Hidden support from unpromising data sets strongly unites snakes with anguimorph ‘lizards’

Abstract

A combined analysis of nuclear, mitochondrial and morphological data robustly resolves snakes as the sister taxon to anguimorph ‘lizards’. Analysed in isolation, nuclear DNA (nDNA) produces a trichotomy between snakes, iguanians and anguimorphs, mitochondrial DNA (mtDNA) is largely uninformative at deeper levels, and morphology tends to nest snakes deep within anguimorphs or with various legless squamate groups. When analysed simultaneously, the nuclear signal is sufficiently strong that mtDNA and morphology are constrained to choose between alternative resolutions of the iguanian–anguimorph–snake trichotomy (generated by the nDNA) – and both support the snake–anguimorph solution. Combined analyses of fast‐evolving or idiosyncratically evolving markers (mtNDA, morphology) with conservative traits (e.g. nuclear genes) might be the best way to resolve ancient, closely spaced divergences. Fast or idiosyncratic markers potentially provide the most information about short, ancient internodes, but can converge on spurious trees if analysed in isolation. However, if constrained to only choosing between plausible trees, such data can contribute unique and valuable phylogenetic signal that resolves such problematic divergences.

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

“…We further corroborate previous studies in also placing Anguimorpha with Iguania [16-20]. In contrast, some other studies have placed anguimorphs with snakes as the sister group to iguanians [127,128]. …”

Phylogenetic analysis and temporal diversification of mosquitoes (Diptera: Culicidae) based on nuclear genes and morphology

“…However, examination of phylogenies resulting from individual genes revealed that topological incongruence was generally limited to certain poorly supported nodes. It has been suggested that different data sets may have a common phylogenetic signal recoverable only upon combined analysis [47,48], and, under the hypothesis that combining data from multiple genes may potentially overcome misleading signal in individual genes [49], we conducted further analyses to compare results from a concatenated data set with results obtained from ML and BI.…”

Amniote vertebral microanatomy - what are the major trends?

“…Statistical tests were performed using a consensus phylogeny derived from several published phylogenies (Motokawa, 2004;Livezey & Zusi, 2007;Lee, 2009Lee, , 2013Kan et al, 2010;Meredith et al, 2011;Yu et al, 2011;Hedges, 2012;Wiens et al, 2012;Yang et al, 2013; Fig. Statistical tests were performed using a consensus phylogeny derived from several published phylogenies (Motokawa, 2004;Livezey & Zusi, 2007;Lee, 2009Lee, , 2013Kan et al, 2010;Meredith et al, 2011;Yu et al, 2011;Hedges, 2012;Wiens et al, 2012;Yang et al, 2013; Fig.…”