Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species

Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

(2020) Tony Kess et al.   Ecology and Evolution

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation

(2020) Claire Mérot et al.   TRENDS IN ECOLOGY & EVOLUTION

Taming the Turmoil Within: New Insights on the Containment of Transposable Elements

(2020) Erin S. Kelleher et al.   TRENDS IN GENETICS

Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

(2020) Hugo Cayuela et al.   MOLECULAR ECOLOGY

Comparative population genomics confirms little population structure in two commercially targeted carcharhinid sharks

(2019) Claudia Junge et al.   MARINE BIOLOGY

LFMM 2: Fast and accurate inference of gene-environment associations in genome-wide studies

(2019) Kevin Caye et al.   MOLECULAR BIOLOGY AND EVOLUTION

Disentangling structural genomic and behavioral barriers in a sea of connectivity

(2019) Julia M.I. Barth et al.   MOLECULAR ECOLOGY

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

(2019) Xiaojun Zhang et al.   Nature Communications

Aquatic Landscape Genomics and Environmental Effects on Genetic Variation

(2019) Jared A. Grummer et al.   TRENDS IN ECOLOGY & EVOLUTION

Free-access copy-number variant detection tools for targeted next-generation sequencing data

(2019) Iria Roca et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Going beyond SNPs: the role of structural genomic variants in adaptive evolution and species diversification

(2019) Maren Wellenreuther et al.   MOLECULAR ECOLOGY

The genomic pool of standing structural variation outnumbers single nucleotide polymorphism by three-fold in the marine teleost Chrysophrys auratus

(2019) Andrew Catanach et al.   MOLECULAR ECOLOGY

Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster ( Homarus americanus ) as a case study

(2019) Yann Dorant et al.   Ecology and Evolution

Genome-wide genotype-expression relationships reveal both copy number and single nucleotide differentiation contribute to differential gene expression between stickleback ecotypes

(2019) Yun Huang et al.   Genome Biology and Evolution

Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift

(2019) David C. Rinker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of the dynamic aberrant landscape of DNA methylation and gene expression during arsenic-induced cell transformation

(2019) Francisco M. Barajas-Olmos et al.   GENE

An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features

(2019) Beth A. Rowan et al.   GENETICS

Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex

(2019) Clément Rougeux et al.   MOLECULAR ECOLOGY

Present and Future Adaptation of Marine Species Assemblages: DNA-Based Insights into Climate Change from Studies of Physiology, Genomics, and Evolution

(2019) Stephen Palumbi et al.   OCEANOGRAPHY

Genome survey and identification of polymorphic microsatellites provide genomic information and molecular markers for the red crab Charybdis feriatus (Linnaeus, 1758) (Decapoda: Brachyura: Portunidae)

(2019) Shaobin Fang et al.   JOURNAL OF CRUSTACEAN BIOLOGY

DNA methylation reprogramming, TE derepression, and postzygotic isolation of nascent animal species

(2019) M. Laporte et al.   Science Advances

Stock structure and connectivity of the American lobster (Homarus americanus) in the southern Gulf of St. Lawrence: Do benthic movements matter?

(2018) Bryan L. Morse et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Genomic resources and comparative analyses of two economical penaeid shrimp species, Marsupenaeus japonicus and Penaeus monodon

(2018) Jianbo Yuan et al.   Marine Genomics

Asymmetric oceanographic processes mediate connectivity and population genetic structure, as revealed by RADseq, in a highly dispersive marine invertebrate (Parastichopus californicus )

(2018) Amanda Xuereb et al.   MOLECULAR ECOLOGY

Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations

(2018) Brenna R. Forester et al.   MOLECULAR ECOLOGY

Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (Haliotis laevigata ), along a longitudinal environmental gradient

(2018) Jonathan Sandoval-Castillo et al.   MOLECULAR ECOLOGY

Intercontinental karyotype–environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly

(2018) Claire Mérot et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Role of Transposable Elements in Speciation

(2018) Antonio Serrato-Capuchina et al.   Genes

Copy number variation (CNV) and insecticide resistance in mosquitoes: evolving knowledge or an evolving problem?

(2018) David Weetman et al.   Current Opinion in Insect Science

A climate-associated multispecies cryptic cline in the northwest Atlantic

(2018) Ryan R. E. Stanley et al.   Science Advances

Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

(2018) Rufaida Dhuhai Al-Breiki et al.   BMC GENOMICS

Seascape genomics of eastern oyster (Crassostrea virginica ) along the Atlantic coast of Canada

(2018) Simon Bernatchez et al.   Evolutionary Applications

Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations

(2018) Julien Prunier et al.   MOLECULAR ECOLOGY

Local adaptation along an environmental cline in a species with an inversion polymorphism

(2017) M. Wellenreuther et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Seascape genomics reveals fine-scale patterns of dispersal for a reef fish along the ecologically divergent coast of Northwestern Australia

(2017) Joseph D. DiBattista et al.   MOLECULAR ECOLOGY

Rapid response to changing environments during biological invasions: DNA methylation perspectives

(2017) Xuena Huang et al.   MOLECULAR ECOLOGY

Dosage sensitivity is a major determinant of human copy number variant pathogenicity

(2017) Alan M. Rice et al.   Nature Communications

Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans

(2017) Kristian Alfsnes et al.   Ecology and Evolution

In the hunt for genomic markers of metabolic resistance to pyrethroids in the mosquito Aedes aegypti: An integrated next-generation sequencing approach

