The ancestry of a sample of sequences subject to recombination.
The ancestry of a sample of sequences subject to recombination.
复制标题
进行重组的序列样本的祖先。
作者：
C. Wiuf;J. Hein
本文讨论了恒定种群大小为2N的重组聚结线虫的遗传序列。我们在模拟样品历史的基础上研究了一些变量，并得出了一些分析结果。考虑序列中最左边的核苷酸。我们表明，当比较两个序列时，与最左边的核苷酸共享最近共同祖先（MRCA）的核苷酸数量约为log(1 + 4N Lr)/4Nr，其中L表示核苷酸的序列长度，r表示每一代任何两个相邻核苷酸之间的重组率。对于较大的样本，与最左边的核苷酸共享MRCA的核苷酸数量减少，几乎与4N Lr无关。此外，我们表明，当两个序列比较时，共享MRCA的序列片段平均由3/8Nr核苷酸组成，当整个种群采样时，这一数字减少到1/4Nr核苷酸。介绍了两个序列上的两个核苷酸的家谱之间的相关性的测量。我们分析表明，即使核苷酸相隔很大的遗传距离，但共享MRCA，家谱将显示只有很少的相关性。这是令人惊讶的，因为两个核苷酸共享MRCA的时间与遗传距离成反比。通过模拟，直到样本中所有位置找到MRCA的平均时间随着序列长度的增加呈对数增长，并且大大低于理论预测的上限。在模拟的基础上，发现整个群体重组后的聚结的重要性质反映在小样本的性质上。
In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is approximately log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.