Forked Tongues Revisited: Molecular Apomorphies Support Morphological Hypotheses of Squamate Evolution

McMahan, Caleb D.; Freeborn, Layla; Wheeler, Ward C.; Crother, Brian I.

doi:10.1643/ch-14-015

Cited by 17 publications

(12 citation statements)

References 37 publications

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“…Combined analyses of molecular and morphological data have also supported the molecular trees [12,13], and have shown that the support for the morphological tree is problematic. Nevertheless, some authors have continued to question the placement of iguanians by molecular data [6,14,15].…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

Streicher

Wiens

2017

Biol. Lett.

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Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates.

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Section: Introductionmentioning

confidence: 99%

Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

Streicher

Wiens

2017

Biol. Lett.

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“…Even though our TED analysis includes molecular data for only 21 lineages, the resulting topological reorganization impacts the position of many other lineages. Previous studies have shown that molecular data can modify the position of fossils (e.g., Wiens et al 2010; Arcila et al 2015), but these topological changes cannot be corroborated with independent data sources, leading some to doubt whether they represent improvements in phylogenetic accuracy (McMahan et al 2015). In our morphological analyses (Figs.…”

Section: Discussionmentioning

confidence: 99%

A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Koch

Thompson

2020

Preprint

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12Several unique properties of echinoids (sea urchins) make them useful for exploring 13 macroevolutionary dynamics, including their remarkable fossil record that can be incorporated 14 into explicit phylogenetic hypotheses. However, this potential cannot be exploited without a 15 robust resolution of the echinoid tree of life. We revisit the phylogeny of crown group 16 Echinoidea using both the largest phylogenomic dataset compiled for the clade, as well as a 17 large-scale morphological matrix with a dense fossil sampling. We also gather a new 18 compendium of both tip and node age constraints, allowing us to combine phylogenomic, 19 morphological and stratigraphic data using a total-evidence dating approach. For this, we 20 develop a novel method for subsampling phylogenomic datasets that selects loci with high 21 phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our approach 22 restructure much of the higher-level phylogeny of echinoids, and demonstrates that combining 23 different data sources increases topological accuracy. We are able to resolve multiple alleged 24 conflicts between molecular and morphological datasets, such as the position of Echinothurioida 25 and Echinoneoida, as well as unravelling the relationships between sand dollars and their closest 26 relatives. We then use this topology to trace the evolutionary history of echinoid body size 27 through more than 270 million years, revealing a complex pattern of convergent evolution to 28 stable peaks in macroevolutionary adaptive landscape. Our efforts show how combining 29 phylogenomic and paleontological evidence offers new ways of exploring evolutionary forces 30 operating across deep timescales.31 32

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“…Many have expressed doubts that this matter is settled [ 29 , 31 , 44 , 45 , 68 ]. Some authors have even chosen to continue employing a scleroglossan phylogenetic framework [ 69 , 70 ], while others have used both topologies to explore the evolutionary history of novel characters and particular sub-taxa [ 71 – 75 ], further indicating that a consensus has yet to be reached.…”

Section: Introductionmentioning

confidence: 99%

Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata

Koch

Gauthier

2018

PLoS ONE

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Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.

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Forked Tongues Revisited: Molecular Apomorphies Support Morphological Hypotheses of Squamate Evolution

Cited by 17 publications

References 37 publications

Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata

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