Data from: Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster

Sequencing of pools of individuals (Pool-Seq) represents a reliable and cost-effective approach for estimating genome-wide SNP and transposable element insertion frequencies. However, Pool-Seq does not provide direct information on haplotypes so that for example obtaining inversion frequencies has not been possible until now. Here, we have developed a new set of diagnostic marker SNPs for 7 cosmopolitan inversions in Drosophila melanogaster that can be used to infer inversion frequencies from Pool-Seq data. We applied our novel marker set to Pool-Seq data from an experimental evolution study and from North American and Australian latitudinal clines. In the experimental evolution data, we find evidence that positive selection has driven the frequencies of In(3R)C and In(3R)Mo to increase over time. In the clinal data, we confirm the existence of frequency clines for In(2L)t, In(3L)P and In(3R)Payne in both North America and Australia and detect a previously unknown latitudinal cline for In(3R)Mo in North America. The inversion markers developed here provide a versatile and robust tool for characterizing inversion frequencies and their dynamics in Pool-Seq data from diverse D. melanogaster populations.

混合样本测序（Pool-Seq）是一种可靠且具成本效益的手段，可用于估算全基因组单核苷酸多态性（SNP）与转座元件插入频率。然而，Pool-Seq无法直接提供单倍型信息，因此直至此前，获取染色体倒位频率始终难以实现。本研究针对黑腹果蝇（Drosophila melanogaster）的7种广布染色体倒位，开发了一套全新的诊断性标记SNP，可用于基于Pool-Seq数据推断染色体倒位频率。我们将这套新型标记套装应用于三组Pool-Seq数据：分别来自一项实验演化研究，以及北美与澳大利亚的纬度渐变群样本。在实验演化数据中，我们发现证据表明：正选择推动了In(3R)C与In(3R)Mo的频率随时间推移逐步升高。在纬度渐变群数据中，我们证实了In(2L)t、In(3L)P与In(3R)Payne在北美与澳大利亚均存在频率渐变群，并在北美地区发现了此前未被报道的In(3R)Mo纬度渐变群。本研究开发的染色体倒位标记，可为来自不同黑腹果蝇群体的Pool-Seq数据提供一种通用且可靠的工具，用于解析染色体倒位频率及其动态变化。