Identifying the minimum number of microsatellite loci needed to assess population genetic structure: A case study in fly culturing

Small, isolated populations are constantly threatened by loss of genetic diversity due to drift. Such situations are found, for instance, in laboratory culturing. In guarding against diversity loss, monitoring of potential changes in population structure is paramount; this monitoring is most often achieved using microsatellite markers, which can be costly in terms of time and money when many loci are scored in large numbers of individuals. Here, we present a case study reducing the number of microsatellites to the minimum necessary to correctly detect the population structure of two <i>Drosophila nigrosparsa</i> populations. The number of loci was gradually reduced from 11 to 1, using the Allelic Richness (AR) and Private Allelic Richness (PAR) as criteria for locus removal. The effect of each reduction step was evaluated by the number of genetic clusters detectable from the data and by the allocation of individuals to the clusters; in the latter, excluding ambiguous individuals was tested to reduce the rate of incorrect assignments. We demonstrate that more than 95% of the individuals can still be correctly assigned when using eight loci and that the major population structure is still visible when using two highly polymorphic loci. The differences between sorting the loci by AR and PAR were negligible. The method presented here will most efficiently reduce genotyping costs when small sets of loci (“core sets”) for long-time use in large-scale population screenings are compiled.

小型隔离种群始终面临因遗传漂变导致的遗传多样性丧失威胁。此类情况常见于实验室培养体系中。为防范遗传多样性丧失，监测种群结构的潜在变化至关重要；此类监测通常借助微卫星标记（microsatellite marker）完成，但当对大量个体的众多基因座进行分型时，该方法会耗费大量时间与资金成本。本研究通过一则案例分析，将微卫星标记的数量缩减至可准确检测两个暗果蝇（Drosophila nigrosparsa）种群结构的最低必要水平。本研究以等位基因丰富度（Allelic Richness, AR）与私有等位基因丰富度（Private Allelic Richness, PAR）作为基因座筛选标准，将基因座数量从11个逐步缩减至1个。每一步缩减的效果均通过数据可检测到的遗传簇数量，以及个体向遗传簇的聚类分配结果进行评估；在后一项评估中，本研究通过剔除歧义个体的方式，尝试降低错配率。研究结果表明，仅使用8个基因座时，仍可实现95%以上个体的准确聚类分配；仅使用2个高多态性基因座时，种群的核心结构依然可被清晰识别。基于AR与PAR进行基因座排序的结果差异可忽略不计。本研究提出的方法可在为大规模种群筛查构建长期使用的小型基因座集合（即"核心基因座集"）时，最有效地降低基因分型成本。