Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

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

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Genomic Evidence for Adaptive Inversion Clines inDrosophila melanogaster

(2016) Martin Kapun et al.   MOLECULAR BIOLOGY AND EVOLUTION

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata)

(2016) Paul F. Gugger et al.   Tree Genetics & Genomes

Recombination Rate Evolution and the Origin of Species

(2016) Daniel Ortiz-Barrientos et al.   TRENDS IN ECOLOGY & EVOLUTION

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

(2016) Jieming Chen et al.   Nature Communications

Detection and Removal of PCR Duplicates in Population Genomic ddRAD Studies by Addition of a Degenerate Base Region (DBR) in Sequencing Adapters

(2016) Hannah Schweyen et al.   BIOLOGICAL BULLETIN

Commentary: When does understanding phenotypic evolution require identification of the underlying genes?

(2015) Mark D. Rausher et al.   EVOLUTION

Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

(2015) Elisa G. Dierickx et al.   Evolutionary Applications

Phylogeny and biogeography of the American live oaks (QuercussubsectionVirentes): a genomic and population genetics approach

(2015) Jeannine Cavender-Bares et al.   MOLECULAR ECOLOGY

A practical guide to environmental association analysis in landscape genomics

(2015) Christian Rellstab et al.   MOLECULAR ECOLOGY

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

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

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

Phylogenomics of polyploidFothergilla(Hamamelidaceae) by RAD-tag based GBS-insights into species origin and effects of software pipelines

(2015) Zhe-Chen Qi et al.   Journal of Systematics and Evolution

The genomics of ecological vicariance in threespine stickleback fish

(2015) Marius Roesti et al.   Nature Communications

Towards the identification of the loci of adaptive evolution

(2015) Carolina Pardo-Diaz et al.   Methods in Ecology and Evolution

Nucleotide diversity patterns of three divergent soybean populations: evidences for population-dependent linkage disequilibrium and taxonomic status ofGlycine gracilis

(2015) Yunsheng Wang et al.   Ecology and Evolution

RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish ( Coregonus clupeaformis ) Species Pairs

(2015) Martin Laporte et al.   G3-Genes Genomes Genetics

Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level

(2015) Chandrasekhar Natarajan et al.   PLoS Genetics

Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

(2015) Alice Kujur et al.   Frontiers in Plant Science

The genomes of two key bumblebee species with primitive eusocial organization

(2015) Ben M Sadd et al.   GENOME BIOLOGY

Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

(2014) Maja P Greminger et al.   BMC GENOMICS

Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato

(2014) Nicola J. Nadeau et al.   GENOME RESEARCH

On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure

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

Selection on Meiosis Genes in Diploid and Tetraploid Arabidopsis arenosa

(2014) Kevin M. Wright et al.   MOLECULAR BIOLOGY AND EVOLUTION

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

Genome-wide single-generation signatures of local selection in the panmictic European eel

(2014) J. M. Pujolar et al.   MOLECULAR ECOLOGY

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

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

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera

(2014) Andreas Wallberg et al.   NATURE GENETICS

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

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

The genetics of divergence and reproductive isolation between ecotypes ofPanicum hallii

(2014) David B. Lowry et al.   NEW PHYTOLOGIST

Advances and limits of using population genetics to understand local adaptation

(2014) Peter Tiffin et al.   TRENDS IN ECOLOGY & EVOLUTION

De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach

(2013) Venkatramana Pegadaraju et al.   BMC GENOMICS

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice

(2013) Jesse N. Weber et al.   NATURE

Enhancers: five essential questions

(2013) Len A. Pennacchio 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

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Recent updates and developments to plant genome size databases

(2013) Sònia Garcia et al.   NUCLEIC ACIDS RESEARCH

Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome, Sequence-Based Association Genetics in Medicago truncatula

(2013) John Stanton-Geddes et al.   PLoS One

Diversity, Differentiation, and Linkage Disequilibrium: Prospects for Association Mapping in the Malaria Vector Anopheles arabiensis

(2013) Clare Diana Marsden et al.   G3-Genes Genomes Genetics

Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon

(2012) Ross D Houston et al.   BMC GENOMICS

Special features of RAD Sequencing data: implications for genotyping

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

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations

(2012) Hoa T. Truong et al.   PLoS One

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

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Population genomics of wild and laboratory zebrafish (Danio rerio)

(2011) ANDREW R. WHITELEY et al.   MOLECULAR ECOLOGY

Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis)

(2011) MARTIN C. FISCHER et al.   MOLECULAR ECOLOGY

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

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

Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne

(2011) W. F. Pfender et al.   THEORETICAL AND APPLIED GENETICS

Evolutionary genetics of plant adaptation

(2011) Jill T. Anderson et al.   TRENDS IN GENETICS

Low linkage disequilibrium in wild Anopheles gambiae s.l. populations

(2010) Caroline Harris et al.   BMC GENETICS

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep

(2010) J.M. MILLER et al.   Molecular Ecology Resources

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

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

Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

(2010) Melissa H Pespeni et al.   GENOME BIOLOGY

A Quantitative Survey of Local Adaptation and Fitness Trade‐Offs

(2009) Joe Hereford   AMERICAN NATURALIST

Multilocus Patterns of Nucleotide Diversity and Divergence Reveal Positive Selection at Candidate Genes Related to Cold Hardiness in Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii)

(2009) A. J. Eckert et al.   GENETICS

Extensive linkage disequilibrium in a wild bird population

(2009) M H Li et al.   HEREDITY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia guttata)

(2008) C. N. Balakrishnan et al.   GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle

(2008) I. J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA