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. The 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.从分子标记数据中鉴定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。高水平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，同时也会对隐性遗传结构的准确推断造成影响。鉴定亲缘与非亲缘个体在育种计划中同样具有重要意义，可为育种配对与个体易地移植的决策提供参考。我们研发了一款名为Friends and Family的Windows可执行程序，其搭载图形用户界面，可基于COANCESTRY、GenAlEx等软件生成的两两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临界值，输出一份所有样本彼此间均无亲缘关系的样本列表。此非亲缘数据集可用于下游分析，例如遗传标记评估或遗传结构推断。还可将该分析结果与全数据集的结果进行对比，以明确亲缘个体对分析产生的影响。我们展示了该程序的一项应用实例：在一组实证数据集内，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Friends and Family程序。