Estimating the pattern of nucleotide substitution
Abstract
Knowledge of the pattern of nucleotide substitution is important both to our understanding of molecular sequence evolution and to reliable estimation of phylogenetic relationships. The method of parsimony analysis, which has been used to estimate substitution patterns in real sequences, has serious drawbacks and leads to results difficult to interpret. In this paper a model-based maximum likelihood approach is proposed for estimating substitution patterns in real sequences. Nucleotide substitution is assumed to follow a homogeneous Markov process, and the general reversible process model (REV) and the unrestricted model without the reversibility assumption are used. These models are also applied to examine the adequacy of the model of Hasegawa et al. (J. Mol. Evol. 1985;22:160-174) (HKY85). Two data sets are analyzed. For the psi eta-globin pseudogenes of six primate species, the REV models fits the data much better than HKY85, while, for a segment of mtDNA sequences from nine primates, REV cannot provide a significantly better fit than HKY85 when rate variation over sites is taken into account in the models. It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation. The use of the unrestricted model does not appear to be worthwhile.
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Models previously used to study animal phylogeny (WAG+G, LG+G, GTR+G, PF-schemes, CAT-GTR+G) fell short of adequately describing among-site amino acid preferences in both WhelanD20 and Chang datasets.
“We showed that for both datasets, models that have previously been used to study the animal phylogeny fell short, to various degrees, of adequately describing among-site amino acid preferences”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [23]
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Self-citation
- Authors
- Yang, Z.
- Affiliations
- University of Cambridge (GB)
- Corresponding author
- Yang, Ziheng
- ORCID
- Yang, Ziheng
- Venue
- Journal of Molecular Evolution
- Published
- 1994-07
- Volume
- 39
- Issue
- 1
- Pages
- 105-11
- ISSN
- 0022-2844 (ISSN-L)
- 1432-1432
- OpenAlex
- W2026551295
- Cited by
- 1,076
- References
- 32
- Citations by year
- 2026: 10 · 2025: 17 · 2024: 20 · 2023: 22 · 2022: 14 · 2021: 19 · 2020: 28 · 2019: 28 · 2018: 22 · 2017: 26 · 2016: 24 · 2015: 28 · 2014: 42 · 2013: 19 · 2012: 29
- FWCI
- 5.27
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Journal of Molecular Evolution (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- nucleotide substitution patterns, substitution rate heterogeneity, Markov processes, model fit assessment, mitochondrial DNA, phylogenetic analysis
- MeSH terms
- Animals, Base Sequence, DNA, Mitochondrial, Biological Evolution, Globins, Humans, Markov Chains, Models, Genetic, Phylogeny, Primates, Probability, Pseudogenes, Genetic Variation
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