Corrigendum to: Drosophila Evolution over Space and Time (DEST): a New Population Genomics Resource

Population genomics of marine fishes: identifying adaptive variation in space and time

Molecular Ecology ◽

10.1111/j.1365-294x.2009.04272.x ◽

2009 ◽

Vol 18 (15) ◽

pp. 3128-3150 ◽

Cited By ~ 213

Author(s):

EINAR E. NIELSEN ◽

JAKOB HEMMER-HANSEN ◽

PETER FOGED LARSEN ◽

DORTE BEKKEVOLD

Keyword(s):

Population Genomics ◽

Marine Fishes ◽

Adaptive Variation ◽

Space And Time

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Rapid evolution in insect pests: the importance of space and time in population genomics studies

Current Opinion in Insect Science ◽

10.1016/j.cois.2017.12.008 ◽

2018 ◽

Vol 26 ◽

pp. 8-16 ◽

Cited By ~ 21

Author(s):

Benjamin Pélissié ◽

Michael S Crossley ◽

Zachary Paul Cohen ◽

Sean D Schoville

Keyword(s):

Population Genomics ◽

Insect Pests ◽

Rapid Evolution ◽

Space And Time

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

Molecular Biology and Evolution ◽

10.1093/molbev/msab259 ◽

2021 ◽

Author(s):

Martin Kapun ◽

Joaquin C B Nunez ◽

María Bogaerts-Márquez ◽

Jesús Murga-Moreno ◽

Margot Paris ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Population Genomics ◽

Natural Populations ◽

Easy Access ◽

Data Repository ◽

Bioinformatics Pipeline ◽

Space And Time ◽

Sequencing Technologies ◽

Spatio Temporal ◽

Demographic Inference

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data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in 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.

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

10.1101/2021.02.01.428994 ◽

2021 ◽

Author(s):

Martin Kapun ◽

Joaquin C. B. Nunez ◽

María Bogaerts-Márquez ◽

Jesús Murga-Moreno ◽

Margot Paris ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Population Genomics ◽

Natural Populations ◽

Easy Access ◽

Data Repository ◽

Bioinformatics Pipeline ◽

Space And Time ◽

Sequencing Technologies ◽

Different Seasons ◽

Spatio Temporal

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 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution and population structure 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 population samples from over 100 locations in >20 countries on four continents based on a combination of 121 unpublished and 150 previously published genomic datasets. 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. 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.

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