2013/07/09 by Martin Kapun, Hester van Schalkwyk, Kapun, Martin +7 · 1 citation
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #FOS: Biological sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE) #q-bio.PE
paper · pdf · doi:10.48550/arxiv.1307.2461
31 pages, 4 main figures, 1 main table, 7 supporting figures, 11 supporting tables
arxiv created 2013/07/09 · openalex publication_date 2013/07/09 · arxiv updated 2013/07/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.