A1 Journal article (refereed)
Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource (2021)

Kapun, M., Nunez, J. C. B., Bogaerts-Márquez, M., Murga-Moreno, J., Paris, M., Outten, J., Coronado-Zamora, M., Tern, C., Rota-Stabelli, O., García, G. M. P., Casillas, S., Orengo, D. J., Puerma, E., Kankare, M., Ometto, L., Loeschcke, V., Onder, B. S., Abbott, J. K., Schaeffer, S. W., . . . Bergland, A. O. (2021). Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource. Molecular Biology and Evolution, 38(12), 5782-5805. https://doi.org/10.1093/molbev/msab259

JYU authors or editors

Publication details

All authors or editors: Kapun, Martin; Nunez, Joaquin C B; Bogaerts-Márquez, María; Murga-Moreno, Jesús; Paris, Margot; Outten, Joseph; Coronado-Zamora, Marta; Tern, Courtney; Rota-Stabelli, Omar; García, Guerreiro Maria P; et al.

Journal or series: Molecular Biology and Evolution

ISSN: 0737-4038

eISSN: 1537-1719

Publication year: 2021

Publication date: 01/09/2021

Volume: 38

Issue number: 12

Pages range: 5782-5805

Publisher: Oxford University Press (OUP)

Publication country: United States

Publication language: English

DOI: https://doi.org/10.1093/molbev/msab259

Publication open access: Openly available

Publication channel open access: Partially open access channel

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/79175

Abstract

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

Keywords: population genetics; genomics; genome; evolution; bioinformatics; Drosophila melanogaster

Free keywords: Drosophila melanogaster; population genomics; SNPs; evolution; adaptation; demography

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Related projects

Ministry reporting: Yes

Reporting Year: 2021

JUFO rating: 3