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Cited by 390Genomics and Phylogenetic StudiesEvolution and Genetic DynamicsGenetic diversity and population structure

Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

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Hwang, Dick G., Green, Phil·2004·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0404142101PMC PMC521089
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Abstract

We describe a model of neutral DNA evolution that allows substitution rates at a site to depend on the two flanking nucleotides (“context”), the branch of the phylogenetic tree, and position within the sequence and implement it by using a flexible and computationally efficient Bayesian Markov chain Monte Carlo approach. We then apply this approach to characterize phylogenetic variation in context-dependent substitution patterns in a 1.7-megabase genomic region in 19 mammalian species. In contrast to other substitution types, CpG transition substitutions have accumulated in a relatively clock-like fashion. More broadly, our results support the notion that context-dependent DNA replication errors, cytosine deamination, and biased gene conversion are major sources of naturally occurring mutations whose relative contributions have varied in mammalian evolution as a result of changes in generation times, effective population sizes, and recombination rates.

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  • CpG transitions accumulate in a more clocklike manner than other mutations.

    “Given such a general challenge to the molecular clock assumption, it may be wise to infer demographic history from mutations such as CpG transitions that accumulate in a more clocklike way than other mutations (8,20).”

    From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [20]

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Authors
Hwang, D. G., & Green, P.
Affiliations
Howard Hughes Medical Institute (US)
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2004-08-03
Volume
101
Issue
39
Pages
13994-14001
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.0404142101
PMC
PMC521089
OpenAlex
W2007890023
Cited by
390
References
51
Citations by year
2026: 8 · 2025: 7 · 2024: 9 · 2023: 12 · 2022: 15 · 2021: 31 · 2020: 17 · 2019: 13 · 2018: 9 · 2017: 13 · 2016: 26 · 2015: 13 · 2014: 20 · 2013: 16 · 2012: 21
FWCI
7.00
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Howard Hughes Medical Institute
  • National Institutes of Health
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
mammalian evolution, cytosine deamination, biased gene conversion, DNA replication errors, mutation rate, phylogenetic variation, recombination rate, effective population size, generation time, Bayesian Markov chain Monte Carlo, sequence evolution models
MeSH terms
Animals, Base Sequence, Bayes Theorem, Cats, Cattle, DNA, Dogs, Horses, Humans, Markov Chains, Models, Genetic, Monte Carlo Method, Mutation, Phylogeny, Rabbits, Swine, Transcription, Genetic, Evolution, Molecular, Mice, Rats

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