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.
Keywords
Markov chain Monte CarloBiologyContext (archaeology)Substitution (logic)Phylogenetic treeMarkov chainGeneticsComputational biologyEvolutionary biologyBayesian probabilityGeneComputer scienceMathematicsStatisticsArtificial intelligence
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Publication Info
- Year
- 2004
- Type
- article
- Volume
- 101
- Issue
- 39
- Pages
- 13994-14001
- Citations
- 412
- Access
- Closed
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Cite This
Dick G. Hwang,
Phil Green
(2004).
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution.
Proceedings of the National Academy of Sciences
, 101
(39)
, 13994-14001.
https://doi.org/10.1073/pnas.0404142101
Identifiers
- DOI
- 10.1073/pnas.0404142101