Data from: Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions

Drosophila subobscura presents a rich and complex chromosomal inversion polymorphism. It can thus be considered a model system i) to study the mechanisms originating inversions and how inversions affect the levels and patterns of variation in the inverted regions, and ii) to study adaptation at both the single-gene and chromosomal inversion levels. It is therefore important to infer its demographic history since previous information indicated that its nucleotide variation is not at mutation-drift equilibrium. For that purpose, we sequenced 16 non-coding regions distributed across those parts of the J chromosome not affected by inversions in the studied population and possibly either by other selective events. The pattern of variation detected in these 16 regions is similar to that previously reported within different chromosomal arrangements, suggesting that the latter results would, thus, mainly reflect recent demographic events rather than the partial selective sweep imposed by the origin and frequency increase of inversions. Among the simple demographic models considered in our ABC analysis of variation at the 16 regions, the model best supported by the data implies a population size expansion soon after the penultimate glacial period. This model constitutes a better null model and it is therefore an important resource for subsequent studies aiming among others to uncover selective events across the species genome. Our results also highlight the importance of introducing the possibility of multiple hits in the coalescent simulations with an outgroup.

暗果蝇（Drosophila subobscura）具有丰富且复杂的染色体倒位多态性（chromosomal inversion polymorphism），因此可作为理想的模式研究系统：其一，用于探究染色体倒位的形成机制，以及倒位如何影响倒位区域内的变异水平与分布模式；其二，用于在单基因与染色体倒位两个层面开展适应性进化研究。鉴于已有研究表明其核苷酸变异并未处于突变-漂移平衡状态，因此推断其种群历史至关重要。为此，我们对研究种群中J染色体（J chromosome）上未受倒位影响、且大概率未受其他选择事件干扰的区域，测序了16个非编码区域（non-coding regions）。我们在这16个区域中检测到的变异模式，与此前不同染色体倒位排列中报道的结果相似，这暗示后者的结果主要反映了近期的种群历史事件，而非由倒位的起源与频率上升所引发的局部选择性清除（selective sweep）。在针对这16个区域的变异开展的近似贝叶斯计算（Approximate Bayesian Computation，ABC）分析所考量的简单种群历史模型中，数据最支持的模型表明，该种群在倒数第二次冰期之后迅速发生了种群扩张。该模型为更优的零模型，因此可为后续旨在揭示该物种全基因组范围内选择事件等在内的研究提供重要的研究资源。本研究结果同时凸显了，在引入外类群（outgroup）的溯祖模拟（coalescent simulations）中纳入多重击中可能性的重要性。