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

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

(2019) Gabriel E. Rech et al.   PLoS Genetics

Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

(2019) Daphné Reiss et al.   PLoS Genetics

Dynamics of Transposable Element Invasions with piRNA Clusters

(2019) Robert Kofler   MOLECULAR BIOLOGY AND EVOLUTION

Coupling, Reinforcement, and Speciation

(2018) Roger K. Butlin et al.   AMERICAN NATURALIST

Evolutionary Conflict between Mobile DNA and Host Genomes

(2018) Michael J. Song et al.   AMERICAN NATURALIST

Evidence for positive selection on recent human transposable element insertions

(2018) Lavanya Rishishwar et al.   GENE

RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

(2018) William H. Palmer et al.   GENETICS

Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention

(2018) Kyria Roessler et al.   Genome Biology and Evolution

Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling

(2018) Alexander T Xue et al.   Genome Biology and Evolution

Multiple and Independent Phases of Transposable Element Amplification in the Genomes of Piciformes (Woodpeckers and Allies)

(2018) Joseph D Manthey et al.   Genome Biology and Evolution

Sex chromosome repeats tip the balance towards speciation

(2018) Michael J. O'Neill et al.   MOLECULAR ECOLOGY

Supervised Machine Learning for Population Genetics: A New Paradigm

(2018) Daniel R. Schrider et al.   TRENDS IN GENETICS

diploS/HIC: An Updated Approach to Classifying Selective Sweeps

(2018) Andrew D. Kern et al.   G3-Genes Genomes Genetics

RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

(2018) William H. Palmer et al.   GENETICS

The Role of Transposable Elements in Speciation

(2018) Antonio Serrato-Capuchina et al.   Genes

The P element invaded rapidly and caused hybrid dysgenesis in natural populations of Drosophila simulans in Japan

(2018) Yusaku Yoshitake et al.   Ecology and Evolution

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distinguishing Among Modes of Convergent Adaptation Using Population Genomic Data

(2017) Kristin M. Lee et al.   GENETICS

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

(2017) Christoph Stritt et al.   Genome Biology and Evolution

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

(2017) Cibele G. Sotero-Caio et al.   Genome Biology and Evolution

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

(2017) Eugene J. Gardner et al.   GENOME RESEARCH

Transposable Element-Mediated Balancing Selection at Hsp90 Underlies Embryo Developmental Variation

(2017) Bing Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting Long-Term Balancing Selection Using Allele Frequency Correlation

(2017) Katherine M. Siewert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

(2017) Alexander Suh et al.   MOLECULAR ECOLOGY

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

(2017) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

Coevolution between transposable elements and recombination

(2017) Tyler V. Kent et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transposable Element Domestication As an Adaptation to Evolutionary Conflicts

(2017) Diwash Jangam et al.   TRENDS IN GENETICS

Identification of pathogenic retrotransposon insertions in cancer predisposition genes

(2017) Yaping Qian et al.   Cancer Genetics

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

(2017) Michael G. Nelson et al.   G3-Genes Genomes Genetics

Distinguishing Among Modes of Convergent Adaptation Using Population Genomic Data

(2017) Kristin M. Lee et al.   GENETICS

LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

(2017) Eric Disdero et al.   Mobile DNA

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

(2017) Jinfeng Chen et al.   PeerJ

LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis

(2017) Robert P. Ruggiero et al.   Frontiers in Genetics

The meaning of intragenomic conflict

(2017) Andy Gardner et al.   Nature Ecology & Evolution

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Benchmarking computational tools for polymorphic transposable element detection

(2016) Lavanya Rishishwar et al.   BRIEFINGS IN BIOINFORMATICS

The Evolution of Line-1 in Vertebrates

(2016) Stéphane Boissinot et al.   Genome Biology and Evolution

The devil is in the details: the effect of population structure on demographic inference

(2016) P Orozco-terWengel   HEREDITY

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

(2016) Robert Kofler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation inDrosophila melanogaster

(2016) Alan O. Bergland et al.   MOLECULAR ECOLOGY

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

(2016) Arjen E. van’t Hof et al.   NATURE

Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing

(2016) Jérôme Nicod et al.   NATURE GENETICS

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Accumulation of transposable elements inHoxgene clusters during adaptive radiation ofAnolislizards

