群体遗传学模拟软件应用现状.pdfVIP

Hereditas (Beijing) 2016 年 8 月, 38(8): 707 ―717 综 述 群体遗传学模拟软件应用现状 1,2 1 高峰 ，李海鹏 1. 中国科学院计算生物学重点实验室，中国科学院-德国马普学会计算生物学伙伴研究所，上海 200031 ； 2. 中国科学院大学，北京100049 摘要 : 随着下一代测序技术的不断进步与测序价格的不断下降，越来越多物种的全基因组信息被公开。作为研 究群体遗传变异模式工具之一的模拟软件必然将发挥越来越重要的作用。依据时间推演方向的不同，模拟软件 可以分为依时间向前和向后推演，二者各有所长，功能上互相补充，分别适合于不同的模拟需求。这些软件在 研究进化动力的影响、估计进化动力参数与验证不同进化假设以及新方法有效性等方面起着重要作用。本文简 要介绍了群体遗传学相关理论知识，详细比较了近 10 年来发表的32 款模拟软件，并对模拟软件的未来发展方 向给出了建议。 关键词 : 群体遗传学；计算机模拟；依时间向前；依时间向后 Application of computer simulators in population genetics Feng Gao1,2, Haipeng Li1 1. CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China; 2. University of Chinese Academy of Sciences, Beijing 100049, China Abstract : The genomes of more and more organisms have been sequenced due to the advances in next-generation sequencing technologies. As a powerful tool, computer simulators play a critical role in studying the genome-wide DNA polymorphism pattern . Simulations can be performed both for- wards-in-time and backwards-in-time, which complement each other and are suitable for meeting different needs, such as studying the effect of evolutionary dynamics, the estimation of parameters, and the valida- tion of evolutionary hypotheses as well as new methods . In this review, we briefly introduced population genetics related theoretical framework and provided a detailed comparison of 32 simulators published over the last ten years. The future development of new simulators was also discussed. Keywords: population genetics ; computer simulation; forwards-in-time; backwards-in-time 收稿日期: 2016−03−22; 修回日期: 2016−04−25 基金项目: 中国科学院先导B 项目(编号：XD和国家自然科学基金项目(编号资助[Supported by the Strategic Priority Research Program of the Chinese