Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
Genes (Basel). 2020 May 19;11(5):566. doi: 10.3390/genes11050566.
Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each Y-STR in these sets performs well during this procedure. In this study, a total of 20,927 haplotypes of a Yfiler Plus set were collected from 41 global populations. Different configurations were observed in multidimensional scaling (MDS) plots based on pairwise genetic distances evaluated using a Yfiler set and a Yfiler Plus set, respectively. Subsequently, 23 single-copy Y-STRs were characterized in the evaluation of population differentiation using the mean of allele frequency difference (mAFD) between populations. Our results indicated that DYS392 had the largest mAFD value (0.3802) and YGATAH4 had the smallest value (0.1845). On the whole, larger pairwise genetic distances could be obtained using the set with the top fifteen markers from these 23 single-copy Y-STRs, and clear clustering or separation of populations could be observed in the MDS plot in comparison with those using the set with the minimum fifteen markers. In conclusion, the mAFD value is reliable to characterize Y-STRs for efficiency in the evaluation of population differentiation.
Y 染色体短串联重复序列（Y-STRs）广泛应用于人类研究，用于评估群体亚结构或群体分化。先前的研究表明，可使用多套单倍型来评估群体分化。然而，目前尚不清楚这些单倍型集中的每个 Y-STR 在该过程中的表现是否良好。在这项研究中，从 41 个全球群体中收集了总共 20927 个 Yfiler Plus 试剂盒的单倍型。基于使用 Yfiler 试剂盒和 Yfiler Plus 试剂盒分别评估的成对遗传距离，在多维尺度（MDS）图中观察到不同的配置。随后，使用群体间等位基因频率差异（mAFD）的平均值评估 23 个单拷贝 Y-STR 在群体分化评估中的特征。结果表明，DYS392 的 mAFD 值最大（0.3802），YGATAH4 的 mAFD 值最小（0.1845）。总的来说，与使用最小 15 个标记的试剂盒相比，使用这 23 个单拷贝 Y-STR 中前 15 个标记的试剂盒可以获得更大的成对遗传距离，并且在 MDS 图中可以清楚地观察到群体聚类或分离。结论是，mAFD 值可用于可靠地描述 Y-STR，以评估群体分化的效率。
