Population divergence time estimation using individual lineage label switching.
Population divergence time estimation using individual lineage label switching.
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DOI：
10.1093/g3journal/jkac040
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发表时间：
2022-04-04
期刊：
影响因子：
--
通讯作者：
Palczewski M
中科院分区：
文献类型：
--
作者：
Beerli P;Ashki H;Mashayekhi S;Palczewski M
从多位点遗传数据中估计分化时间在群体遗传学和系统发育学中已经变得很常见。我们提出了一种新的贝叶斯推理方法，将发散时间视为随机变量。分歧时间是根据家谱中各个谱系上的分裂事件的集合计算的。这种分裂事件的时间是从截断正态分布的风险函数中得出的。这允许轻松集成到Migrate等程序中使用的标准联合框架。通过对5个种群的数据集进行重新分析，其中包括3个现代种群(非洲人、欧洲人、亚洲人)和2个古代样本(阿拉泰和乌斯特·伊斯特姆)，我们探索了在广泛的分歧时间值上模拟种群分裂的新推断方法的准确性。对没有后续基因流的简单发散模型的评估显示出很高的准确性，而用迁徙模型进行隔离的结果的准确性取决于迁移率的大小。高移民率导致样本的最新共同祖先的时间，回顾时间，早于分歧时间。即使有许多独立的地点，在高移民率的情况下准确估计分歧时间也是有问题的。我们与其他软件工具的比较表明，我们在Migrate中实现的谱系转换方法与IMa2p相当。软件Migrate可以在计算机集群上并行运行大量序列基因座(>；1,000)。
Divergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayesian inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The time for such a splitting event is drawn from a hazard function of the truncated normal distribution. This allows easy integration into the standard coalescence framework used in programs such as Migrate. We explore the accuracy of the new inference method with simulated population splittings over a wide range of divergence time values and with a reanalysis of a dataset of 5 populations consisting of 3 present-day populations (Africans, Europeans, Asian) and 2 archaic samples (Altai and Ust’Isthim). Evaluations of simple divergence models without subsequent geneflow show high accuracy, whereas the accuracy of the results of isolation with migration models depends on the magnitude of the immigration rate. High immigration rates lead to a time of the most recent common ancestor of the sample that, looking backward in time, predates the divergence time. Even with many independent loci, accurate estimation of the divergence time with high immigration rates becomes problematic. Our comparison to other software tools reveals that our lineage-switching method, implemented in Migrate, is comparable to IMa2p. The software Migrate can run large numbers of sequence loci (>1,000) on computer clusters in parallel.
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影响因子：
10.7
作者：
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通讯作者：
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影响因子：
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DOI：
10.1073/pnas.081068098
发表时间：
2001-04-10
影响因子：
11.1
作者：
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通讯作者：
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