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

Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsWe 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.

Evolution of nuchal glands, unusual defensive organs of Asian natricine snakes (Serpentes: Colubridae), inferred from a molecular phylogeny

“…Although differing in some details, recent molecular phylogenetic analyses of the Natricinae (Figueroa et al., 2016; Guo et al., 2012, 2014; Pyron, Burbrink et al., 2013; Pyron, Kandambi et al., 2013), including ours, agree on the general pattern of relationships among the major lineages. A basal dichotomy separates the subfamily into two major clades.…”

“…Those two, in turn, are sister to a clade containing the Asian genera Opisthotropis and Sinonatrix . A clade containing two endemic Sri Lankan genera, Aspidura and Haplocerus , is variously recovered as sister to this North American–Eurasian clade (Pyron, Burbrink et al., 2013; Pyron, Kandambi et al., 2013) or as the most basal branch of the natricine clade (our study, but with weak support).…”

Heterogeneous tempo and mode of evolutionary diversification of compounds in lizard chemical signals

“…These analyses were performed on a time‐calibrated molecular phylogenetic tree for our focal lizards, extracted from Pyron, Burbrink, and Wiens's (2013) supertree for squamate reptiles (lizards and snakes).…”

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

“…Another extreme approach is to include hundreds or thousands of species but for a smaller number of genes: this is the typical approach in supermatrix studies (e.g. Pyron and Wiens, 2011;Jetz et al, 2012;Pyron et al, 2013). Whether it is better to sample more taxa or more genes to resolve higher-level phylogenies was once a major debate in systematics (e.g.…”