Approximating the coalescent with recombination
Approximating the coalescent with recombination
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DOI：
10.1098/rstb.2005.1673
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发表时间：
2005-07-29
影响因子：
6.3
通讯作者：
Cardin, NJ
中科院分区：
文献类型：
--
作者：
McVean, GAT;Cardin, NJ
结合重组描述了自然种群DNA序列样本中家谱历史的分布和遗传变异的结果模式。然而，使用模型作为推理的基础目前受到估计可能性的计算挑战的严重限制。我们讨论了为什么合并与重组是如此具有挑战性的工作，并探索是否更简单的模型，推理更容易处理，可能证明对基于家谱的推理有用。我们介绍了一种简化的聚结过程，其中没有重叠祖先物质的谱系之间的聚结被禁止。当沿着序列产生谱系时，结果过程具有简单的马尔可夫结构，但在描述遗传变异模式和作为统计推断的基础方面，与完整模型具有非常相似的特性。
The coalescent with recombination describes the distribution of genealogical histories and resulting patterns of genetic variation in samples of DNA sequences from natural populations. However, using the model as the basis for inference is currently severely restricted by the computational challenge of estimating the likelihood. We discuss why the coalescent with recombination is so challenging to work with and explore whether simpler models, under which inference is more tractable, may prove useful for genealogy-based inference. We introduce a simplification of the coalescent process in which coalescence between lineages with no overlapping ancestral material is banned. The resulting process has a simple Markovian structure when generating genealogies sequentially along a sequence, yet has very similar properties to the full model, both in terms of describing patterns of genetic variation and as the basis for statistical inference.