(2016) Nathalie Feiner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptation to Global Change: A Transposable Element–Epigenetics Perspective

(2016) Olivier Rey et al.   TRENDS IN ECOLOGY & EVOLUTION

The Ecology and Evolutionary Dynamics of Meiotic Drive

(2016) Anna K. Lindholm et al.   TRENDS IN ECOLOGY & EVOLUTION

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis

(2016) Rebeca Campos-Sánchez et al.   PLoS Computational Biology

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

Roles for retrotransposon insertions in human disease

(2016) Dustin C. Hancks et al.   Mobile DNA

Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon

(2015) Vladimir V Kapitonov et al.   Biology Direct

ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data

(2015) Chuan Jiang et al.   BMC BIOINFORMATICS

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps

(2015) D. R. Schrider et al.   GENETICS

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

Exploring the Phenotypic Space and the Evolutionary History of a Natural Mutation inDrosophila melanogaster

(2015) Anna Ullastres et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

(2015) Ryan J. Haasl et al.   MOLECULAR ECOLOGY

Unique transposon landscapes are pervasive acrossDrosophila melanogastergenomes

(2015) Reazur Rahman et al.   NUCLEIC ACIDS RESEARCH

Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition

(2015) Chaoyang Cheng et al.   PLANT JOURNAL

The recent invasion of naturalDrosophila simulanspopulations by the P-element

(2015) Robert Kofler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

Transposons play an important role in the evolution and diversification of centromeres among closely related species

(2015) Dongying Gao et al.   Frontiers in Plant Science

Population Genomics of Transposable Elements inDrosophila

(2014) Maite G. Barrón et al.   Annual Review of Genetics

Tangram: a comprehensive toolbox for mobile element insertion detection

(2014) Jiantao Wu et al.   BMC GENOMICS

Transcriptional properties and splicing of the flamenco piRNA cluster

(2014) C. Goriaux et al.   EMBO REPORTS

On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure

(2014) Anna Ferrer-Admetlla et al.   MOLECULAR BIOLOGY AND EVOLUTION

The transposable elementBari-Jhehmediates oxidative stress response in Drosophila

(2014) Lain Guio et al.   MOLECULAR ECOLOGY

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

(2014) Anna-Sophie Fiston-Lavier et al.   NUCLEIC ACIDS RESEARCH

TEMP: a computational method for analyzing transposable element polymorphism in populations

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

Transposable element islands facilitate adaptation to novel environments in an invasive species

(2014) Lukas Schrader et al.   Nature Communications

A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data

(2014) Michael DeGiorgio et al.   PLoS Genetics

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes

(2014) Yann Lesecque et al.   PLoS Genetics

Genome-Wide Inference of Ancestral Recombination Graphs

(2014) Matthew D. Rasmussen et al.   PLoS Genetics

An Age-of-Allele Test of Neutrality for Transposable Element Insertions

(2013) J. P. Blumenstiel et al.   GENETICS

Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

(2013) Marc Tollis et al.   Genome Biology and Evolution

A road map for molecular ecology

(2013) Rose L. Andrew et al.   MOLECULAR ECOLOGY

Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters

(2013) Kyuha Choi et al.   NATURE GENETICS

Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins

(2013) Nataša Lindič et al.   Retrovirology

Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network

(2013) C. E. Ellison et al.   SCIENCE

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Intrinsic immunity against retrotransposons by APOBEC cytidine deaminases

(2013) Atsushi Koito et al.   Frontiers in Microbiology

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

RECURRENT AND RECENT SELECTIVE SWEEPS IN THE piRNA PATHWAY

(2012) Alfred Simkin et al.   EVOLUTION

Accumulation and Rapid Decay of Non-LTR Retrotransposons in the Genome of the Three-Spine Stickleback

(2012) Eryn Blass et al.   Genome Biology and Evolution

The Diversity of Class II Transposable Elements in Mammalian Genomes Has Arisen from Ancestral Phylogenetic Splits during Ancient Waves of Proliferation through the Genome

