The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Assessing Concordance of Fossil Calibration Points in Molecular Clock Studies: An Example Using Turtles
Abstract
Although still controversial, estimation of divergence times using molecular data has emerged as a powerful tool to examine the tempo and mode of evolutionary change. Two primary obstacles in improving the accuracy of molecular dating are heterogeneity in DNA substitution rates and accuracy of the fossil record as calibration points. Recent methodological advances have provided powerful methods that estimate relative divergence times in the face of heterogeneity of nucleotide substitution rates among lineages. However, relatively little attention has focused on the accuracy of fossil calibration points that allow one to translate relative divergence times into absolute time. We present a new cross-validation method that identifies inconsistent fossils when multiple fossil calibrations are available for a clade and apply our method to a molecular phylogeny of living turtles with fossil calibration times for 17 of the 22 internal nodes in the tree. Our cross-validation procedure identified seven inconsistent fossils. Using the consistent fossils as calibration points, we found that despite their overall antiquity as a lineage, the most species-rich clades of turtles diversified well within the Cenozoic. Many of the truly ancient lineages of turtles are currently represented by a few, often endangered species that deserve high priority as conservation targets.
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
Evolutionary divergence and convergence in proteins.
ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020
Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977
Estimating the rate of evolution of the rate of molecular evolution
Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317 · cited 2×
“1995; Cooper and Penny 1997), to methods that include all of the data and attempt to estimate local rates for branches and lineages in the phylogeny using nonparametric, semiparametric, and Bayesian methodologies (Sanderson 1997, 2002; Thorne et al. 1998).”
MethodA nonparametric approach to estimating divergence times in the absence of rate constancy.
Sanderson, M. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025731 · Cited by 1,156 · cited 2×
“Subsequent to the discovery of significant rate heterogeneity, we estimated divergence times using the penalized likelihood method (Sanderson 2002), as implemented in the computer program r8s (Sanderson 2003). For each iteration of divergence time estimation, cross-validation determined the optimal smoothing parameter…”
MethodReading the entrails of chickens: molecular timescales of evolution and the illusion of precision
Graur, D., & Martin, W. (2004) · Trends in Genetics · doi:10.1016/j.tig.2003.12.003 · Cited by 669
Bromham, L., & Penny, D. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1020 · Cited by 615
Mass survival of birds across the Cretaceous–Tertiary boundary: Molecular evidence.
Cooper, A., & Penny, D. (1997) · Science · doi:10.1126/science.275.5303.1109 · Cited by 472
Benton, M. J., & Ayala, F. J. (2003) · Science · doi:10.1126/science.1077795 · Cited by 252
Dating the Time of Origin of Major Clades: Molecular Clocks and the Fossil Record
Smith, A. B., & Peterson, K. J. (2002) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev.earth.30.091201.140057 · Cited by 193 · cited 3×
“By using multiple calibration points, a variance in the age estimate for a given node in the phylogeny, using different fossil dates, can potentially be used to calculate confidence intervals around molecular age estimates (Smith and Peterson 2002).”
BackgroundMethodThe Power of Relative Rates Tests Depends on the Data
Bromham, L., Penny, D., Rambaut, A., & Hendy, M. D. (2000) · Journal of Molecular Evolution · doi:10.1007/s002399910034 · Cited by 168
Cited by
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., & Rasnitsyn, A. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys058 · Cited by 930
Best Practices for Justifying Fossil Calibrations
Parham, J. F., Donoghue, P. C. J., Bell, C. J., Calway, T. D., Head, J. J., Holroyd, P. A., Inoue, J. G., Irmis, R. B., Joyce, W. G., Ksepka, D. T., et al. (2012) · Systematic Biology · doi:10.1093/sysbio/syr107 · Cited by 780
Taxon sampling and the accuracy of phylogenetic analyses
(2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08016 · Cited by 553
Campione, N. E., & Evans, D. C. (2012) · BMC Biology · doi:10.1186/1741-7007-10-60 · Cited by 475
Phylotranscriptomic consolidation of the jawed vertebrate timetree
Irisarri, I., Baurain, D., Brinkmann, H., Delsuc, F., Sire, J.-Y., Kupfer, A., Petersen, J., Jarek, M., Meyer, A., Vences, M., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0240-5 · Cited by 299
On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
Eme, L., Sharpe, S. C., Brown, M. W., & Roger, A. J. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016139 · Cited by 287
The impact of fossils and taxon sampling on ancient molecular dating analyses
Hug, L. A., & Roger, A. J. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm115 · Cited by 144
Sharpe*, S. C., Eme*, L., Brown, M. W., & Roger, A. J. (2015) · Advances in Marine Genomics · doi:10.1007/978-94-017-9642-2_1 · Cited by 49
Battistuzzi, F. U., Billing-Ross, P., Murillo, O., Filipski, A., & Kumar, S. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv075 · Cited by 34
The mouth, the anus, and the blastopore—open questions about questionable openings
Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37
Genomic, phylogenetic, and cell biological insights into metazoan origins
Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24
Metadata
- Authors
- Near, T. J., Meylan, P. A., & Shaffer, H. B.
- Venue
- The American Naturalist
- Publisher
- University of Chicago Press
- Published
- 2005-02
- Volume
- 165
- Issue
- 2
- Pages
- 137-146
- ISSN
- 0003-0147 (ISSN-L)
- 1537-5323
- OpenAlex
- W2059419868
- Cited by
- 269
- References
- 11
- FWCI
- 16.83
- Type
- journal article
- Language
- en
- Open access
- closed
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
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.
