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Sequencing of pools of individuals (Pool-Seq) represents a reliable and cost-effective approach for estimating genome-wide SNP and transposable elementinsertion frequencies. However, Pool-Seq does not provide direct information onhaplotypes so that for example obtaining inversion frequencies has not beenpossible until now. Here, we have developed a new set of diagnostic marker SNPsfor 7 cosmopolitan inversions in Drosophila melanogaster that can be used toinfer inversion frequencies from Pool-Seq data. We applied our novel marker setto Pool-Seq data from an experimental evolution study and from North Americanand Australian latitudinal clines. In the experimental evolution data, we findevidence that positive selection has driven the frequencies of In(3R)C andIn(3R)Mo to increase over time. In the clinal data, we confirm the existence offrequency clines for In(2L)t, In(3L)P and In(3R)Payne in both North America andAustralia and detect a previously unknown latitudinal cline for In(3R)Mo inNorth America. The inversion markers developed here provide a versatile androbust tool for characterizing inversion frequencies and their dynamics inPool- Seq data from diverse D. melanogaster populations.

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