Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

Abstract

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.

Phylogenetic relationships of Amazonian anole lizards (Dactyloa): Taxonomic implications, new insights about phenotypic evolution and the timing of diversification

“…Moreover, the divergence time estimates presented by Nicholson et al (2012) were based on a single mitochondrial marker, yet mitochondrial genes are known to mislead deep divergence time estimation due to substitution saturation (Brandley et al, 2011;Lukoschek et al, 2012;Mulcahy et al, 2012), sometimes resulting in 3-10-fold overestimations (Zheng et al, 2011). To improve estimates of divergence times for Amazonian anoles, we built a dated phylogeny for the pleurodont iguanian clade (sensu Wiens et al, 2012) using five nuclear genes and well-known fossils for calibration points. For that, we combined newly generated sequences of Amazonian lizards in the genera Dactyloa and Norops (Dactyloidae) and Polychrus (Polychrotidae) with published sequences of 12 other pleurodont taxa, emphasizing the South American genera (see online Supplementary data 2 for taxa, voucher and Genbank accession numbers).…”

New insight into the evolution of the vertebrate respiratory system and the discovery of unidirectional airflow in iguana lungs

“…Unidirectional flow has been purported to serve ectotherms by harnessing the heart as a pump for air during periods of breath-holding (apnea) (12). Light can be shed on this pattern of evolution with observations of more squamates (snakes, lizards), which are the most diverse and largest (∼9,000 species) group of living reptiles (24).…”

EarlyHomoand the role of the genus in paleoanthropology

“…Indeed, a meta-analysis of terrestrial vertebrate taxonomies (Amphibia, Aves, Eutheria, Metatheria, Squamates) illustrates that diversity within Homo is compatible with the diversity within genera in these major clades. The distribution of generic diversity is wide (Figure 4) in all clades, and the eight species currently recognized within Homo falls well within expectations for vertebrate taxonomy (Faurby & Svenning, 2015;Jetz, Thomas, Joy, Hartmann, & Mooers, 2012;May-Collado, Kilpatrick, & Agnarsson, 2015;Pyron & Weins, 2011;Wiens et al, 2012;Pyron et al, 2013). Furthermore, in all of those vertebrate taxonomies, identifying paraphyletic taxa and reassigning them to monophyletic taxa was a major goal of the research, and continues to be a major focus of phylogenetic research.…”