosymninae (weakly placed as the sister-group to Oxyrhabdium), Pseudaspidinae, Psammophiinae, and Pseudoxyrhophiinae (Figure 23). In Lamprophiidae, most genera are monophyletic based on our sampling (Figure 23). However, within Aparallactinae, Xenocalamus is strongly placed within Amblyodipsas, and in Atractaspidinae, Homoroselaps is weakly placed in Atractaspis. In Lamprophiinae, Lamprophis is paraphyletic with respect to Lycodonomorphus but support for the relevant clades is weak. The enigmatic genera Buhoma from Africa and Psammodynastes from Asia were both previously considered incertae sedis within Lamprophiidae [41]. Here they are weakly placed as sister taxa, and more importantly, they form a strongly supported clade with the African genus Pseudaspis (Pseudaspidinae; SHL = 95; Figure 23). Therefore, we expand Pseudaspidinae to include these two genera. The genus Micrelaps (putatively an aparallactine; [1]) is weakly placed as the sister taxon to Lamprophiidae + Elapidae. Along with Oxyrhabdium (see above) and Montaspis [40], this genus is treated as incertae sedis in our classification (Appendix I). If future studies strongly support these relationships, they may require a new family for Micrelaps and possibly a new subfamily for Oxyrhabdium, though placement of these taxa has been highly variable in previous studies [40,41,44,81]. Monophyly of Elapidae is strongly supported (Figure 24), and Calliophis melanurus is strongly supported as the sister group to all other elapids (see also [44]). Within Elapidae (Figure 24), relationships are generally concordant with previous taxonomy, with some exceptions. The genera Toxicocalamus, Simoselaps, and Echiopsis are all divided across multiple clades, with strong support for many of the relevant branches. A recent study has provided a generic re-classification of the sea snakes (Hydrophis group) to resolve the extensive paraphyly of genera found in previous studies (e.g. [46,179,180]). Our results support this classification. Monophyly of Colubridae and most of its subfamilies (sensu [41,44]) are strongly supported (Figures 1, 25, 26, 27, 28). However, relationships among many of these subfamilies are weakly supported (Figure 1), as in most previous studies [41,43,45,181]. The subfamilies Calamariinae and Pseudoxenodontinae are strongly supported as sister taxa, and weakly
Page 1 and 2: BMC Evolutionary Biology This Provi
Page 3 and 4: Conclusions We present a new large-
Page 5 and 6: clades that were previously studied
Page 7 and 8: Figure 19 Species-level squamate ph
Page 9 and 10: Cricosaura [105]. We also recognize
Page 11 and 12: Ophioscincus are polyphyletic with
Page 13 and 14: We find strong support for monophyl
Page 15 and 16: studies have also begun to revise s
Page 17: Relationships in this group are gen
Page 21 and 22: Finally, within a weakly supported
Page 23 and 24: previous studies of 8 datasets have
Page 25 and 26: Throughout the paper, we refer to t
Page 27 and 28: for ND2 (45%, 960 bp), 1556 for ND4
Page 29 and 30: Authors' contributions RAP and JJW
Page 31 and 32: Lacertoides, Lamprolepis, Lampropho
Page 33 and 34: Darlingtonia, Diadophis, Diaphorole
Page 35 and 36: 10. Wiens JJ, Brandley MC, Reeder T
Page 37 and 38: 38. Vidal N, Marin J, Morini M, Don
Page 39 and 40: 64. Castoe TA, Doan TM, Parkinson C
Page 41 and 42: 94. Anisimova M, Gascuel O: Approxi
Page 43 and 44: 122. Miralles A, Fuenmayor GR, Boni
Page 45 and 46: 149. Noonan BP, Chippindale PT: Vic
Page 47 and 48: 178. Vidal N, Branch WR, Pauwels OS
Page 49 and 50: 207. Edgar RC: MUSCLE: multiple seq
Page 51 and 52: Figure 2 &∃ &##% &∃ %&∃ &
Page 53 and 54: 100 C Figure 4 (i) (ii) Gekkonidae
Page 55 and 56: E Figure 6 Scincidae 100 Typhlosaur
Page 57 and 58: G Figure 8 Lygosominae cont. 100 97
Page 59 and 60: I Figure 10 Lygosominae cont. 90 10
Page 61 and 62: K Figure 12 99 100 84 100 Rhineura
Page 63 and 64: M Figure 14 Xenosauridae 100 Xenosa
Page 65 and 66: O Figure 16 Uromasticinae (i) 100 A
Page 67 and 68: Q Figure 18 (i) (ii) Leiocephalidae
Page 69 and 70:
S Figure 20 100 90 100 100 T-AA 97
Page 71 and 72:
U Figure 22 Acrochordidae (i) (ii)
Page 73 and 74:
W Figure 24 100 Elapidae Calliophis
Page 75 and 76:
Y Figure 26 Colubrinae cont. 64 83
Page 77 and 78:
AA Figure 28 (i) 100 Dipsadinae Con
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