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

TL;DR

This study introduces diagnostic SNP markers enabling the inference of chromosomal inversion frequencies from Pool-Seq data in Drosophila melanogaster, revealing evolutionary dynamics and latitudinal clines across populations.

Contribution

We developed a novel set of SNP markers for 7 inversions, allowing inversion frequency estimation from Pool-Seq data, which was previously not possible.

Findings

Increased frequencies of In(3R)C and In(3R)Mo under positive selection.

Confirmed known latitudinal clines for multiple inversions.

Discovered a new latitudinal cline for In(3R)Mo in North America.

Abstract

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.