(2017) Frederic Faucon et al.   PLoS Neglected Tropical Diseases

The evolution and population diversity of human-specific segmental duplications

(2017) Megan Y. Dennis 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

Canadian Coastal Seas and Great Lakes Sea Surface Temperature Climatology and Recent Trends

(2016) Pierre Larouche et al.   CANADIAN JOURNAL OF REMOTE SENSING

Shape plasticity in response to water velocity in the freshwater blennySalaria fluviatilis

(2016) M. Laporte et al.   JOURNAL OF FISH BIOLOGY

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

(2016) L. Bernatchez   JOURNAL OF FISH BIOLOGY

Genomics of local adaptation with gene flow

(2016) Anna Tigano et al.   MOLECULAR ECOLOGY

Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus )

(2016) Laura Benestan et al.   MOLECULAR ECOLOGY

Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations

(2016) Garrett J. McKinney et al.   Molecular Ecology Resources

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

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

Adaptation to Global Change: A Transposable Element–Epigenetics Perspective

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

Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod

(2016) Paul R. Berg et al.   Scientific Reports

Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes

(2016) Keith W. Dunaway et al.   Cell Reports

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

(2016) Alvaro Martinez Barrio et al.   eLife

Canadian Coastal Seas and Great Lakes Sea Surface Temperature Climatology and Recent Trends

(2016) Pierre Larouche et al.   CANADIAN JOURNAL OF REMOTE SENSING

Draft genome of the Chinese mitten crab, Eriocheir sinensis

(2016) Linsheng Song et al.   GigaScience

Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks

(2015) Baocheng Guo et al.   BMC BIOLOGY

The impact of human copy number variation on gene expression: Figure 1

(2015) Eric R. Gamazon et al.   Briefings in Functional Genomics

Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era

(2015) Pierre-Alexandre Gagnaire et al.   Evolutionary Applications

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

Potential effect of variation in water temperature on development time of American lobster larvae

(2015) Brady K. Quinn et al.   ICES JOURNAL OF MARINE SCIENCE

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)

(2015) Laura Benestan et al.   MOLECULAR ECOLOGY

Global diversity, population stratification, and selection of human copy-number variation

(2015) Peter H. Sudmant et al.   SCIENCE

Growth, Female Size, and Sex Ratio Variability in American Eel of Different Origins in Both Controlled Conditions and the Wild: Implications for Stocking Programs

(2015) Caroline L. Côté et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Tempo and Mode of Transposable Element Activity in Drosophila

(2015) Robert Kofler et al.   PLoS Genetics

Dose-Response Analysis Using R

(2015) Christian Ritz et al.   PLoS One

Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing

(2015) Melissa C. Keinath et al.   Scientific Reports

Hellbender Genome Sequences Shed Light on Genomic Expansion at the Base of Crown Salamanders

(2014) C. Sun et al.   Genome Biology and Evolution

Conserving marine biodiversity: insights from life-history trait candidate genes in Atlantic cod (Gadus morhua)

(2013) Jakob Hemmer-Hansen et al.   CONSERVATION GENETICS

MARSPEC: ocean climate layers for marine spatial ecology

(2013) Elizabeth J. Sbrocco et al.   ECOLOGY

Effect of temperature on development rate of larvae from cold-water American lobster (Homarus americanus)

(2013) Brady K. Quinn et al.   JOURNAL OF CRUSTACEAN BIOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Signals of selection in outlier loci in a widely dispersing species across an environmental mosaic

(2013) Melissa H. Pespeni et al.   MOLECULAR ECOLOGY

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

(2013) Luke W. Pembleton et al.   Molecular Ecology Resources

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

A Coastal Seawater Temperature Dataset for Biogeographical Studies: Large Biases between In Situ and Remotely-Sensed Data Sets around the Coast of South Africa

(2013) Albertus J. Smit et al.   PLoS One

Ten years of landscape genetics

(2013) Stéphanie Manel et al.   TRENDS IN ECOLOGY & EVOLUTION

Properties and rates of germline mutations in humans

(2013) Catarina D. Campbell et al.   TRENDS IN GENETICS

Copy number variation in the genomes of domestic animals

(2012) A. Clop et al.   ANIMAL GENETICS

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo et al.   BIOINFORMATICS

Antifreeze protein gene amplification facilitated niche exploitation and speciation in wolffish

(2012) Mariève Desjardins et al.   FEBS Journal

Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

(2012) Jon E. Hess et al.   MOLECULAR ECOLOGY

Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

(2012) Andrea D. McCue et al.   PLoS Genetics

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering

(2010) Eva Freyhult et al.   BMC BIOINFORMATICS

Lobster larval transport in the southern Gulf of St. Lawrence

(2010) JOËL CHASSÉ et al.   FISHERIES OCEANOGRAPHY

Nuclear DNA content variation associated with muscle fiber hypertrophic growth in decapod crustaceans

(2010) Ana Gabriela Jimenez et al.   GENOME

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Global analysis of thermal tolerance and latitude in ectotherms

(2010) J. M. Sunday et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Towards a comprehensive structural variation map of an individual human genome

(2010) Andy W Pang et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The adaptive role of transposable elements in the Drosophila genome

(2009) Josefa González et al.   GENE

Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity

(2009) NADIA AUBIN-HORTH et al.   MOLECULAR ECOLOGY

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis

(2008) Iuliana Ionita-Laza et al.   GENOMICS

Genome size evolution: Within-species variation in genome size

(2008) C Biémont   HEREDITY

Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish

(2008) Z. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster

(2008) J. J. Emerson et al.   SCIENCE