title: Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster.
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 seven 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.
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna, A-1210, Austria; Vienna graduate school of Population Genetics, Iowa City, IA, 52242, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Kapun
authors.forename: Hester
authors.initials: H
authors.lastname: van Schalkwyk
authors.forename: Bryant
authors.initials: B
authors.lastname: McAllister
authors.forename: Thomas
authors.initials: T
authors.lastname: Flatt
authors.forename: Christian
authors.initials: C
authors.lastname: Schlötterer
mesh_terms: D000818:Animals; D001315:Australia; D007446:Chromosome Inversion; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D007621:Karyotyping; D015810:Linkage Disequilibrium; D009656:North America; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers
keywords: Pool-Seq; experimental evolution; genomics; inversions; population genetics