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

Martin Kapun; Hester van Schalkwyk; Bryant McAllister; Thomas Flatt; Christian Schlötterer

doi:10.1111/mec.12594

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

Journal article

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

Martin Kapun, Hester van Schalkwyk, Bryant McAllister, Thomas Flatt and Christian Schlötterer

Molecular ecology, Vol.23(7), pp.1813-1827

04/2014

DOI: 10.1111/mec.12594

PMCID: PMC4359753

PMID: 24372777

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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.

Haplotypes

Genetics, Population

Genetic Markers

Chromosome Inversion

Drosophila melanogaster - genetics

North America

Sequence Analysis, DNA

Linkage Disequilibrium

Genetic Variation

Animals

Karyotyping

Polymorphism, Single Nucleotide

Australia

Evolution, Molecular

Details

Title: Subtitle: Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster
Creators: Martin Kapun - Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna, A-1210, Austria; Vienna graduate school of Population Genetics, Iowa City, IA, 52242, USA
Hester van Schalkwyk
Bryant McAllister
Thomas Flatt
Christian Schlötterer
Resource Type: Journal article
Publication Details: Molecular ecology, Vol.23(7), pp.1813-1827
DOI: 10.1111/mec.12594
PMID: 24372777
PMCID: PMC4359753
NLM abbreviation: Mol Ecol
ISSN: 0962-1083
eISSN: 1365-294X
Publisher: England
Grant note: W 1225 / Austrian Science Fund FWF
Language: English
Date published: 04/2014
Academic Unit: Biology
Record Identifier: 9983992062302771

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