RADseq approaches and applications for forest tree genetics

Adaptation in plant genomes: Bigger is different

(2018) Wenbin Mei et al.   AMERICAN JOURNAL OF BOTANY

The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis ) and limber pine (P. flexilis )

(2018) Mitra Menon et al.   MOLECULAR ECOLOGY

Phylogeny and biogeography of East Asian evergreen oaks ( Quercus section Cyclobalanopsis ; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia

(2018) Min Deng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic relationships of Aurantioideae (Rutaceae) based on RAD-Seq

(2018) Yukio Nagano et al.   Tree Genetics & Genomes

The genomics of local adaptation in trees: are we out of the woods yet?

(2018) Brandon M. Lind et al.   Tree Genetics & Genomes

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

(2017) Kasey K. Pham et al.   GENOME

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)

(2017) Sorel Fitz-Gibbon et al.   GENOME

Construction of a SNP-based genetic linkage map for kiwifruit using next-generation restriction-site-associated DNA sequencing (RADseq)

(2017) Chun-Yan Liu et al.   MOLECULAR BREEDING

The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)

(2017) Ayako Izuno et al.   MOLECULAR ECOLOGY

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA

(2017) Brandon M. Lind et al.   MOLECULAR ECOLOGY

Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River

(2017) S. Elizabeth Alter et al.   MOLECULAR ECOLOGY

RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al . (2016)

(2017) Garrett J. McKinney et al.   Molecular Ecology Resources

Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations

(2017) Julian M. Catchen et al.   Molecular Ecology Resources

Responsible RAD: Striving for best practices in population genomic studies of adaptation

(2017) David B. Lowry et al.   Molecular Ecology Resources

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee ( Coffea ) and insights into the evolution of caffeine content in its species

(2017) Perla Hamon et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A genetic legacy of introgression confounds phylogeny and biogeography in oaks

(2017) John D. McVay et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

(2017) Alan Brelsford et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data

(2017) P. Fuentes-Utrilla et al.   Tree Genetics & Genomes

Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan

(2017) A. Imai et al.   Tree Genetics & Genomes

Genomic Quantitative Genetics to Study Evolution in the Wild

(2017) Phillip Gienapp et al.   TRENDS IN ECOLOGY & EVOLUTION

FRAGMATIC: in silico locus prediction and its utility in optimizing ddRADseq projects

(2017) Tyler K. Chafin et al.   Conservation Genetics Resources

Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)

(2017) Kazuki Mori et al.   Scientific Reports

Seed dispersal at alpine treeline: an assessment of seed movement within the alpine treeline ecotone

(2017) Jeremy S. Johnson et al.   Ecosphere

Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits

(2017) Amel Oueslati et al.   PLoS One

Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering

(2017) Richard G. J. Hodel et al.   Scientific Reports

Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae

(2016) R. Massatti et al.   AMERICAN JOURNAL OF BOTANY

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

(2016) Sean Hoban et al.   AMERICAN NATURALIST

The first high-density sequence characterized SNP-based linkage map of olive (Olea europaea L. subsp. europaea) developed using genotyping by sequencing

(2016) Annalisa Marchese et al.   Australian Journal of Crop Science

RADIS:analysis ofRAD-seq data for interspecific phylogeny

(2016) Astrid Cruaud et al.   BIOINFORMATICS

Weakly supervised learning of biomedical information extraction from curated data

(2016) Suvir Jain et al.   BMC BIOINFORMATICS

How and how much does RAD-seq bias genetic diversity estimates?

(2016) Marie Cariou et al.   BMC EVOLUTIONARY BIOLOGY

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences – a case study in the tree genus Milicia

(2016) Kasso Daïnou et al.   BMC EVOLUTIONARY BIOLOGY

De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies

(2016) Mohaddeseh Mousavi et al.   BMC GENOMICS

Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.)

(2016) Mengmeng Lu et al.   BMC GENOMICS

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers

(2016) Jasmin Zohren et al.   MOLECULAR ECOLOGY

Divergence maintained by climatic selection despite recurrent gene flow: a case study ofCastanopsis carlesii(Fagaceae)

(2016) Ye Sun et al.   MOLECULAR ECOLOGY

Population genomic evidence for adaptive differentiation in the Baltic Sea herring

(2016) Baocheng Guo et al.   MOLECULAR ECOLOGY

Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp,Carassius carassius,L.

