Genomic resources and their influence on the detection of the signal of positive selection in genome scans

RAD Sequencing Highlights Polygenic Discrimination of Habitat Ecotypes in the Panmictic American Eel

(2015) Scott A. Pavey et al.   CURRENT BIOLOGY

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

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

A practical guide to environmental association analysis in landscape genomics

(2015) Christian Rellstab et al.   MOLECULAR ECOLOGY

Whole-genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep

(2015) Marty Kardos et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Detection of selective sweeps in structured populations: a comparison of recent methods

(2015) Alexandra I. Vatsiou et al.   MOLECULAR ECOLOGY

The red coral (Corallium rubrum ) transcriptome: a new resource for population genetics and local adaptation studies

(2015) M. Pratlong et al.   Molecular Ecology Resources

Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals

(2015) David J. Combosch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

The fine-scale genetic structure of the British population

(2015) Stephen Leslie et al.   NATURE

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Genomic variation across landscapes: insights and applications

(2015) Jason G. Bragg et al.   NEW PHYTOLOGIST

Combining niche modelling and landscape genetics to study local adaptation: A novel approach illustrated using alpine plants

(2015) Jonathan Rolland et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Building coral reef resilience through assisted evolution

(2015) Madeleine J. H. van Oppen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Greenlandic Inuit show genetic signatures of diet and climate adaptation

(2015) M. Fumagalli et al.   SCIENCE

Genomic determinants of coral heat tolerance across latitudes

(2015) G. B. Dixon et al.   SCIENCE

Prevalence of adiposity and associated cardiometabolic risk factors in the samoan genome-wide association study

(2014) Nicola L. Hawley et al.   AMERICAN JOURNAL OF HUMAN BIOLOGY

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Keeping It Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana

(2014) Christian D. Huber et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome scan methods against more complex models: when and how much should we trust them?

(2014) Pierre de Villemereuil et al.   MOLECULAR ECOLOGY

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

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

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

LANDSCAPE GENOMICS IN ATLANTIC SALMON (SALMO SALAR): SEARCHING FOR GENE-ENVIRONMENT INTERACTIONS DRIVING LOCAL ADAPTATION

(2013) Bourret Vincent et al.   EVOLUTION

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

(2013) Pierre-Alexandre Gagnaire et al.   EVOLUTION

Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish

(2013) Ian R. Bradbury et al.   Evolutionary Applications

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pervasive selection or is it…? why areFSToutliers sometimes so frequent?

(2013) Nicolas Bierne et al.   MOLECULAR ECOLOGY

RAD-Seq derived markers flank the shell colour and banding loci of theCepaea nemoralissupergene

(2013) Paul M. Richards et al.   MOLECULAR ECOLOGY

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Development of anArabis alpinagenomic contig sequence data set and application to single nucleotide polymorphisms discovery

(2013) Stéphane Lobréaux et al.   Molecular Ecology Resources

Avatars of information: towards an inclusive evolutionary synthesis

(2013) Étienne Danchin   TRENDS IN ECOLOGY & EVOLUTION

Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure

(2013) Hua Chen et al.   G3-Genes Genomes Genetics

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

(2013) Philippe Gayral et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Adaptive Genetic Variation on the Landscape: Methods and Cases

(2012) Sean D. Schoville et al.   Annual Review of Ecology Evolution and Systematics

Uninformative polymorphisms bias genome scans for signatures of selection

(2012) Marius Roesti et al.   BMC EVOLUTIONARY BIOLOGY

Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples

(2012) S. Boitard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation

(2012) STÉPHANIE MANEL et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

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

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

(2012) Pierre De Wit et al.   MOLECULAR ECOLOGY

The impact of global climate change on genetic diversity within populations and species

(2012) Steffen U. Pauls et al.   MOLECULAR ECOLOGY

Human-specific evolution of killer cell immunoglobulin-like receptor recognition of major histocompatibility complex class I molecules

(2012) P. Parham et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What is needed for next-generation ecological and evolutionary genomics?

(2012) Scott A. Pavey et al.   TRENDS IN ECOLOGY & EVOLUTION

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education

(2012) Taras K Oleksyk et al.   GigaScience

Detection of outlier loci and their utility for fisheries management

(2011) Michael A. Russello et al.   Evolutionary Applications

The Genetic Consequences of Spatially Varying Selection in the Panmictic American Eel ( Anguilla rostrata )

(2011) Pierre-Alexandre Gagnaire et al.   GENETICS

The n = 1 constraint in population genomics

(2011) C. A. BUERKLE et al.   MOLECULAR ECOLOGY

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

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

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

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

(2011) J. L. Strasburg et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

(2011) Simon W. Baxter et al.   PLoS One

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

Applications of landscape genetics in conservation biology: concepts and challenges

(2010) Gernot Segelbacher et al.   CONSERVATION GENETICS

INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCI

(2010) Jay F. Storz et al.   EVOLUTION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field

(2010) STÉPHANIE MANEL et al.   MOLECULAR ECOLOGY

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

Characterization of missing human genome sequences and copy-number polymorphic insertions

(2010) Jeffrey M Kidd et al.   NATURE METHODS

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

How We Are Evolving

(2010) Jonathan K. Pritchard   SCIENTIFIC AMERICAN

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

Human-Specific Evolution and Adaptation Led to Major Qualitative Differences in the Variable Receptors of Human and Chimpanzee Natural Killer Cells

(2010) Laurent Abi-Rached et al.   PLoS Genetics

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

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

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Spatial patterns of variation due to natural selection in humans

(2009) John Novembre et al.   NATURE REVIEWS GENETICS

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Genome Scan for Positive Selection in Thoroughbred Horses

(2009) Jingjing Gu et al.   PLoS One

Genetics and ecological speciation

(2009) D. Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Identifying Selected Regions from Heterozygosity and Divergence Using a Light-Coverage Genomic Dataset from Two Human Populations

(2008) Taras K. Oleksyk et al.   PLoS One

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One