Data from: Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms

Understanding the genetic mechanisms of adaptive population divergence is one of the most fundamental endeavours in evolutionary biology and is becoming increasingly important as it will allow predictions about how organisms will respond to global environmental crisis. This is particularly important for the honey bee, a species of unquestionable ecological and economical importance that has been exposed to increasing human-mediated selection pressures. Here, we conducted a single nucleotide polymorphism (SNP)-based genome scan in honey bees collected across an environmental gradient in Iberia and used four FST-based outlier tests to identify genomic regions exhibiting signatures of selection. Additionally, we analysed associations between genetic and environmental data for the identification of factors that might be correlated or act as selective pressures. With these approaches, 4.4% (17 of 383) of outlier loci were cross-validated by four FST-based methods, and 8.9% (34 of 383) were cross-validated by at least three methods. Of the 34 outliers, 15 were found to be strongly associated with one or more environmental variables. Further support for selection, provided by functional genomic information, was particularly compelling for SNP outliers mapped to different genes putatively involved in the same function such as vision, xenobiotic detoxification and innate immune response. This study enabled a more rigorous consideration of selection as the underlying cause of diversity patterns in Iberian honey bees, representing an important first step towards the identification of polymorphisms implicated in local adaptation and possibly in response to recent human-mediated environmental changes.

解析适应性种群分化的遗传机制，是进化生物学领域最基础的研究课题之一，且其重要性与日俱增——该研究可为预测生物如何应对全球环境危机提供依据。这一点对于蜜蜂而言尤为关键：作为具有毋庸置疑的生态与经济价值的物种，蜜蜂正面临日益加剧的人类介导选择压力。本研究针对伊比利亚半岛环境梯度下采集的蜜蜂样本，开展了基于单核苷酸多态性（single nucleotide polymorphism, SNP）的基因组扫描，并采用4种基于FST的离群位点检测方法，以筛选呈现选择信号的基因组区域。此外，我们还通过遗传数据与环境数据的关联分析，探究可能与选择压力相关或本身即为选择压力的环境因子。经上述分析，383个离群位点中有4.4%（17个）被4种FST方法交叉验证，8.9%（34个）被至少3种方法交叉验证。在这34个离群位点中，15个与一项或多项环境变量存在显著关联。功能基因组信息为选择作用提供了进一步的支撑证据：对于定位至不同基因的SNP离群位点而言，若这些基因被推测参与同一生物学功能（如视觉、外源性物质解毒及先天免疫应答），则该支撑证据尤为确凿。本研究严谨验证了选择作用是伊比利亚蜜蜂种群多样性模式的潜在成因，为鉴定参与本地适应、乃至响应近期人类介导环境变化的多态性位点迈出了重要的第一步。