(2012) E. H. B. Hellen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription

(2012) Thomas Conrad et al.   NATURE REVIEWS GENETICS

Conflictual speciation: species formation via genomic conflict

(2012) Bernard Crespi et al.   TRENDS IN ECOLOGY & EVOLUTION

Recombination Drives Vertebrate Genome Contraction

(2012) Kiwoong Nam et al.   PLoS Genetics

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

Retroelements versus APOBEC3 family members: No great escape from the magnificent seven

(2012) Juan F. Arias et al.   Frontiers in Microbiology

Co-evolution between transposable elements and their hosts: a major factor in genome size evolution?

(2011) J. Arvid Ågren et al.   CHROMOSOME RESEARCH

Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles

(2011) C. Gilbert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Joint analysis of demography and selection in population genetics: where do we stand and where could we go?

(2011) JUNRUI LI et al.   MOLECULAR ECOLOGY

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Retrotransposons that maintain chromosome ends

(2011) M.-L. Pardue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterozygote advantage as a natural consequence of adaptation in diploids

(2011) D. Sellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans

(2011) Shmuel Sattath et al.   PLoS Genetics

Chromosomes, Conflict, and Epigenetics: Chromosomal Speciation Revisited

(2010) Judith D. Brown et al.   Annual Review of Genomics and Human Genetics

A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

(2010) C. Biemont   GENETICS

Pervasive Horizontal Transfer of Rolling-Circle Transposons among Animals

(2010) Jainy Thomas et al.   Genome Biology and Evolution

Population Genomics of Transposable Elements in Drosophila melanogaster

(2010) D. A. Petrov et al.   MOLECULAR BIOLOGY AND EVOLUTION

CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR

(2010) Mikel Zaratiegui et al.   NATURE

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & EVOLUTION

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

(2010) Josefa González et al.   PLoS Genetics

Epigenetic histone modifications of human transposable elements: genome defense versus exaptation

(2010) Ahsan Huda et al.   Mobile DNA

The adaptive role of transposable elements in the Drosophila genome

(2009) Josefa González et al.   GENE

Independent and parallel lateral transfer of DNA transposons in tetrapod genomes

(2009) Peter Novick et al.   GENE

Transposons in the MHC: the Yin and Yang of the vertebrate immune system

(2009) C van Oosterhout   HEREDITY

A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster

(2009) J. Gonzalez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Small RNAs and the control of transposons and viruses in Drosophila

(2009) Ronald P. van Rij et al.   TRENDS IN MICROBIOLOGY

Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes

(2009) Carolina Bartolomé et al.   GENOME BIOLOGY

Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura

(2008) María Pilar García Guerreiro et al.   BMC EVOLUTIONARY BIOLOGY

Haemophilia A mutations in the UK: results of screening one-third of the population

(2008) P. M. Green et al.   BRITISH JOURNAL OF HAEMATOLOGY

COMPARING CLINES ON MOLECULAR AND PHENOTYPIC TRAITS IN HYBRID ZONES: A WINDOW ON TENSION ZONE MODELS

(2008) Laurène Gay et al.   EVOLUTION

Contrasting Patterns of Transposable-Element Insertion Polymorphism and Nucleotide Diversity in Autotetraploid and Allotetraploid Arabidopsis Species

(2008) K. M. Hazzouri et al.   GENETICS

The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements

(2008) E. S. Dolgin et al.   GENETICS

An infectious progenitor for the murine IAP retrotransposon: Emergence of an intracellular genetic parasite from an ancient retrovirus

(2008) D. Ribet et al.   GENOME RESEARCH

Inferring the Strength of Selection in Drosophila under Complex Demographic Models

(2008) J. Gonzalez et al.   MOLECULAR BIOLOGY AND EVOLUTION

A common sequence motif associated with recombination hot spots and genome instability in humans

(2008) Simon Myers et al.   NATURE GENETICS

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata

(2008) Jeffrey Ross-Ibarra et al.   PLoS One

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

(2008) S. Lockton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A new theory of MHC evolution: beyond selection on the immune genes

(2008) C. van Oosterhout   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES