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Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna

https://doi.org/10.1101/2020.09.21.307181

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-030-30363-1_12openalex-snapshot

Vertebrate Genome Size and the Impact of Transposable Elements in Genome Evolution

inferredcites →https://doi.org/10.1007/s00239-008-9118-0openalex-snapshot

The Association Between Breeding System and Transposable Element Dynamics in Daphnia Pulex

inferredcites →https://doi.org/10.1016/0043-1354(94)90157-0openalex-snapshot

ADaM, an artificial freshwater for the culture of zooplankton

inferredcites →https://doi.org/10.1016/0092-8674(90)90016-8openalex-snapshot

High-frequency P element loss in Drosophila is homolog dependent

inferredcites →https://doi.org/10.1016/j.gde.2018.02.011openalex-snapshot

Exaptation of transposable element coding sequences

inferredcites →https://doi.org/10.1016/j.tig.2019.01.002openalex-snapshot

Substitutions Are Boring: Some Arguments about Parallel Mutations and High Mutation Rates

inferredcites →https://doi.org/10.1016/j.ympev.2015.03.009openalex-snapshot

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

inferredcites →https://doi.org/10.1017/s0016672300021455openalex-snapshot

The population dynamics of transposable elements

inferredcites →https://doi.org/10.1038/nature17951openalex-snapshot

The industrial melanism mutation in British peppered moths is a transposable element

inferredcites →https://doi.org/10.1038/nrg1348openalex-snapshot

Microsatellites: simple sequences with complex evolution

inferredcites →https://doi.org/10.1038/s41467-019-11385-5openalex-snapshot

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

inferredcites →https://doi.org/10.1038/s41467-019-13555-xopenalex-snapshot

The epigenomic landscape of transposable elements across normal human development and anatomy

inferredcites →https://doi.org/10.1038/s41467-020-15149-4openalex-snapshot

Horizontal transfer and evolution of transposable elements in vertebrates

inferredcites →https://doi.org/10.1038/s41576-018-0050-xopenalex-snapshot

Computational tools to unmask transposable elements

inferredcites →https://doi.org/10.1038/s41576-019-0172-9openalex-snapshot

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

inferredcites →https://doi.org/10.1038/s41576-020-0251-yopenalex-snapshot

Measuring and interpreting transposable element expression

inferredcites →https://doi.org/10.1073/pnas.1716459114openalex-snapshot

Tracking the genome-wide outcomes of a transposable element burst over decades of amplification

inferredcites →https://doi.org/10.1086/698482openalex-snapshot

Evolutionary Conflict between Mobile DNA and Host Genomes

inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

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/bts187openalex-snapshot

pIRS: Profile-based Illumina pair-end reads simulator

inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot

CD-HIT: accelerated for clustering the next-generation sequencing data

inferredcites →https://doi.org/10.1093/gbe/evw264openalex-snapshot

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

inferredcites →https://doi.org/10.1093/gbe/evw302openalex-snapshot

Insertion polymorphisms of mobile genetic elements in sexual and asexual populations of Daphnia pulex

inferredcites →https://doi.org/10.1093/gbe/evx050openalex-snapshot

Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster

inferredcites →https://doi.org/10.1093/gbe/evy252openalex-snapshot

Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches

inferredcites →https://doi.org/10.1093/molbev/msaa142openalex-snapshot

High and Highly Variable Spontaneous Mutation Rates in Daphnia

inferredcites →https://doi.org/10.1093/molbev/msq337openalex-snapshot

Population Genomics of Transposable Elements in Drosophila melanogaster

inferredcites →https://doi.org/10.1093/molbev/msv261openalex-snapshot

No Accumulation of Transposable Elements in Asexual Arthropods

inferredcites →https://doi.org/10.1093/molbev/msw185openalex-snapshot

The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes

inferredcites →https://doi.org/10.1093/molbev/msx155openalex-snapshot

Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species

inferredcites →https://doi.org/10.1093/molbev/msz118openalex-snapshot

Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

inferredcites →https://doi.org/10.1093/nar/gkw294openalex-snapshot

Redundans: an assembly pipeline for highly heterozygous genomes

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040188openalex-snapshot

The genomic rate of transposable element movement in Drosophila melanogaster.

