A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes - PubMed (original) (raw)

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

R Alexander Pyron et al. BMC Evol Biol. 2013.

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.

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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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