Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees

Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations. We find that in general, levels of genetic differentiation between highland and lowland populations are very low, consistent with them being a single panmictic population. However, we identify two loci on chromosomes 7 and 9, each several hundred kilobases in length, which exhibit near fixation for different haplotypes between highland and lowland populations. The highland haplotypes at these loci are extremely rare in samples from the rest of the world. Patterns of segregation of genetic variants suggest that recombination between haplotypes at each locus is suppressed, indicating that they comprise independent structural variants. The haplotype on chromosome 7 harbors nearly all octopamine receptor genes in the honey bee genome. These have a role in learning and foraging behavior in honey bees and are strong candidates for adaptation to highland habitats. Molecular analysis of a putative breakpoint indicates that it may disrupt the coding sequence of one of these genes. Divergence between the highland and lowland haplotypes at both loci is extremely high suggesting that they are ancient balanced polymorphisms that greatly predate divergence between the extant honey bee subspecies.解析适应的遗传基础是生物学领域的核心研究课题之一。栖息于东非山地森林的西方蜜蜂（Apis mellifera）种群，与其周边低地稀树草原的同类种群在行为与形态上存在显著差异，这一现象大概率反映了二者对各自栖息环境的适应性演化。本研究对来自两组种群的39份高地与低地蜜蜂样本开展全基因组测序，以明确它们的演化亲缘关系，并鉴定这些推测性适应性特征的遗传基础。 研究结果显示，总体而言高地与低地种群间的遗传分化水平极低，符合二者同属一个泛交种群（panmictic population）的特征。但我们在7号与9号染色体上各发现一个长度达数百千碱基的基因座（locus，复数形式为loci），这两个基因座在高地与低地种群中几乎固定了不同的单倍型（haplotype）。上述基因座上的高地单倍型在全球其他区域的样本中极为罕见。 遗传变异的分离模式表明，每个基因座上的单倍型间重组受到抑制，提示二者属于独立的结构变异（structural variant）。7号染色体上的单倍型包含了西方蜜蜂基因组中几乎全部的章鱼胺受体基因（octopamine receptor gene），这类基因在西方蜜蜂的学习与觅食行为中发挥关键作用，是适应高地栖息环境的有力候选基因。对一处推测断裂点（putative breakpoint）的分子分析显示，该断裂点可能会破坏其中一个基因的编码序列。 两个基因座上高地与低地单倍型间的分化程度极高，表明它们是古老的平衡多态性（balanced polymorphism），其形成时间远早于现存西方蜜蜂亚种间的分化事件。