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类群的多样性格局，对诸多分类单元而言均颇具挑战性，伊比利亚蜜蜂亦不例外。针对伊比利亚蜜蜂的遗传变异调查，是所有蜜蜂亚种相关研究中覆盖规模最广泛的系列之一。此类研究已揭示出差异化且复杂的多样性格局，但相关成因尚未完全阐明。本研究采用一套覆盖西方蜜蜂16条染色体的全基因组数据集，包含309个经中性检验的单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点，对711只单倍体雄蜂进行基因分型；同时结合线粒体DNA（mitochondrial DNA, mtDNA）的一个基因间位点开展联合分析，以揭示伊比利亚蜜蜂全分布区内的种群结构历史格局。总体而言，通过多种聚类分析方法及地理梯度分析，对核基因座数据进行种群结构推断所得的格局显示：存在两个主要类群，二者形成一条清晰的渐变带，沿东北-西南轴线横贯伊比利亚半岛——该格局与线粒体DNA的分析结果高度一致。尽管初级渐变或距离隔离机制可解释观测到的梯度变异，但我们的研究结果更契合另一假说：即此前在冰期避难所中发生分化的种群，后续发生了二次接触——这一假说已在越来越多的伊比利亚半岛特有类群研究中被提出。尽管当前伊比利亚蜜蜂的养殖管理强度较高，但人类活动介导的过程，似乎对塑造伊比利亚蜜蜂的遗传结构仅起到了微弱作用。本研究凸显了伊比利亚蜜蜂多样性格局的复杂性，并进一步证实伊比利亚半岛作为西方蜜蜂（Apis mellifera）种质资源库的重要价值。