(2016) Daniel L. Jeffries et al.   MOLECULAR ECOLOGY

Selection against recombinant hybrids maintains reproductive isolation in hybridizingPopulusspecies despite F1fertility and recurrent gene flow

(2016) Camille Christe et al.   MOLECULAR ECOLOGY

ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments

(2016) F. Mora-Márquez et al.   Molecular Ecology Resources

GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome

(2016) A. Hapke et al.   Molecular Ecology Resources

Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates

(2016) Emily D. Fountain et al.   Molecular Ecology Resources

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

(2016) David B. Lowry et al.   Molecular Ecology Resources

Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

(2016) Naiara Rodríguez-Ezpeleta et al.   Molecular Ecology Resources

Harnessing the power of RADseq for ecological and evolutionary genomics

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

Towards integration of population and comparative genomics in forest trees

(2016) Pär K. Ingvarsson et al.   NEW PHYTOLOGIST

Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L.

(2016) Oliver Gailing et al.   PLANT MOLECULAR BIOLOGY REPORTER

Convergent local adaptation to climate in distantly related conifers

(2016) S. Yeaman et al.   SCIENCE

RAD-seq phylogenomics recovers a well-resolved phylogeny of a rapid radiation of mutualistic and antagonistic yucca moths

(2016) CLIVE T. DARWELL et al.   SYSTEMATIC ENTOMOLOGY

Pedigrees or markers: Which are better in estimating relatedness and inbreeding coefficient?

(2016) Jinliang Wang   THEORETICAL POPULATION BIOLOGY

Rapid evolutionary response to a transmissible cancer in Tasmanian devils

(2016) Brendan Epstein et al.   Nature Communications

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

Evolutionary potential and adaptation of Banksia attenuata (Proteaceae) to climate and fire regime in southwestern Australia, a global biodiversity hotspot

(2016) Tianhua He et al.   Scientific Reports

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation inRobinia pseudoacaciaL.

(2016) Cindy F. Verdu et al.   Ecology and Evolution

Ecological genomics of local adaptation inCornus floridaL. by genotyping by sequencing

(2016) Andrew L. Pais et al.   Ecology and Evolution

GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data

(2016) Thomas F. Cooke et al.   PLoS Genetics

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

(2016) Chunfa Tong et al.   PLoS One

Multiplexed-shotgun-genotyping data resolve phylogeny within a very recently derived insular lineage

(2015) Mark E. Mort et al.   AMERICAN JOURNAL OF BOTANY

Estimating phylogenetic trees from genome-scale data

(2015) Liang Liu et al.   Annals of the New York Academy of Sciences

Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

(2015) Omnia Gamal El-Dien et al.   BMC GENOMICS

Historical introgression among the American live oaks and the comparative nature of tests for introgression

(2015) Deren A. R. Eaton et al.   EVOLUTION

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

(2015) J. Wang et al.   GENETICS

Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life

(2015) Santiago Herrera et al.   Genome Biology and Evolution

Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)

(2015) Wirulda Pootakham et al.   GENOMICS

A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods

(2015) B Ratcliffe et al.   HEREDITY

Evolution, plasticity and evolving plasticity of phenology in the tree speciesAlnus glutinosa

(2015) H. De Kort et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Field heritability of a plant adaptation to fire in heterogeneous landscapes

(2015) M. C. Castellanos et al.   MOLECULAR ECOLOGY

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

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

Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus

(2015) Aaron B. A. Shafer et al.   MOLECULAR ECOLOGY

Highly variable reproductive isolation among pairs ofCatostomusspecies

(2015) Elizabeth G. Mandeville et al.   MOLECULAR ECOLOGY

RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

(2015) M. Laporte et al.   MOLECULAR ECOLOGY

Targeted capture in evolutionary and ecological genomics

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

Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations

(2015) Matthew D. McGee et al.   MOLECULAR ECOLOGY

Rapid diversification associated with ecological specialization in NeotropicalAdelphabutterflies

(2015) Emily R. Ebel et al.   MOLECULAR ECOLOGY

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

High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)

(2015) C. Plomion et al.   Molecular Ecology Resources

AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data

(2015) Michael G. Sovic et al.   Molecular Ecology Resources

Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients inPopulus trichocarpa

(2015) Jason A. Holliday et al.   NEW PHYTOLOGIST

Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history ofEucalyptus grandis

(2015) Orzenil B. Silva-Junior et al.   NEW PHYTOLOGIST

A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240Eucalyptustree genomes across 12 species

(2015) Orzenil B. Silva-Junior et al.   NEW PHYTOLOGIST

Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot

(2015) Ovidiu Paun et al.   SYSTEMATIC BIOLOGY

Construction of a high density linkage map and its application in the identification of QTLs for soluble sugar and organic acid components in apple

