ArticleMolecular biology and evolution2014
Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66 citing papers in PubMed.
- Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci.eLife · 2026Article
- Retention of a single Cenp-C gene in different syntenic locations in the montium group of Drosophila species.Heredity · 2026Article
- Adaptive evolution of Topoisomerase II triggers reproductive isolation in Drosophila.bioRxiv : the preprint server for biology · 2026Article
- Chromosomal Rearrangements and Transposable Elements in Locally Adapted Island Drosophila.Genome biology and evolution · 2026Article
- Retention of a singlebioRxiv : the preprint server for biology · 2025Article
- Sex-biased duplicates are rapidly generated duringbioRxiv : the preprint server for biology · 2025Article
- Dinucleotide preferences underlie apparent codon preference reversals in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genomic Islands of Divergence Between Drosophila yakuba Subspecies are Predominantly Driven by Chromosomal Inversions and the Recombination Landscape.Molecular ecology · 2025Article
- Sex-Specific Ultraviolet Radiation Tolerance AcrossEcology and evolution · 2025Article
- Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila.Molecular biology and evolution · 2024Article
- IntroUNET: Identifying introgressed alleles via semantic segmentation.PLoS genetics · 2024Article
- IntroUNET: identifying introgressed alleles via semantic segmentation.bioRxiv : the preprint server for biology · 2024Article
- Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.Journal of evolutionary biology · 2023Article
- Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species.PLoS genetics · 2023Article
- Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans.PLoS biology · 2023Article
- Copy Number Variation of theAnimals : an open access journal from MDPI · 2022Article
- Species-specific chromatin landscape determines how transposable elements shape genome evolution.eLife · 2022Article
- Cross-species incompatibility between a DNA satellite and the Drosophila Spartan homolog poisons germline genome integrity.Current biology : CB · 2022Article
- Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans.Nature ecology & evolution · 2022Article
- P-elements strengthen reproductive isolation within the Drosophila simulans species complex.Evolution; international journal of organic evolution · 2021Article
6 more citing papers are in PubMed but not listed here.
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Abstract
We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of Drosophila yakuba and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting that deleterious impacts are common. Drosophila simulans shows larger numbers of whole gene duplications in comparison to larger proportions of gene fragments in D. yakuba. Drosophila simulans displays an excess of high-frequency variants on the X chromosome, consistent with adaptive evolution through duplications on the D. simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited noncoding sequence in D. yakuba and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these results suggest that tandem duplications often result in complex variation beyond whole gene duplications that offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease, as well as to adaptive evolutionary change.
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