A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis
A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis
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DOI：
10.1101/766741
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发表时间：
2019-09
期刊：
影响因子：
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通讯作者：
Thomas Flouris;Xiyun Jiao;B. Rannala;Ziheng Yang
中科院分区：
文献类型：
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作者：
Thomas Flouris;Xiyun Jiao;B. Rannala;Ziheng Yang
最近的分析表明，跨物种的基因流动或渐渗是常见的自然，特别是在物种分化。基因组序列数据可以用来推断基因渗入事件，估计时间和强度的基因渗入，提供了一个重要的手段，以促进我们的理解的作用，基因流的物种形成。在这里，我们在我们的贝叶斯马尔可夫链蒙特卡罗（MCMC）程序BPP中实现了多物种合并基因渗入（MSci）模型，这是多物种合并（MSC）模型的扩展，以纳入基因渗入。MSCI模型适应深度聚结（或不完全谱系分选）和渐渗，并提供了使用基因组序列数据进行推断的自然框架。计算机模拟证实了该方法的良好统计特性，尽管通常需要数百或数千个位点来可靠地估计渐渗概率。对紫锥云杉数据集的重新分析证实了同倍体杂交物种形成的假设。我们估计的基因渗入概率使用的基因组序列数据，从6种蚊子在冈比亚按蚊种复合体，这在整个基因组中变化很大，可能是由差异选择对基因渗入等位基因。
Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.