Data from: Friends and Family: a software program for identification of unrelated individuals from molecular marker data

The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as COANCESTRY and GenAlEx. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user-defined relatedness cut-off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. These results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy-Weinberg equilibrium test outcome for microsatellite markers in an empirical data set. Friends and Family can be obtained from https://github.com/DeondeJager/Friends-and-Family.

从分子标记数据中识别亲缘与非亲缘个体往往颇具难度，尤其当缺乏系谱信息且数据集规模庞大时。高度的亲缘关系或近交程度会影响基因型频率，进而干扰遗传标记评估，以及对隐藏遗传结构的准确推断。亲缘与非亲缘个体的识别在育种项目中同样至关重要，可为育种配对与个体移植的决策提供依据。本文介绍一款名为Friends and Family的Windows可执行程序，其搭载图形用户界面，可基于COANCESTRY、GenAlEx等软件生成的成对亲缘关系矩阵或表格，筛选出非亲缘个体。该程序可根据用户自定义的亲缘关系截断值，输出一组彼此间均无亲缘关系的样本列表。这类无亲缘关系的数据集可用于后续分析，例如遗传标记评估或遗传结构推断。还可将其与全数据集的分析结果进行对比，以明确亲缘个体对分析过程的影响。我们通过实证案例展示了该程序的一项应用：在某实证数据集内，移除亲缘个体如何改变了微卫星标记的哈迪-温伯格平衡（Hardy-Weinberg equilibrium）检验结果。用户可从https://github.com/DeondeJager/Friends-and-Family获取该程序。