Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)

The honeybee (Apis mellifera) has been threatened by multiple factors, including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A.m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A.m. mellifera colonies. Microsatellites have been preferred for identification of A.m. mellifera stocks across conservation centers. However, owing to high-throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite dataset to detect structure and introgression with that of different datasets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellites. Contrary to every SNP dataset, microsatellites were unable to clearly separate the two European lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level microsatellites’ performance was relatively poor at the upper range of introgression, a result reflected by their lower precision. Although mean accuracy was relatively high across datasets (>91%), microsatellites were the least accurate and the top-ranked informative 144 SNPs were the most accurate. Comparisons amongst the SNP datasets showed that those combining SNPs flanking microsatellites performed worst. Our results suggest that SNPs are more powerful for identification of A.m. mellifera colonies, especially when they are selected by information content.西方蜜蜂（Apis mellifera）正受到多种因素的威胁，包括病虫害、农药，以及因种群替换和基因渐渗而丧失的本地适应性基因复合体。在西欧，本土西方蜜蜂西方亚种（M谱系）的遗传完整性正受到威胁，原因是与东欧血统的商业亚种（C谱系）开展的蜂王贸易与集约化繁育。有效的保护行动需要可靠的分子工具来鉴定纯系西方蜜蜂蜂群。目前，各保护中心普遍采用微卫星标记（microsatellites）来鉴定西方蜜蜂种群。然而，单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）具有高通量、实验室间易于转移且基因分型错误率低的优势，其有望成为主流分子标记。本研究对比了一套广泛使用的微卫星标记数据集在检测种群结构与基因渐渗方面的分辨能力，以及多套不同的单核苷酸多态性数据集——这些数据集结合了数量不等的SNPs，这些SNPs均依据其信息含量以及与微卫星标记的基因组邻近性筛选得到。与所有单核苷酸多态性数据集均不同的是，微卫星标记无法在主成分分析（Principal Component Analysis，PCA）空间中清晰区分这两个欧洲谱系。两种标记类型的平均渐渗比例完全一致，但在个体水平上，微卫星标记在高渐渗程度区间内的表现相对较差，这一结果也体现在其较低的精度上。尽管各数据集的平均识别精度相对较高（>91%），但微卫星标记的精度最低，而筛选出的前144个高信息性SNPs的精度最高。对单核苷酸多态性数据集的进一步对比显示，侧翼包含微卫星标记的SNPs组合数据集表现最差。本研究结果表明，单核苷酸多态性在鉴定西方蜜蜂蜂群方面具有更优的性能，尤其是当这些SNPs依据信息含量进行筛选时。