The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Comparison of Likelihood and Bayesian Methods for Estimating Divergence Times Using Multiple Gene Loci and Calibration Points, with Application to a Radiation of Cute-Looking Mouse Lemur Species
Abstract
Divergence time and substitution rate are seriously confounded in phylogenetic analysis, making it difficult to estimate divergence times when the molecular clock (rate constancy among lineages) is violated. This problem can be alleviated to some extent by analyzing multiple gene loci simultaneously and by using multiple calibration points. While different genes may have different patterns of evolutionary rate change, they share the same divergence times. Indeed, the fact that each gene may violate the molecular clock differently leads to the advantage of simultaneous analysis of multiple loci. Multiple calibration points provide the means for characterizing the local evolutionary rates on the phylogeny. In this paper, we extend previous likelihood models of local molecular clock for estimating species divergence times to accommodate multiple calibration points and multiple genes. Heterogeneity among different genes in evolutionary rate and in substitution process is accounted for by the models. We apply the likelihood models to analyze two mitochondrial protein-coding genes, cytochrome oxidase II and cytochrome b, to estimate divergence times of Malagasy mouse lemurs and related outgroups. The likelihood method is compared with the Bayes method of Thorne et al. (1998, Mol. Biol. Evol. 15:1647-1657), which uses a probabilistic model to describe the change in evolutionary rate over time and uses the Markov chain Monte Carlo procedure to derive the posterior distribution of rates and times. Our likelihood implementation has the drawbacks of failing to accommodate uncertainties in fossil calibrations and of requiring the researcher to classify branches on the tree into different rate groups. Both problems are avoided in the Bayes method. Despite the differences in the two methods, however, data partitions and model assumptions had the greatest impact on date estimation. The three codon positions have very different substitution rates and evolutionary dynamics, and assumptions in the substitution model affect date estimation in both likelihood and Bayes analyses. The results demonstrate that the separate analysis is unreliable, with dates variable among codon positions and between methods, and that the combined analysis is much more reliable. When the three codon positions were analyzed simultaneously under the most realistic models using all available calibration information, the two methods produced similar results. The divergence of the mouse lemurs is dated to be around 7-10 million years ago, indicating a surprisingly early species radiation for such a morphologically uniform group of primates.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“In spite of their increasingly widespread application, there have been few studies into the accuracy of relaxed-clock models (for exceptions, see Kishino, Thorne, and Bruno 2001;Yang and Yoder 2003;Perez-Losada, Hoeg, and Crandall 2004).”
From Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation (2005) · cites this paper as Yang and Yoder 2003
Citations
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,377
Self-citationEvolutionary 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
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
Self-citationKendall's Advanced Theory of Statistics.
Aa, Stuart, A., & Ord, K. (1995) · Journal of the American Statistical Association · doi:10.2307/2291187 · Cited by 2,663
Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
Self-citationKendall's Advanced Theory of Statistics.
Kemp, A. W., Stuart, A., & Ord, J. K. (1994) · Journal of the Royal Statistical Society Series D (The Statistician) · doi:10.2307/2348968 · Cited by 1,393
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 by
Sorted by citations
Items 301–356 of 356
Clercq, L. L., Kotzé, A., Grobler, J. P., & Dalton, D. L. (2023) · Journal of Molecular Evolution · doi:10.1007/s00239-023-10106-3 · Cited by 1
Rogers, A. R. (2013) · Elsevier eBooks · doi:10.1016/b978-0-08-095975-7.01206-7
Bukontaite, R. (2015) · KTH Publication Database DiVA (KTH Royal Institute of Technology)
2. Dating Methods and Corresponding Chronometers in Astrobiology
Gargaud, M., Albarède, F., Boiteau, L., Chaussidon, M., Douzery, E., & Montmerle, T. (2006) · Earth Moon and Planets · doi:10.1007/s11038-006-9086-6
Schrago, C. G., & Voloch, C. M. (2014) · Genetics and Molecular Research · doi:10.4238/2014.march.6.1
Page, M. M. (2011) · Brock University Digital Repository (Brock University)
Heath, T. A. (2008) · Texas ScholarWorks (Texas Digital Library)
Debate over which mammals roamed with the dinosaurs
Callaway, E. (2014) · Nature · doi:10.1038/nature.2014.14522
Comparison of methods and tests on trees
Yang, Z. (2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198567028.003.0006
Self-citationYang, Z. (2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.003.0007 · Cited by 1
Self-citationComparison of phylogenetic methods and tests on trees
Yang, Z. (2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.003.0005
Self-citationAndrews, P. (2016) · Cambridge University Press eBooks · doi:10.1017/cbo9781316180938.004
Molecular clock and estimation of species divergence times
