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.