(2015) Baiquan Ma et al.   Tree Genetics & Genomes

The genetic architecture of local adaptation I: the genomic landscape of foxtail pine (Pinus balfouriana Grev. & Balf.) as revealed from a high-density linkage map

(2015) Christopher J. Friedline et al.   Tree Genetics & Genomes

High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species

(2015) Shota Sakaguchi et al.   Tree Genetics & Genomes

A RAD-based linkage map of kiwifruit (Actinidia chinensis Pl.) as a tool to improve the genome assembly and to scan the genomic region of the gender determinant for the marker-assisted breeding

(2015) Davide Scaglione et al.   Tree Genetics & Genomes

Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)

(2015) Wirulda Pootakham et al.   Frontiers in Plant Science

Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

(2015) Janna L. Fierst   Frontiers in Genetics

Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS)

(2015) Verónica Guajardo et al.   PLoS One

Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae)

(2015) Yan Hou et al.   PLoS One

Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch]

(2015) Douglas Gary Bielenberg et al.   PLoS One

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

(2015) Luxian Liu et al.   PLoS One

Genome-Wide Association Mapping of Phenotypic Traits Subject to a Range of Intensities of Natural Selection in Timema cristinae

(2014) Aaron A. Comeault et al.   AMERICAN NATURALIST

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Sampling strategies for frequency spectrum-based population genomic inference

(2014) John D Robinson et al.   BMC EVOLUTIONARY BIOLOGY

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

(2014) Wesley A. Larson et al.   Evolutionary Applications

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

(2014) J. L. Wegrzyn et al.   GENETICS

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

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

An evaluation of seed zone delineation using phenotypic and population genomic data on black alderAlnus glutinosa

(2014) Hanne De Kort et al.   JOURNAL OF APPLIED ECOLOGY

Genomic Analyses of Three Malaria Vectors Reveals Extensive Shared Polymorphism but Contrasting Population Histories

(2014) Samantha M. O’Loughlin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unexpected ancestry ofPopulusseedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

(2014) Dorothea Lindtke et al.   MOLECULAR ECOLOGY

Demystifying the RAD fad

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

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

(2014) Zachariah Gompert et al.   MOLECULAR ECOLOGY

Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

(2014) Camillo Bérénos et al.   MOLECULAR ECOLOGY

A role for migration-linked genes and genomic islands in divergence of a songbird

(2014) Kristen Ruegg et al.   MOLECULAR ECOLOGY

Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree speciesAlnus glutinosa

(2014) Hanne De Kort et al.   MOLECULAR ECOLOGY

Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

(2014) L. Zhou et al.   MOLECULAR ECOLOGY

First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species,Pinus halepensisMill

(2014) S. Pinosio et al.   Molecular Ecology Resources

Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq

(2014) M.-J. Karam et al.   Molecular Ecology Resources

SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches

(2014) Olivier Lepais et al.   Molecular Ecology Resources

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers

(2014) Jin Pan et al.   Molecular Ecology Resources

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

(2014) Luke M Evans et al.   NATURE GENETICS

High-resolution genetic maps ofEucalyptusimproveEucalyptus grandisgenome assembly

(2014) Jérôme Bartholomé et al.   NEW PHYTOLOGIST

Conservation and divergence of gene expression plasticity followingc. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

(2014) Sam Yeaman et al.   NEW PHYTOLOGIST

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

(2014) Jeffrey C. Glaubitz et al.   PLoS One

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

Rapid SNP Discovery and a RAD-Based High-Density Linkage Map in Jujube (Ziziphus Mill.)

(2014) Jin Zhao et al.   PLoS One

Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

(2014) Luca Bianco et al.   PLoS One

The genetic diversity and introgression of Juglans regia and Juglans sigillata in Tibet as revealed by SSR markers

(2014) Hua Wang et al.   Tree Genetics & Genomes

Advances and limits of using population genetics to understand local adaptation

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

Genomic selection: genome-wide prediction in plant improvement

(2014) Zeratsion Abera Desta et al.   TRENDS IN PLANT SCIENCE

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

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

(2014) Jonathan B. Puritz et al.   PeerJ

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

Assisted Gene Flow to Facilitate Local Adaptation to Climate Change

(2013) Sally N. Aitken et al.   Annual Review of Ecology Evolution and Systematics

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

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

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

(2013) A. J. Eckert et al.   GENETICS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

(2013) Filipe G. Vieira et al.   GENOME RESEARCH

Potential for evolutionary responses to climate change - evidence from tree populations

