Inferring spatial phylogenetic variation along nucleotide sequences: A multiple changepoint model
Inferring spatial phylogenetic variation along nucleotide sequences: A multiple changepoint model
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DOI：
10.1198/016214503000215
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发表时间：
2003-06-01
影响因子：
3.7
通讯作者：
Sinsheimer, JS
中科院分区：
文献类型：
--
作者：
Suchard, MA;Weiss, RE;Sinsheimer, JS
我们发展了一个贝叶斯多变点模型来推断空间系统发育变异（SPV）沿沿着对齐的分子序列数据。SPV发生在经历生物重组的生物序列中，或者当进化速率和选择压力沿着序列沿着变化时。这种贝叶斯方法允许估计关于重组、交换位置和所有其他模型参数的不确定性。该模型假设的网站沿着的数据分成一个未知数量的连续段，每个可能不同的生物体之间的进化关系，进化速率和转换：颠换比。我们开发了一个过渡内核，使用可逆跳马尔可夫链蒙特卡罗来拟合我们的模型，并从模拟和真实的数据中得出推断。通过模拟，我们研究了最小长度的重组片段，我们的模型可以检测到几个层次的进化分歧。我们研究了报告的人类免疫缺陷病毒（HIV）-1分离株的全基因组，该分离株与据称的重组病毒有关，该病毒被认为是俄罗斯静脉注射吸毒者中HIV-1感染流行爆发的病原体。我们发现基因组的区域在进化历史和选择压力方面有所不同。有强有力的证据表明，沿着基因组的多次交叉和选择压力的变化在整个vif通过env基因的频繁转移。
We develop a Bayesian multiple changepoint model to infer spatial phylogenetic variation (SPV) along aligned molecular sequence data. SPV occurs in sequences from organisms that have undergone biological recombination or when evolutionary rates and selective pressures vary, along the sequences. This Bayesian approach permits estimation of uncertainty regarding recombination, the crossing-over locations, and all other model parameters. The model assumes that the sites along the data separate into an unknown number of contiguous segments, each with possibly different evolutionary relationships between organisms, evolutionary rates, and transition: transversion ratios. We develop a transition kernel, use reversible-jump Markov chain Monte Carlo to fit our model, and draw inference from both simulated and real data. Through simulation, we examine the minimal length recombinant segment that our model can detect for several levels of evolutionary divergence. We examine the entire genome of a reported human immunodeficiency virus (HIV)-1 isolate, related to a purported recombinant virus thought to be the causative agent of an epidemic outbreak of HIV-1 infection among intravenous drug users in Russia. We find that regions of the genome differ in their evolutionary history and selective pressures. There is strong evidence for multiple crossovers along the genome and frequent shifts in selective pressure changes throughout the vif through env genes.