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, 10 (3), e0118199

Integrated Analyses Resolve Conflicts Over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa


Integrated Analyses Resolve Conflicts Over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

Tod W Reeder et al. PLoS One.


Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Fig 1
Fig 1. Estimated phylogeny of squamate reptiles from likelihood analysis of combined morphological and molecular data, after removal of four “rogue” fossil taxa (-lnL = 979285.16; see S8 Fig. for tree including all taxa).
Red dots indicate clades with bootstrap values from 90–100%, black dots indicate values from 70–89% (values <70% not shown; for bootstrap values for all branches see S9 Fig.). Fossil taxa are indicated with “≪” and green branches. The four abbreviated fossil taxa in gray at the base of the phylogeny are the four rogue taxa (Eichstaetisaurus, Huehuecuetzpalli, Sineoamphisbaenia, AMNH FR 21444), shown in their phylogenetic positions as inferred in the combined analysis including all taxa (S8 Fig.). Photos include representatives of Dibamidae (Anelytropsis), Gekkota (Carphodactylidae: Underwoodisaurus), Scincoidea (Scincidae: Plestiodon), Amphisbaenia (Bipedidae: Bipes), Mosasauria (Tylosaurus), Serpentes (Boidae: Exiliboa), Anguimorpha (Xenosauridae: Xenosaurus), Polyglyphanodontia (Polyglyphanodon), Acrodonta (Agamidae: Calotes), and Pleurodonta (Phrynosomatidae: Sceloporus). See Acknowledgments for photo credits (except for Anelytropsis from T. M. Townsend).

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Grant support

This project was supported by a United States National Science Foundation grant, with awards to T.W.R. (EF 0334967), J.W.S. (EF 0334966) and J.J.W. (EF 0334923). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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