(2013) Florian J. Alberto et al.   GLOBAL CHANGE BIOLOGY

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

(2013) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

Partitioning of genetic variation across the genome using multimarker methods in a wild bird population

(2013) Matthew R. Robinson et al.   MOLECULAR ECOLOGY

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners

(2013) Nathalie Pavy et al.   Molecular Ecology Resources

A 34K SNP genotyping array forPopulus trichocarpa: Design, application to the study of natural populations and transferability to otherPopulusspecies

(2013) A. Geraldes et al.   Molecular Ecology Resources

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grassMiscanthus sinensis

(2013) Gancho T. Slavov et al.   NEW PHYTOLOGIST

Geographical and environmental gradients shape phenotypic trait variation and genetic structure inPopulus trichocarpa

(2013) Athena D. McKown et al.   NEW PHYTOLOGIST

Genome-wide association mapping for wood characteristics inPopulusidentifies an array of candidate single nucleotide polymorphisms

(2013) Ilga Porth et al.   NEW PHYTOLOGIST

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform

(2013) Charles Chen et al.   Tree Genetics & Genomes

Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate

(2013) V. L. Sork et al.   Tree Genetics & Genomes

Isolation, characterization and genotyping of single nucleotide polymorphisms in the non-model tree species Frangula alnus (Rhamnaceae)

(2013) Hanne De Kort et al.   Conservation Genetics Resources

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

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

(2013) Philippe Gayral et al.   PLoS Genetics

Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

(2013) Fei Lu et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

GENOMIC REGIONS WITH A HISTORY OF DIVERGENT SELECTION AFFECT FITNESS OF HYBRIDS BETWEEN TWO BUTTERFLY SPECIES

(2012) Zachariah Gompert et al.   EVOLUTION

HYBRID SPECIATION AND INDEPENDENT EVOLUTION IN LINEAGES OF ALPINE BUTTERFLIES

(2012) Chris C. Nice et al.   EVOLUTION

Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.)

(2012) M. F. R. Resende et al.   GENETICS

Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species

(2012) Kai N. Stölting et al.   MOLECULAR ECOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

(2012) Nian Wang et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

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

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle 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

Genome-wide association genetics of an adaptive trait in lodgepole pine

(2012) THOMAS L. PARCHMAN et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest treePopulus trichocarpa

(2012) Gancho T. Slavov et al.   NEW PHYTOLOGIST

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees

(2012) Marcos D. V. Resende et al.   NEW PHYTOLOGIST

Effects of interspecific recombination on functional traits in trees revealed by metabolomics and genotyping-by-resequencing

(2012) Celine Caseys et al.   Plant Ecology & Diversity

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.)

(2012) Satish Kumar 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

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

SNP markers trace familial linkages in a cloned population of Pinus taeda—prospects for genomic selection

(2012) Jaime Zapata-Valenzuela et al.   Tree Genetics & Genomes

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Variation in actual relationship as a consequence of Mendelian sampling and linkage

(2011) W.G. HILL et al.   Genetics Research

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen 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

Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments

(2011) M. F. R. Resende et al.   NEW PHYTOLOGIST

Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes

(2011) P. A. Hohenlohe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

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

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

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.)

(2010) T. Quesada et al.   GENETICS

Genome-wide association and genomic selection in animal breedingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Ben Hayes et al.   GENOME

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis)

(2010) Jason A. Holliday et al.   NEW PHYTOLOGIST

Revisiting protein heterozygosity in plants—nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris

(2010) Tanja Pyhäjärvi et al.   Tree Genetics & Genomes

Genomic selection in forest tree breeding

(2010) Dario Grattapaglia et al.   Tree Genetics & Genomes

Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population

(2010) H. D. Daetwyler et al.   Animal Production Science

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Association Genetics of Coastal Douglas Fir ( Pseudotsuga menziesii var. menziesii , Pinaceae). I. Cold-Hardiness Related Traits

(2009) Andrew J. Eckert et al.   GENETICS

Understanding and using quantitative genetic variation

(2009) W. G. Hill   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

Population, quantitative and comparative genomics of adaptation in forest trees

(2008) David B Neale et al.   CURRENT OPINION IN PLANT BIOLOGY

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

Adaptation, migration or extirpation: climate change outcomes for tree populations

(2008) Sally N. Aitken et al.   Evolutionary Applications

Heritability in the genomics era — concepts and misconceptions

(2008) Peter M. Visscher et al.   NATURE REVIEWS GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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