The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
MRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck, J. P., & Ronquist, F. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.8.754 · Cited by 21,937
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Bayesian inference of species trees from multilocus data
Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453
Kasturiratne, A., Wickremasinghe, A. R., de Silva, N., Gunawardena, N. K., Pathmeswaran, A., Premaratna, R., Savioli, L., Lalloo, D. G., & de Silva, H. J. (2008) · PLoS Medicine · doi:10.1371/journal.pmed.0050218 · Cited by 1,935
High-resolution species trees without concatenation
Edwards, S. V., Liu, L., & Pearl, D. K. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607004104 · Cited by 588
Vidal, N., & Hedges, S. B. (2005) · Comptes Rendus. Biologies · doi:10.1016/j.crvi.2005.10.001 · Cited by 461
Townsend, T. M., Larson, A., Louis, E., & Macey, J. R. (2004) · Systematic Biology · doi:10.1080/10635150490522340 · Cited by 458
Self-citationMissing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data
Wiens, J. J., & Morrill, M. C. (2011) · Systematic Biology · doi:10.1093/sysbio/syr025 · Cited by 452
Self-citationWiens, J. J., Brandley, M. C., & Reeder, T. W. (2006) · Evolution · doi:10.1554/05-328.1 · Cited by 354
Self-citationRokas, A., & Carroll, S. B. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040352 · Cited by 315
Cited by
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
Pyron, R., Burbrink, F. T., & Wiens, J. J. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-93 · Cited by 1,641
Self-citationEarly origin of viviparity and multiple reversions to oviparity in squamate reptiles
Pyron, R. A., & Burbrink, F. T. (2014) · Ecology Letters · doi:10.1111/ele.12168 · Cited by 313
Constraints on the timescale of animal evolutionary history
Benton, M., Donoghue, P., Vinther, J., Asher, R., Friedman, M., & Near, T. (2015) · Palaeontologia Electronica · doi:10.26879/424 · Cited by 284
Exploring gaps, biases, and research priorities in the evidence for reptile conservation actions
Speight, O., Morgan, W. H., White, T. B., Sainsbury, K. A., Bouskila, A., Rotem, G., Smith, R. K., Sutherland, W. J., Watson, M. J., & Christie, A. P. (2025) · Conservation Biology · doi:10.1111/cobi.70073 · Cited by 11
Metadata
- Authors
- Wiens, J. J., Hutter, C. R., Mulcahy, D. G., Noonan, B. P., Townsend, T. M., Sites, J. W., & Reeder, T. W.
- Venue
- Biology Letters
- Publisher
- The Royal Society
- Published
- 2012-09-19
- Volume
- 8
- Issue
- 6
- Pages
- 1043-1046
- ISSN
- 1744-9561 (ISSN-L)
- 1744-957X
- OpenAlex
- W1988783684
- Cited by
- 324
- References
- 15
- FWCI
- 24.40
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. https://app.cochat.ai/papers/10.1098/rsbl.2012.0703
- The paper
- Wiens, J. J., Hutter, C. R., Mulcahy, D. G., Noonan, B. P., Townsend, T. M., Sites, J. W., & Reeder, T. W. (2012). Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters. https://doi.org/10.1098/rsbl.2012.0703
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
