Arthofer Wolfgang, Heussler Carina, Krapf Patrick, Schlick-Steiner Birgit C, Steiner Florian M
a Molecular Ecology Group , Institute of Ecology, University of Innsbruck , Technikerstrasse 25, Innsbruck , Austria.
Fly (Austin). 2018 Jan 2;12(1):13-22. doi: 10.1080/19336934.2017.1396400. Epub 2017 Dec 1.
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 Drosophila nigrosparsa 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.
小型孤立种群经常受到因遗传漂变导致的遗传多样性丧失的威胁。例如，在实验室培养中就会出现这种情况。在防止多样性丧失方面，监测种群结构的潜在变化至关重要；这种监测通常使用微卫星标记来实现，当在大量个体中对许多位点进行评分时，这在时间和金钱方面可能成本很高。在这里，我们展示了一个案例研究，即将微卫星数量减少到正确检测两个黑腹果蝇种群的种群结构所需的最低数量。使用等位基因丰富度（AR）和私有等位基因丰富度（PAR）作为去除位点的标准，位点数量从11个逐渐减少到1个。通过从数据中可检测到的遗传簇数量以及个体分配到簇的情况来评估每个减少步骤的效果；在后者中，测试排除不明确个体以降低错误分配率。我们证明，使用8个位点时，仍有超过95%的个体能够被正确分配，并且使用两个高度多态性位点时，主要种群结构仍然可见。按AR和PAR对位点进行排序之间的差异可以忽略不计。当编制用于大规模种群筛查长期使用的少量位点（“核心集”）时，这里提出的方法将最有效地降低基因分型成本。
