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. 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 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），因此可作为模式系统（model system）：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，用于开展单基因及染色体倒位层面的适应性进化研究。鉴于已有研究表明其核苷酸变异并未处于突变-漂移平衡（mutation-drift equilibrium）状态，因此准确推断该物种的种群动态历史至关重要。为此，我们针对研究种群中J染色体未受倒位影响的区段，对分布于该区段的16个非编码区域开展了测序。我们在这16个区域中检测到的变异模式，与此前在不同染色体倒位构型中报道的结果高度相似，这表明后者的结果主要反映的是近期的种群动态事件，而非倒位的起源与频率上升所带来的部分选择性清除效应。在我们针对这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动态模型中，数据支持度最高的模型指向了倒数第二次冰期之后迅速发生的种群扩张事件。该模型是更优的零模型（null model），可为后续旨在揭示该物种全基因组范围内选择性事件的研究提供重要的参考资源。本研究结果同时凸显了，在引入外类群（outgroup）的溯祖模拟（coalescent simulations）中纳入多重突变事件可能性的重要意义。