Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
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DOI：
10.1073/pnas.0404142101
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发表时间：
2004-09-28
影响因子：
11.1
通讯作者：
Green, P
中科院分区：
文献类型：
--
作者：
Hwang, DG;Green, P
我们描述了一个中性 DNA 进化模型，该模型允许一个位点的替换率取决于两个侧翼核苷酸（“上下文”）、系统发育树的分支以及序列中的位置，并通过使用灵活且计算高效的贝叶斯马尔可夫链蒙特卡罗方法来实现该模型。然后，我们应用这种方法来表征 19 种哺乳动物物种 1.7 兆碱基基因组区域中上下文相关替换模式的系统发育变异。与其他取代类型相比，CpG 转换取代以相对类似时钟的方式累积。更广泛地说，我们的结果支持这样的观点，即背景依赖性 DNA 复制错误、胞嘧啶脱氨和有偏差的基因转换是自然发生的突变的主要来源，其相对贡献在哺乳动物进化中由于世代时间、有效种群规模和重组率的变化而变化。
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.