ArticleGenetics2015
The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.
Article in Genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
187 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila.Genetics · 2024Pooled it
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- Dietary restriction is evolutionarily conserved on the phenotypic and mechanistic level.EMBO reports · 2026Article
- Gene-level complexity explains genome-wide variation in the distribution of fitness effects.Molecular biology and evolution · 2026Article
- Estimating the evolutionary fitness of specific synonymous codon changes.Molecular biology and evolution · 2026Article
- A recombinantbioRxiv : the preprint server for biology · 2026Article
- Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein.PLoS genetics · 2026Article
- ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.Genome biology · 2026Article
- Alternative 3' Polyadenylation Responses to Acute Ethanol Exposure Differ Between Drosophila Populations.Research square · 2026Article
- The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Estimating the evolutionary fitness of specific synonymous codon changes.bioRxiv : the preprint server for biology · 2026Article
- The distribution of fitness effects of new mutations in regulatory regions of thebioRxiv : the preprint server for biology · 2026Article
- Article
- Polymorphic 3D genome architecture mediated by transposable elements.bioRxiv : the preprint server for biology · 2026Article
- Rapid compensatory evolution within a multiprotein complex preserves telomere integrity.Science (New York, N.Y.) · 2025Article
- Natural Selection in Transcription Factor-DNA Interaction Motifs: A Comparative and Population Genomics Perspective.Genome biology and evolution · 2025Article
- Gene age shapes functional and evolutionary properties of theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Epistasis among clustered lineage-specific adaptive amino acid substitutions in the Drosophila Trio protein.bioRxiv : the preprint server for biology · 2025Article
- Gene and transposable element expression in response to stress in temperate and tropical populations of Drosophila.Mobile DNA · 2025Article
- Genetic variation in recalcitrant repetitive regions of theGenome research · 2025Article
127 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.