Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

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Abstract
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, 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data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in 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 data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. 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 data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
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Funding Information
  • Austrian Science Foundation (FWF P32275)
  • European Research Council
  • European Union’s Horizon 2020 Research and Innovation Programme (H2020-ERC-2014-CoG-647900)
  • Spanish Ministry of Science and Innovation (BFU-2011-24397)
  • Swiss National Science Foundation (PP00P3_133641, PP00P3_165836, 31003A_182262)
  • German Research Foundation
  • National Institutes of Health (R35 GM119686)
  • Research Council of Finland (322980)
  • Danish Natural Science Research Council (4002-00113B)
  • FS Deutsche Forschungsgemeinschaft (STA1154/4-1, 408908608)
  • Deutsche Forschungsgemeinschaft (274388701, 347368302)
  • FPI Fellowship (BES-2012-052999)
  • ET Israel Science Foundation (1737/17)
  • Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178)
  • Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007)
  • TM NSERC (RGPIN-2018-05551)

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