Population genomics of the eastern cottonwood (Populus deltoides )

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

(2017) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

(2016) Jing Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The programstructuredoes not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem

(2016) Sebastien J. Puechmaille   Molecular Ecology Resources

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

Towards integration of population and comparative genomics in forest trees

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

Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

(2016) Annette M. Fahrenkrog et al.   NEW PHYTOLOGIST

Convergent local adaptation to climate in distantly related conifers

(2016) S. Yeaman et al.   SCIENCE

The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2

(2015) M. E. Roux et al.   EMBO JOURNAL

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

(2015) J. Wang et al.   GENETICS

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

Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

(2015) A. Geraldes 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

Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages ofPopulus alba(Salicaceae), a widespread forest tree

(2015) Kai N. Stölting et al.   NEW PHYTOLOGIST

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

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation inPopulus

(2015) Lijun Liu et al.   PLANT JOURNAL

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

Evolutionary Quantitative Genomics of Populus trichocarpa

(2015) Ilga Porth et al.   PLoS One

Effective filtering strategies to improve data quality from population-based whole exome sequencing studies

(2014) Andrew R Carson et al.   BMC BIOINFORMATICS

LANDSCAPE GENOMICS OFPOPULUS TRICHOCARPA: THE ROLE OF HYBRIDIZATION, LIMITED GENE FLOW, AND NATURAL SELECTION IN SHAPING PATTERNS OF POPULATION STRUCTURE

(2014) Armando Geraldes et al.   EVOLUTION

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

(2014) Katie E. Lotterhos 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

Carbon sequestration: Managing forests in uncertain times

(2014) Valentin Bellassen et al.   NATURE

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

(2014) Luke M Evans et al.   NATURE GENETICS

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations ofPopulus trichocarpa

(2014) Athena D. McKown et al.   NEW PHYTOLOGIST

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

(2014) Wan-Ping Lee et al.   PLoS One

4P: fast computing of population genetics statistics from large DNA polymorphism panels

(2014) Andrea Benazzo et al.   Ecology and Evolution

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Nicolas Bierne et al.   MOLECULAR ECOLOGY

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Breeding with rare defective alleles (BRDA): a naturalPopulus nigraHCT mutant with modified lignin as a case study

(2013) Bartel Vanholme et al.   NEW PHYTOLOGIST

Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of naturalPopulus trichocarpaaccessions

(2013) Ilga Porth 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

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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

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

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

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Comparative SNP and Haplotype Analysis Reveals a Higher Genetic Diversity and Rapider LD Decay in Tropical than Temperate Germplasm in Maize

(2011) Yanli Lu et al.   PLoS One

Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene

(2011) Fabio Marroni et al.   Tree Genetics & Genomes

Conditions Under Which Genome-Wide Association Studies Will be Positively Misleading

(2010) A. Platt et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Affinity Purification of theArabidopsis26 S Proteasome Reveals a Diverse Array of Plant Proteolytic Complexes

(2010) Adam J. Book et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests

(2010) J. A. HOLLIDAY et al.   MOLECULAR ECOLOGY

Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem

(2010) Jill L. Wegrzyn et al.   NEW PHYTOLOGIST

WD40 proteins propel cellular networks

(2010) Christian U. Stirnimann et al.   TRENDS IN BIOCHEMICAL SCIENCES

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Nucleotide diversity among natural populations of a North American poplar (Populus balsamifera , Salicaceae)

(2009) Amy L. Breen et al.   NEW PHYTOLOGIST

ThePopulusGenome Integrative Explorer (PopGenIE): a new resource for exploring thePopulusgenome

(2009) Andreas Sjödin et al.   NEW PHYTOLOGIST

Genome-wide scans for footprints of natural selection

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

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

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

Correcting Estimators of   and Tajima's D for Ascertainment Biases Caused by the Single-Nucleotide Polymorphism Discovery Process

(2008) A. Ramirez-Soriano et al.   GENETICS

Multilocus Patterns of Nucleotide Polymorphism and the Demographic History of Populus tremula

(2008) P. K. Ingvarsson   GENETICS

Gene expression profiling and silencing reveal that monolignol biosynthesis plays a critical role in penetration defence in wheat against powdery mildew invasion

(2008) N. H. Bhuiyan et al.   JOURNAL OF EXPERIMENTAL BOTANY