Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer
Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer
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DOI：
10.1111/1755-0998.13175
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发表时间：
2020-05-25
影响因子：
7.7
通讯作者：
Corbett-Detig, Russ
中科院分区：
文献类型：
--
作者：
Schumer, Molly;Powell, Daniel L.;Corbett-Detig, Russ
很明显，物种间的杂交比以前认识到的要普遍得多。因此，我们现在知道，许多现代物种的基因组，包括我们自己的基因组，都是由过去杂交事件产生的区域拼凑而成的。越来越多的研究人员感兴趣的是使用当地祖先推断方法解开基因组的哪些区域起源于每个亲本物种。由于混合物的不同影响，这种兴趣在不同的领域都有，从人类遗传学到生态学和进化生物学的研究。然而，当地祖先推断方法对一系列可能影响准确性的生物和技术参数敏感。在这里，我们提出了成对的模拟和祖先推理管道，mixnmatch和ancestryinferor，以帮助研究人员计划和执行本地祖先推理研究。mixnmatch可以模拟任意复杂的亲本和杂交种群的人口统计历史、杂交选择以及覆盖率和污染等技术变量。AncestryInferor将来自模拟的或真实的个体的测序读段作为输入，并实现有效的局部祖先推断流水线。我们使用mixnmatch进行了一系列模拟，以确定影响本地祖先推断准确性的因素，并突出两个管道的有用功能。mixnmatch是用于杂交模拟的强大工具，而ancestryinferor便于对真实的或模拟数据进行局部祖先推断。
It has become clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate fields, from human genetics to research in ecology and evolutionary biology. However, local ancestry inference methods are sensitive to a range of biological and technical parameters which can impact accuracy. Here we present paired simulation and ancestry inference pipelines, mixnmatch and ancestryinfer, to help researchers plan and execute local ancestry inference studies. mixnmatch can simulate arbitrarily complex demographic histories in the parental and hybrid populations, selection on hybrids, and technical variables such as coverage and contamination. ancestryinfer takes as input sequencing reads from simulated or real individuals, and implements an efficient local ancestry inference pipeline. We perform a series of simulations with mixnmatch to pinpoint factors that influence accuracy in local ancestry inference and highlight useful features of the two pipelines. mixnmatch is a powerful tool for simulations of hybridization while ancestryinfer facilitates local ancestry inference on real or simulated data.