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.
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There have been few studies into the accuracy of relaxed-clock models.
“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
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- 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
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