inferredcites →https://doi.org/10.1098/rspb.2013.2744openalex-snapshot

Adaptive phenotypic plasticity and local adaptation for temperature tolerance in freshwater zooplankton

inferredcites →https://doi.org/10.1101/gr.247965.118openalex-snapshot

Pedigree-based estimation of human mobile element retrotransposition rates

inferredcites →https://doi.org/10.1101/gr.827603openalex-snapshot

Sequence Divergence Within Transposable Element Families in the Drosophila melanogaster Genome

inferredcites →https://doi.org/10.1111/1365-2656.12421openalex-snapshot

Genetic, ecological and geographic covariables explaining host range and specificity of a microsporidian parasite

inferredcites →https://doi.org/10.1111/j.1095-8312.2008.01185.xopenalex-snapshot

Genome size evolution and polyploidy in the Daphnia pulex complex (Cladocera: Daphniidae)

inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03698.xopenalex-snapshot

Daphnia comes of age: an ecological model in the genomic era

inferredcites →https://doi.org/10.1111/j.1558-5646.2011.01337.xopenalex-snapshot

DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES

inferredcites →https://doi.org/10.1111/mec.14794openalex-snapshot

The impact of transposable elements in adaptive evolution

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.1089370openalex-snapshot

The Origins of Genome Complexity

inferredcites →https://doi.org/10.1126/science.1118884openalex-snapshot

Mutation Pressure and the Evolution of Organelle Genomic Architecture

inferredcites →https://doi.org/10.1128/9781555819217.ch25openalex-snapshot

Mechanisms of DNA Transposition

inferredcites →https://doi.org/10.1139/gen-2013-0004openalex-snapshot

Larger Daphnia at lower temperature: a role for cell size and genome configuration?

inferredcites →https://doi.org/10.1146/annurev-arplant-050213-035811openalex-snapshot

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

inferredcites →https://doi.org/10.1159/000444429openalex-snapshot

Transposons, Genome Size, and Evolutionary Insights in Animals

inferredcites →https://doi.org/10.1186/1471-2164-11-425openalex-snapshot

LTR retroelements in the genome of Daphnia pulex

inferredcites →https://doi.org/10.1186/gb-2010-11-4-r46openalex-snapshot

DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex

inferredcites →https://doi.org/10.1186/gb-2011-12-3-r27openalex-snapshot

A genome-wide view of mutation rate co-variation using multivariate analyses

inferredcites →https://doi.org/10.1186/s12862-015-0339-8openalex-snapshot

Do larger genomes contain more diverse transposable elements?

inferredcites →https://doi.org/10.1186/s12864-020-6763-1openalex-snapshot

Transposable element persistence via potential genome-level ecosystem engineering

inferredcites →https://doi.org/10.1186/s13059-018-1577-zopenalex-snapshot

Ten things you should know about transposable elements

inferredcites →https://doi.org/10.1186/s13100-015-0044-6openalex-snapshot

A call for benchmarking transposable element annotation methods

inferredcites →https://doi.org/10.1186/s13100-017-0103-2openalex-snapshot

Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

inferredcites →https://doi.org/10.1186/s13100-020-00213-zopenalex-snapshot

Transposable elements in Drosophila

inferredcites →https://doi.org/10.1371/journal.pgen.1008872openalex-snapshot

Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements

inferredcites →https://doi.org/10.1371/journal.pone.0185056openalex-snapshot

BBMerge – Accurate paired shotgun read merging via overlap

inferredcites →https://doi.org/10.1534/genetics.109.101147openalex-snapshot

Nucleotide Polymorphism and Within-Gene Recombination in Daphnia magna and D. pulex, Two Cyclical Parthenogens

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.3390/genes10050336openalex-snapshot

Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation

inferredcites →https://doi.org/10.3390/genes10060419openalex-snapshot

On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements

inferredcites →https://doi.org/10.3390/genes9050254openalex-snapshot

The Role of Transposable Elements in Speciation

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3389/fgene.2021.691058openalex-snapshot

A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

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