Data from: Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variation provide support for secondary contact from historical refugia

Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern–southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity.解析伊比利亚半岛特有生物的多样性分布模式，对诸多分类群（taxa）而言均极具挑战性，伊比利亚蜜蜂（Iberian honey bee）亦不例外。针对伊比利亚蜜蜂的遗传变异研究，是全球范围内针对蜜蜂亚种开展的最全面的研究之一。此类研究已揭示出差异化且复杂的多样性分布模式，但相关机制尚未得到完全阐明。本研究采用了覆盖蜜蜂16条染色体的309个经中性检验的单核苷酸多态性（single nucleotide polymorphisms, SNPs）全基因组数据集，该数据集已在711只单倍体雄蜂中完成基因分型。研究团队将上述单核苷酸多态性与线粒体DNA（mitochondrial DNA）的一个基因间位点一并分析，以揭示伊比利亚蜜蜂整个分布范围内的种群结构历史模式。总体而言，通过多种聚类分析方法及地理梯度分析从核基因座中推断出的种群结构模式，与两大聚类群形成的清晰渐变群相一致——该渐变群沿东北-西南轴线横贯伊比利亚半岛，这一模式与线粒体DNA的分布模式极为相似。尽管初级渐变杂交或距离隔离机制能够解释观测到的梯度变异，但本研究结果更符合另一假说：即此前在冰期避难所中隔离的分化种群之间发生了次级接触，这一假说已在越来越多的伊比利亚分类群研究中被提出。尽管当前蜜蜂养殖管理强度极高，但人类活动介导的过程对伊比利亚蜜蜂遗传结构的塑造似乎仅起到了微弱作用。本研究凸显了伊比利亚蜜蜂多样性模式的复杂性，并进一步证实了伊比利亚半岛作为西方蜜蜂（Apis mellifera）多样性储存库的重要价值。