Table 1.
Number of taxa sampled per family or subfamily.
Families are listed in order according to Fig 1. For the taxonomy of families and subfamilies, we use Adalsteinsson et al, [26] for Anomalepididae and Leptotyphlopidae, Pyron and Wallach [29] for Gerrhopilidae, Typhlopidae, and Xenotyphlopidae, Pyron et al [30] for Booidea, and Pyron et al [15] for Alethinophidia. The number of species per clade was taken from The Reptile Database (http://www.reptile-database.org/) on 10/01/2015. Percentages of the number of species sampled do not include taxa not assigned to species status. Paraphyletic taxa are included under their traditional family and/or subfamily. In the Total cell for total number of species, the number not in parentheses equals the sum of the values in the table and the number in the parentheses equals the number returned when a search for Serpentes is conducted in The Reptile Database. Percentage for total number of species sampled is based on 3566 species.
Fig 1.
Abridged phylogeny on final dataset of 1652 snake species and seven outgroup taxa displaying higher-level relationships.
Maximum-likelihood phylogenetic estimate based on 10 concatenated genes. Tips represent families and sub-families. Commonly recognized higher-level clades are labeled in all caps and bold. Species classified as Lamprophiidae incertae sedis are also shown since they did not place within a subfamily. Node values represent SHL support values. Skeleton of the species tree is displayed on the left, colored and labeled as they appear in Figs 2–10.
Fig 2.
Species-level phylogeny on final dataset of 1652 snake species.
Maximum-likelihood phylogenetic estimate based on 10 concatenated genes. Node values represent SHL support values. Seven outgroup taxa are not shown. Colors of clades indicate their position in the overall tree, shown at left. Newly sequenced taxa are highlighted in bold. Skeleton of the species tree is displayed on the left with displayed subfamilies/families highlighted. Letters denoted by i and ii represent parts of the tree where external branches do not connect to the part of the tree immediately preceding it. A) Anomalepididae, Epictinae, Leptotyphlopinae, Gerrhopilidae, Xenotyphlopidae, and Typhlopinae. B) Asiatyphlopinae I, Afrotyphlopinae; Madatyphlopinae, and Asiatyphlopinae II.
Fig 3.
Phylogenetic tree of Serpentes continued.
A) Aniliidae, Tropidophiidae, Calabariidae, Candoiidae, Sanziniidae, Charininae, Ungaliophiinae, Erycidae, and Boidae. Bi) Cylindrophiidae + Anomochilidae, Uropeltidae, Xenopeltidae, Loxocemidae, and Pythonidae. Bii) Bolyeridae, Xenophidiidae, Acrochordidae, Xenodermatidae, and Pareatidae.
Fig 4.
Phylogenetic tree of Serpentes continued.
Ai) Viperinae. Aii) Azemiopinae and Crotalinae. B) Crotalinae continued.
Fig 5.
Phylogenetic tree of Serpentes continued.
A) Homalopsidae, Psammophiinae, Buhoma procterae, Prosymninae, Pseudaspidinae, Atractaspidinae, and Aparallactinae. Bi) Oxyrhabdium leporinum and Lamprophiinae. Bii) Ditypophis sp. + Micrelaps bicoloratus and Pseudoxyrhophiinae.
Fig 6.
Phylogenetic tree of Serpentes continued.
A) Buhoma depressiceps and Elapidae. B) Elapidae continued.
Fig 7.
Phylogenetic tree of Serpentes continued.
A) Sibynophiinae and Natricinae. B) Pseudoxenodontinae and Dipsadinae.
Fig 8.
Phylogenetic tree of Serpentes continued.
A) Dipsadinae continued. B) Dipsadinae continued.
Fig 9.
Phylogenetic tree of Serpentes continued.
A) Grayiinae, Calamariinae, Ahaetullinae subfam. nov., and Colubrinae. Bi) Colubrinae continued. Bii) Colubrinae continued.
Fig 10.
Phylogenetic tree of Serpentes continued.
A) Colubrinae continued. B) Colubrinae continued.