Backward simulation of ancestors of sampled individuals
Backward simulation of ancestors of sampled individuals
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DOI：
10.1016/j.tpb.2004.08.003
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发表时间：
2005-03-01
影响因子：
1.4
通讯作者：
Arjas, E
中科院分区：
文献类型：
--
作者：
Gasbarra, D;Sillanpää, MJ;Arjas, E
如果群体很大并且采样机制是随机的，则通常使用合并来对样本中的单倍型进行建模。然后可以通过衍生的单倍型的随机匹配来形成有序的基因型。然而，当（1）偏离随机交配（例如，繁殖群体中的优势个体或人类的一夫一妻制），或（2）群体较小和/或通过应用某些特定的非随机抽样方案来确定样本中的个体时，这种方法是不现实的，这在考虑谱系数据的统计建模和分析时通常是这种情况。对于这种情况，我们在这里提出一种数据生成方法，其中首先使用合并理论的思想，在时间上向后生成具有不重叠世代的祖先图。等位基因被随机分配给创始人，随后根据重组模型将等位基因从图表中删除，从而及时向前模拟整个基因组上的基因流，而不会产生干扰。可以调整控制图中生成的个体的交配行为的参数（一夫一妻制程度），以匹配特定的人口统计情况，而不限于简单的随机交配。通过模拟示例说明了该方法的性能。该软件（用 C 语言编写）可免费用于研究目的，网址为 http://www.rni.heisinki.fi/-dag/。 (C) 2004 Elsevier Inc. 保留所有权利。
If the population is large and the sampling mechanism is random, the coalescent is commonly used to model the haplotypes in the sample. Ordered genotypes can then be formed by random matching of the derived haplotypes. However, this approach is not realistic when (1) there is departure from random mating (e.g., dominant individuals in breeding populations or monogamy in humans), or (2) the population is small and/or the individuals in the sample are ascertained by applying some particular non-random sampling scheme, as is usually the case when considering the statistical modeling and analysis of pedigree data. For such situations, we present here a data generation method where an ancestral graph with non-overlapping generations is first generated backwards in time, using ideas from coalescent theory. Alleles are randomly assigned to the founders, and subsequently the gene flow over the entire genome is simulated forwards in time by dropping alleles down the graph according to recombination model without interference. The parameters controlling the mating behavior of generated individuals in the graph (degree of monogamy) can be tuned in order to match a particular demographic situation, without restriction to simple random mating.The performance of the approach is illustrated with a simulation example. The software (written in C-language) is freely available for research purposes at http://www.rni.heisinki.fi/-dag/. (C) 2004 Elsevier Inc. All rights reserved.