Data from: Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In Western Europe one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST=1) is introduced when the sample size is small (N≤10) and when sampling only captures a small fraction of a population’s genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training dataset to design four independent SNP assays selected from pairwise FST between the Iberian and C-lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid datasets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia, and South America, in a time- and cost-effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.作为最重要的人工管理传粉者，西方蜜蜂（Apis mellifera L.）正面临日益增多的生存威胁。在西欧，此类威胁之一便是商业品系（具有C谱系血统）的大规模引入，这引发了渐渗杂交，甚至导致本土西方蜜蜂种群（具有M谱系血统）的局部灭绝。本研究从176个全基因组中开发出高信息量单核苷酸多态性（Single Nucleotide Polymorphism，SNPs）简化检测体系，以估算欧洲最多样化且进化最复杂的亚种——伊比利亚蜜蜂（Apis mellifera iberiensis）中的C谱系渐渗情况。我们首先评估了样本量以及地理限制区域采样对高信息量SNP数量的影响。研究证实，当样本量较小（N≤10）且采样仅覆盖种群遗传多样性的极小部分时，会引入固定SNP（FST=1）数量的偏差。上述结果凸显了为具有复杂遗传模式的生物开发可靠简化SNP检测体系时，采用代表性采样的重要性。我们利用训练数据集，基于伊比利亚蜜蜂与C谱系蜜蜂的两两FST筛选出4组独立的SNP检测体系。所设计的检测体系经预留数据集与模拟杂交数据集验证，展现出极高的准确性，可省时且低成本地用于监测伊比利亚本土分布范围以及巴利阿里群岛、马卡罗尼西亚和南美洲等引种范围内的蜜蜂种群。尽管本研究以伊比利亚蜜蜂为模型系统，但其采用的方法在诸多场景中均具有较高应用价值，可用于监测和保护潜在发生杂交的驯养与野生种群。