A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus - PubMed (original) (raw)

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

Alex Figueroa et al. PLoS One. 2016.

Abstract

Background: With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61).

Results: Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades.

Conclusion: Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1

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

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

Fig 3. Phylogenetic tree of Serpentes continued.

A) Aniliidae, Tropidophiidae, Calabariidae, Candoiidae, Sanziniidae, Charininae, Ungaliophiinae, Erycidae, and Boidae. B_i_) Cylindrophiidae + Anomochilidae, Uropeltidae, Xenopeltidae, Loxocemidae, and Pythonidae. B_ii_) Bolyeridae, Xenophidiidae, Acrochordidae, Xenodermatidae, and Pareatidae.

Fig 4

Fig 4. Phylogenetic tree of Serpentes continued.

A_i_) Viperinae. A_ii_) Azemiopinae and Crotalinae. B) Crotalinae continued.

Fig 5

Fig 5. Phylogenetic tree of Serpentes continued.

A) Homalopsidae, Psammophiinae, Buhoma procterae, Prosymninae, Pseudaspidinae, Atractaspidinae, and Aparallactinae. B_i_) Oxyrhabdium leporinum and Lamprophiinae. B_ii_) Ditypophis sp. + Micrelaps bicoloratus and Pseudoxyrhophiinae.

Fig 6

Fig 6. Phylogenetic tree of Serpentes continued.

A) Buhoma depressiceps and Elapidae. B) Elapidae continued.

Fig 7

Fig 7. Phylogenetic tree of Serpentes continued.

A) Sibynophiinae and Natricinae. B) Pseudoxenodontinae and Dipsadinae.

Fig 8

Fig 8. Phylogenetic tree of Serpentes continued.

A) Dipsadinae continued. B) Dipsadinae continued.

Fig 9

Fig 9. Phylogenetic tree of Serpentes continued.

A) Grayiinae, Calamariinae, Ahaetullinae subfam. nov., and Colubrinae. B_i_) Colubrinae continued. B_ii_) Colubrinae continued.

Fig 10

Fig 10. Phylogenetic tree of Serpentes continued.

A) Colubrinae continued. B) Colubrinae continued.

Similar articles

Cited by

References

    1. Harvey PH, Pagel MD. The Comparative Method in Evolutionary Biology (Vol. 239). Oxford: Oxford University Press; 1991.
    1. Huelsenbeck JP, Rannala B. Phylogenetic methods come of age: testing hypotheses in an evolutionary context.Science. 1997; 276: 227–232. - PubMed
    1. Pagel M. Inferring the historical patterns of biological evolution. Nature. 1999; 401: 877–884. - PubMed
    1. Whelan S, Liò P, Goldman N. Molecular phylogenetics: state-of-the-art methods for looking into the past.Trends Genet.2001; 17: 262–272. - PubMed
    1. Driskell AC, Ane C, Burleigh JG, McMahon MM, O'Meara B, Sanderson MJ. Prospects for building the tree of life from large sequence databases. Science. 2004; 306: 1172–1174. - PubMed

MeSH terms

Substances

LinkOut - more resources