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Reconstructing the invasion route of DNA transposons using extant population samples

https://doi.org/10.1101/729889
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Outgoing claims: the papers this work cites, builds on, or argues with.

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KP elements repress P‐induced hybrid dysgenesis in Drosophila melanogaster.
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I elements and the Drosophila genome
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Prevalence of full-size P and KP elements in North American populations of Drosophila melanogaster
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High-frequency P element loss in Drosophila is homolog dependent
inferredcites →https://doi.org/10.1016/0168-9525(89)90039-5openalex-snapshot
Eukaryotic transposable elements and genome evolution
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Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila
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Small RNAs as Guardians of the Genome
inferredcites →https://doi.org/10.1016/j.cell.2009.03.040openalex-snapshot
Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary
inferredcites →https://doi.org/10.1016/j.cell.2012.10.040openalex-snapshot
Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression
inferredcites →https://doi.org/10.1016/j.cell.2014.04.031openalex-snapshot
The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila
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1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
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Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution
inferredcites →https://doi.org/10.1017/s0016672303006505openalex-snapshot
Mutation accumulation and the effect of copia insertions in Drosophila melanogaster
inferredcites →https://doi.org/10.1017/s001667239900395xopenalex-snapshot
A scenario for the hobo transposable element invasion, deduced from the structure of natural populations of Drosophila melanogaster using tandem TPE repeats
inferredcites →https://doi.org/10.1038/443521aopenalex-snapshot
Junk DNA as an evolutionary force
inferredcites →https://doi.org/10.1038/nature11416openalex-snapshot
Paramutation in Drosophila linked to emergence of a piRNA-producing locus
inferredcites →https://doi.org/10.1038/nrg2165openalex-snapshot
A unified classification system for eukaryotic transposable elements
inferredcites →https://doi.org/10.1046/j.1420-9101.1989.2030223.xopenalex-snapshot
Geographical and historical patterns of distribution of hobo elements in Drosophila melanogaster populations
inferredcites →https://doi.org/10.1073/pnas.1313677110openalex-snapshot
Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters
inferredcites →https://doi.org/10.1073/pnas.1500758112openalex-snapshot
The recent invasion of natural Drosophila simulans populations by the P-element
inferredcites →https://doi.org/10.1073/pnas.1613365113openalex-snapshot
Deep sequencing of 10,000 human genomes
inferredcites →https://doi.org/10.1073/pnas.1621178114openalex-snapshot
Massive horizontal transfer of transposable elements in insects
inferredcites →https://doi.org/10.1073/pnas.80.6.1655openalex-snapshot
Evolution of hybrid dysgenesis determinants in Drosophila melanogaster
inferredcites →https://doi.org/10.1073/pnas.82.16.5418openalex-snapshot
P -element distribution in Eurasian populations of Drosophila melanogaster : A genetic and molecular analysis
inferredcites →https://doi.org/10.1073/pnas.96.22.12621openalex-snapshot
Evidence for the recent horizontal transfer of long terminal repeat retrotransposon
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/gbe/evy218openalex-snapshot
The Evolution of Small-RNA-Mediated Silencing of an Invading Transposable Element
inferredcites →https://doi.org/10.1093/genetics/124.2.339openalex-snapshot
Evidence for horizontal transmission of the P transposable element between Drosophila species.
inferredcites →https://doi.org/10.1093/genetics/130.2.315openalex-snapshot
Effects of P element insertions on quantitative traits in Drosophila melanogaster.
inferredcites →https://doi.org/10.1093/genetics/132.3.737openalex-snapshot
Analysis of subtelomeric heterochromatin in the Drosophila minichromosome Dp1187 by single P element insertional mutagenesis.
inferredcites →https://doi.org/10.1093/genetics/133.3.623openalex-snapshot
P element transposition in Drosophila melanogaster: an analysis of sister-chromatid pairs and the formation of intragenic secondary insertions during meiosis.
inferredcites →https://doi.org/10.1093/genetics/49.4.561openalex-snapshot
THE STEPPING STONE MODEL OF POPULATION STRUCTURE AND THE DECREASE OF GENETIC CORRELATION WITH DISTANCE
inferredcites →https://doi.org/10.1093/molbev/msv194openalex-snapshot
The Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome Reveals a Network of Epistatic Fitness Interactions
inferredcites →https://doi.org/10.1093/molbev/msz079openalex-snapshot
Dynamics of Transposable Element Invasions with piRNA Clusters
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025590openalex-snapshot
Multiple UPGMA and Neighbor-joining Trees and the Performance of Some Computer Packages
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025808openalex-snapshot
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040491openalex-snapshot
Molecular characteristics of diverse populations are consistent with the hypothesis of a recent invasion of Drosophila melanogaster by mobile P elements.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040649openalex-snapshot
Distribution of hobo transposable elements in natural populations of Drosophila melanogaster.
