论文标题
代表近亲树的算法
An algorithm to represent inbreeding trees
论文作者
论文摘要
最近的工作证明了从当代英国人口\ cite {nature_01}采集的欧洲血统样本中存在极端近亲繁殖。这一结果再次引起了我们的注意力,这是一个与近交的家谱和多样性有关的数学问题。有限数量的个体的群体可以提供各种遗传关系。 {在先前的工作中\ cite {physreve.92.052132,physreve.90.022125,jarne20191},我们已经解决了使用马尔可夫模型建造近交树来建造近亲树的问题。在这里,我们通过提出算法来生成和表示没有重叠的世代的近亲树来扩展这些研究。我们明确假设一个两性生殖方案,并特别注意节点之间的联系。我们表明,即使对于一个简单的案例,树中有相对较少的节点,也有许多可能的方法可以重新安排世代之间的链接。我们提出一个开源Python代码,以生成树图,邻接矩阵以及每个不同树表示的链接的直方图。我们展示了该映射如何反映树木实现之间的差异,以及在检查这些矩阵时如何提取有价值的信息。该算法包括平均几棵树实现的功能,获得连接分布并计算平均值和平均值。我们使用此功能将树与不同的世代和节点进行比较。此处介绍的代码可在Git-ub中使用,可以轻松修改以应用于涉及个人之间联系的其他感兴趣领域,扩展研究以添加更多不同节点的特征,等等。
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees and diversity. Groups with a finite number of individuals could give a variety of genetic relationships. { In previous works \cite{PhysRevE.92.052132, PhysRevE.90.022125, JARNE20191}, we have addressed the issue of building inbreeding trees for biparental reproduction using Markovian models. Here, we extend these studies by presenting an algorithm to generate and represent inbreeding trees with no overlapping generations. We explicitly assume a two-gender reproductory scheme, and we pay particular attention to the links between nodes. We show that even for a simple case with a relatively small number of nodes in the tree, there are a large number of possible ways to rearrange the links between generations. We present an open-source python code to generate the tree graph, the adjacency matrix, and the histogram of the links for each different tree representation. We show how this mapping reflects the difference between tree realizations, and how valuable information may be extracted upon inspection of these matrices. The algorithm includes a feature to average several tree realizations, obtain the connectivity distribution, and calculate the average and mean value. We used this feature to compare trees with a different number of generations and nodes. The code presented here, available in Git-Hub, may be easily modified to be applied to other areas of interest involving connections between individuals, extend the study to add more characteristics of the different nodes, etc.