Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland.
Genes (Basel). 2019 Apr 18;10(4):308. doi: 10.3390/genes10040308.
Measuring the magnitude of differentiation between populations based on genetic markers is commonplace in ecology, evolution, and conservation biology. The predominant differentiation metric used for this purpose is F. Based on a qualitative survey, numerical analyses, simulations, and empirical data, I here argue that F does not express the relationship to allele frequency differentiation between populations generally considered interpretable and desirable by researchers. In particular, F (1) has low sensitivity when population differentiation is weak, (2) is contingent on the minor allele frequency across the populations, (3) can be strongly affected by asymmetry in sample sizes, and (4) can differ greatly among the available estimators. Together, these features can complicate pattern recognition and interpretation in population genetic and genomic analysis, as illustrated by empirical examples, and overall compromise the comparability of population differentiation among markers and study systems. I argue that a simple differentiation metric displaying intuitive properties, the absolute allele frequency difference , provides a valuable alternative to F. I provide a general definition of applicable to both bi- and multi-allelic markers and conclude by making recommendations on the sample sizes needed to achieve robust differentiation estimates using .
基于遗传标记衡量群体间的分化程度在生态学、进化生物学和保护生物学中是很常见的。为此目的而使用的主要分化度量标准是 F。基于定性调查、数值分析、模拟和经验数据，我在这里认为，F 并没有表达出研究人员普遍认为可解释和可取的种群间等位基因频率分化的关系。具体来说，F（1）在群体分化较弱时灵敏度较低，（2）取决于种群间的次要等位基因频率，（3）可能受到样本大小不对称的强烈影响，（4）在可用估计量之间差异很大。这些特征共同使群体遗传和基因组分析中的模式识别和解释变得复杂，如经验示例所示，并且总体上会损害标记和研究系统之间的群体分化的可比性。我认为，一种具有直观属性的简单分化度量标准，即绝对等位基因频率差异 ，提供了 F 的有价值替代品。我给出了适用于双等位基因和多等位基因标记的 的一般定义，并最后就使用 获得稳健的分化估计所需的样本量提出了建议。