inferredcites →https://doi.org/10.1101/313759openalex-snapshot
Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses
inferredcites →https://doi.org/10.1101/337543openalex-snapshot
Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila
inferredcites →https://doi.org/10.1101/611350openalex-snapshot
Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations
inferredcites →https://doi.org/10.1101/gad.209841.112openalex-snapshot
Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state
inferredcites →https://doi.org/10.1101/gr.095406.109openalex-snapshot
Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
inferredcites →https://doi.org/10.1101/gr.228627.117openalex-snapshot
Molecular dissection of a natural transposable element invasion
inferredcites →https://doi.org/10.1111/1755-0998.13030openalex-snapshot
DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03887.xopenalex-snapshot
G ST and its relatives do not measure differentiation
inferredcites →https://doi.org/10.1111/mec.14961openalex-snapshot
Patterns of transposable element variation and clinality in Drosophila
inferredcites →https://doi.org/10.1111/mec.14963openalex-snapshot
Population‐specific dynamics and selection patterns of transposable element insertions in European natural populations
inferredcites →https://doi.org/10.1126/science.1140494openalex-snapshot
A Slicer-Mediated Mechanism for Repeat-Associated siRNA 5' End Formation in Drosophila
inferredcites →https://doi.org/10.1126/science.1653452openalex-snapshot
Targeted Gene Replacement in Drosophila Via P Element-Induced Gap Repair
inferredcites →https://doi.org/10.1128/9781555817954.ch21openalex-snapshot
P Transposable Elements inDrosophila melanogaster
inferredcites →https://doi.org/10.1139/g89-046openalex-snapshot
Transposable elements and fitness in Drosophila melanogaster
inferredcites →https://doi.org/10.1186/1745-6150-6-1openalex-snapshot
The advantages and disadvantages of horizontal gene transfer and the emergence of the first species
inferredcites →https://doi.org/10.1186/1745-6150-6-19openalex-snapshot
The struggle for life of the genome's selfish architects
inferredcites →https://doi.org/10.1186/1759-8753-5-22openalex-snapshot
piRNA clusters and open chromatin structure
inferredcites →https://doi.org/10.1186/gb-2006-7-11-r112openalex-snapshot
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome
inferredcites →https://doi.org/10.1186/s13059-019-1736-xopenalex-snapshot
Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion
inferredcites →https://doi.org/10.1186/s13059-019-1795-zopenalex-snapshot
A comparison of automatic cell identification methods for single-cell RNA sequencing data
inferredcites →https://doi.org/10.1261/rna.046300.114openalex-snapshot
The capacity of target silencing by Drosophila PIWI and piRNAs
inferredcites →https://doi.org/10.1266/ggs.77.259openalex-snapshot
Full-size P and KP elements predominate in wild Drosophila melanogaster.
inferredcites →https://doi.org/10.1266/jjg.60.531openalex-snapshot
Viability mutations induced by the P elements in Drosophila melanogaster.
inferredcites →https://doi.org/10.1371/journal.pcbi.0010022openalex-snapshot
Combined Evidence Annotation of Transposable Elements in Genome Sequences
inferredcites →https://doi.org/10.1371/journal.pgen.1004775openalex-snapshot
Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila
inferredcites →https://doi.org/10.1534/genetics.113.158147openalex-snapshot
An Age-of-Allele Test of Neutrality for Transposable Element Insertions
inferredcites →https://doi.org/10.1534/genetics.115.174664openalex-snapshot
The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population
inferredcites →https://doi.org/10.1534/genetics.115.184119openalex-snapshot
Reexamining the P-Element Invasion of Drosophila melanogaster Through the Lens of piRNA Silencing
inferredcites →https://doi.org/10.2307/j.ctvjhzrc6openalex-snapshot
Genes in Conflict
inferredcites →https://doi.org/10.3389/fgene.2014.00001openalex-snapshot
Cytoplasmic 5′-3′ exonuclease Xrn1p is also a genome-wide transcription factor in yeast
inferredcites →https://doi.org/10.3389/fgene.2014.00257openalex-snapshot
History of the discovery of a master locus producing piRNAs: the flamenco/COM locus in Drosophila melanogaster
inferredcites →https://doi.org/10.5860/choice.43-5875openalex-snapshot
Genes in conflict: the biology of selfish genetic elements
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Genomic analysis of P elements in natural populations of Drosophila melanogaster
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