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

Correlated patterns of genetic diversity and differentiation across an avian family

(2017) Benjamin M. Van Doren et al.   MOLECULAR ECOLOGY

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

(2017) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

(2017) Ludovic Dutoit et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus

(2017) Junko Yoshida et al.   Scientific Reports

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

(2017) Zachary Baker et al.   eLife

Evolution of bird genomes-a transposon's-eye view

(2016) Aurélie Kapusta et al.   Annals of the New York Academy of Sciences

Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium

(2016) R J Pengelly et al.   HEREDITY

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

Making sense of genomic islands of differentiation in light of speciation

(2016) Jochen B. W. Wolf et al.   NATURE REVIEWS GENETICS

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

(2016) Linnéa Smeds et al.   PLoS Genetics

GC-biased gene conversion links the recombination landscape and demography to genomic base composition

(2015) Carina F. Mugal et al.   BIOESSAYS

DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination inArabidopsis

(2015) Nataliya E. Yelina et al.   GENES & DEVELOPMENT

Quantification of GC-biased gene conversion in the human genome

(2015) Sylvain Glémin et al.   GENOME RESEARCH

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

(2015) Bonnie A. Fraser et al.   MOLECULAR ECOLOGY

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis

(2015) Shay Shilo et al.   PLANT CELL

Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast

(2015) I. Lam et al.   SCIENCE

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC BIOLOGY

Evolutionary analysis of the female-specific avian W chromosome

(2015) Linnéa Smeds et al.   Nature Communications

The Relations Between Recombination Rate and Patterns of Molecular Variation and Evolution in Drosophila

(2014) Brian Charlesworth et al.   Annual Review of Genetics

Abundance, arrangement, and function of sequence motifs in the chicken promoters

(2014) Hideaki Abe et al.   BMC GENOMICS

Germline Methylation Patterns Determine the Distribution of Recombination Events in the Dog Genome

(2014) Jonas Berglund et al.   Genome Biology and Evolution

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

Do the same genes underlie parallel phenotypic divergence in differentLittorina saxatilispopulations?

(2014) A. M. Westram et al.   MOLECULAR ECOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Young but not relatively old retrotransposons are preferentially located in gene-rich euchromatic regions in tomato (Solanum lycopersicum) plants

(2014) Yingxiu Xu et al.   PLANT JOURNAL

Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes

(2014) Linnéa Smeds et al.   Nature Communications

The Drosophila early ovarian transcriptome provides insight to the molecular causes of recombination rate variation across genomes

(2013) Andrew B Adrian et al.   BMC GENOMICS

Twisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Kyuha Choi et al.   NATURE GENETICS

Meiotic recombination in mammals: localization and regulation

(2013) Frédéric Baudat et al.   NATURE REVIEWS GENETICS

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Dynamics of DNA Methylation in Recent Human and Great Ape Evolution

(2013) Irene Hernando-Herraez et al.   PLoS Genetics

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

(2013) Krystyna Nadachowska-Brzyska et al.   PLoS Genetics

Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs

(2013) Adam Auton et al.   PLoS Genetics

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

(2012) A. Auton et al.   SCIENCE

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

(2012) Andrew H. Chan et al.   PLoS Genetics

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

A Hierarchical Combination of Factors Shapes the Genome-wide Topography of Yeast Meiotic Recombination Initiation

(2011) Jing Pan et al.   CELL

Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome

(2011) E. Axelsson et al.   GENOME RESEARCH

Nucleosome Positioning in Saccharomyces cerevisiae

(2011) A. Jansen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Access to DNA establishes a secondary target site bias for the yeast retrotransposon Ty5

(2011) J. A. Baller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The recombination landscape of the zebra finch Taeniopygia guttata genome

(2010) N. Backstrom et al.   GENOME RESEARCH

Population Genomics of Transposable Elements in Drosophila melanogaster

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

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Mammalian recombination hot spots: properties, control and evolution

(2010) Kenneth Paigen et al.   NATURE REVIEWS GENETICS

Prdm9 Controls Activation of Mammalian Recombination Hotspots

(2010) E. D. Parvanov et al.   SCIENCE

Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination

(2010) S. Myers et al.   SCIENCE

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

Poly(dA:dT) tracts: major determinants of nucleosome organization

(2009) Eran Segal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

POSTZYGOTIC ISOLATION OVER MULTIPLE GENERATIONS OF HYBRID DESCENDENTS IN A NATURAL HYBRID ZONE: HOW WELL DO SINGLE-GENERATION ESTIMATES REFLECT REPRODUCTIVE ISOLATION?

(2009) Chris Wiley et al.   EVOLUTION

High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe

(2009) Y. Guo et al.   GENOME RESEARCH

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

(2009) Sanzhen Liu et al.   PLoS Genetics

Meiotic Recombination at the Ends of Chromosomes in Saccharomyces cerevisiae

(2008) A. B. Barton et al.   GENETICS

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

(2008) E. S. Dolgin et al.   GENETICS

Fast and flexible simulation of DNA sequence data

(2008) G. K. Chen et al.   GENOME RESEARCH

High-resolution mapping of meiotic crossovers and non-crossovers in yeast

(2008) Eugenio Mancera et al.   NATURE

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics

DNA sequence and structural properties as predictors of human and mouse promoters

(2007) Pelin Akan et al.   GENE