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A Phylogeny and Revised Classification of Squamata, Including 4161 Species of Lizards and Snakes

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A Phylogeny and Revised Classification of Squamata, Including 4161 Species of Lizards and Snakes

R Alexander Pyron et al. BMC Evol Biol.

Abstract

Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata.

Results: The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.

Conclusions: We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.

Figures

Figure 1
Figure 1
Higher-level squamate phylogeny. Skeletal representation of the 4161-species tree from maximum-likelihood analysis of 12 genes, with tips representing families and subfamilies (following our taxonomic revision; species considered incertae sedis are not shown). Numbers at nodes are SHL values greater than 50%. The full tree is presented in Figures 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28.
Figure 2
Figure 2
Species-level squamate phylogeny. Large-scale maximum likelihood estimate of squamate phylogeny, containing 4161 species. Numbers at nodes are SHL values greater than 50%. A skeletal version of this tree is presented in Figure 1. Bold italic letters indicate figure panels (A-AA). Within panels, branch lengths are proportional to expected substitutions per site, but the relative scale differs between panels.
Figure 3
Figure 3
Species-level squamate phylogeny continued (B).
Figure 4
Figure 4
Species-level squamate phylogeny continued (C).
Figure 5
Figure 5
Species-level squamate phylogeny continued (D).
Figure 6
Figure 6
Species-level squamate phylogeny continued (E).
Figure 7
Figure 7
Species-level squamate phylogeny continued (F).
Figure 8
Figure 8
Species-level squamate phylogeny continued (G).
Figure 9
Figure 9
Species-level squamate phylogeny continued (H).
Figure 10
Figure 10
Species-level squamate phylogeny continued (I).
Figure 11
Figure 11
Species-level squamate phylogeny continued (J).
Figure 12
Figure 12
Species-level squamate phylogeny continued (K).
Figure 13
Figure 13
Species-level squamate phylogeny continued (L).
Figure 14
Figure 14
Species-level squamate phylogeny continued (M).
Figure 15
Figure 15
Species-level squamate phylogeny continued (N).
Figure 16
Figure 16
Species-level squamate phylogeny continued (O).
Figure 17
Figure 17
Species-level squamate phylogeny continued (P).
Figure 18
Figure 18
Species-level squamate phylogeny continued (Q).
Figure 19
Figure 19
Species-level squamate phylogeny continued (R).
Figure 20
Figure 20
Species-level squamate phylogeny continued (S).
Figure 21
Figure 21
Species-level squamate phylogeny continued (T).
Figure 22
Figure 22
Species-level squamate phylogeny continued (U).
Figure 23
Figure 23
Species-level squamate phylogeny continued (V).
Figure 24
Figure 24
Species-level squamate phylogeny continued (W).
Figure 25
Figure 25
Species-level squamate phylogeny continued (X).
Figure 26
Figure 26
Species-level squamate phylogeny continued (Y).
Figure 27
Figure 27
Species-level squamate phylogeny continued (Z).
Figure 28
Figure 28
Species-level squamate phylogeny continued (AA).

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