Yang, Z. (2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198567028.003.0007
Self-citationMolecular Phylogenetics and Biogeography of Threadsnakes (Serpentes: Leptotyphlopidae)
Adalsteinsson, S. A. (2008)
Fossil taxa in the family Pinaceae, and their phylogenetic implications
Klymiuk, A. A. (2011) · ERA: Education and Research Archive (University of Alberta) · doi:10.7939/r3z92d
Quantifying MCMC Exploration of Phylogenetic Tree SpacePreprint
Whidden, C., & Matsen, F. A., IV (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1405.2120
Masters, J. C. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.004
Behaviour of Pottos and Angwantibos
Svensson, M. S., & Luhrs, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.020
Nekaris, K. A. I., & Burrows, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.002
Biomechanics of Loris Locomotion
Hanna, J. B. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.013
Allometric and Phylogenetic Diversity in Lorisiform Orbit Orientation
Nett, E. M., & Ravosa, M. J. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.011
Occupancy Modelling as a Method to Study Slender Loris Density
Williams, E., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.030
Showell, Z. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.024 · Cited by 1
Variational Combinatorial Sequential Monte Carlo Methods for Bayesian Phylogenetic InferencePreprint
Moretti, A. K., Zhang, L.-Y., Naesseth, C. A., Venner, H., Blei, D. M., & Pe’er, I. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2106.00075 · Cited by 1
Ecology and Captive Management
Nekaris, K. A. I., & Burrows, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.015
Research, Trade and Conservation
Nekaris, K. A. I., & Burrows, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.027
Nekaris, K. A. I., & Burrows, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.001
(2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.038
Evolution, Morphology and the Fossil Record
Nekaris, K. A. I., & Burrows, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.003
Yang, Z. (2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.003.0006
Self-citationThe Biogeography of Madagascar: Where to Turn when the Fossils aren't there
Yoder, A. D. (2005) · The Paleontological Society Papers · doi:10.1017/s1089332600001285
Self-citationYang, Z. (2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198567028.003.0010
Self-citationYang, Z. (2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.003.0013
Self-citationMolecular clock and estimation of species divergence times
Yang, Z. (2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.003.0010
Self-citationYang, Z. (2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.003.0008
Self-citationPhylogeny reconstruction: overview
Yang, Z. (2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.003.0003
Self-citationNekaris, K. A. I., & Burrows, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.039
Dating Methods and Corresponding Chronometers in Astrobiology
Gargaud, M., Albarède, F., Boiteau, L., Chaussidon, M., Douzery, E., & Montmerle, T. (2007) · Springer eBooks · doi:10.1007/978-0-387-45083-4_2
Local and relaxed clocks, the best of both worldsPreprint
Fourment, M., & Darling, A. E. (2018) · doi:10.7287/peerj.preprints.26744v1
(2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198567028.002.0004
(2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198567028.005.0001
(2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198567028.002.0005
(2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198567028.002.0006
(2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.002.0005
(2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.002.0003
(2014) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199602605.002.0004
ARTreeFormer: A faster attention-based autoregressive model for phylogenetic inference
Xie, T., Mao, Y., & Zhang, C. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013768
Qin, F., Xue, T., Zhang, X., Yang, X., Yu, J., Gadagkar, S. R., & Yu, S. (2023) · Figshare · doi:10.6084/m9.figshare.24669981
Qin, F., Xue, T., Zhang, X., Yang, X., Yu, J., Gadagkar, S. R., & Yu, S. (2024) · Figshare · doi:10.6084/m9.figshare.24670251
Schrago, C. G., & Mello, B. (2026) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2025.1704212
Metadata
- Authors
- Yang, Z., & Yoder, A. D.
- Affiliations
- University College London (GB)
- Yale University (US)
- Corresponding author
- Yang, Ziheng
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-10-01
- Volume
- 52
- Issue
- 5
- Pages
- 705-716
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2159816280
- Cited by
- 357
- References
- 39
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 4 · 2023: 7 · 2022: 3 · 2021: 5 · 2020: 45 · 2019: 7 · 2018: 17 · 2017: 1 · 2016: 9 · 2015: 10 · 2014: 26 · 2013: 11 · 2012: 8
- FWCI
- 33.58
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Systematic Biology (publishedVersion)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- divergence time estimation, molecular clock, rate heterogeneity, mouse lemurs, cytochrome oxidase II, cytochrome b, mitochondrial protein-coding genes, species radiation, primate phylogeny
- MeSH terms
- Animals, Bayes Theorem, Models, Genetic, Phylogeny, Likelihood Functions, Sequence Alignment, Cheirogaleidae, Evolution, Molecular
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
