Plant responses to global change: next generation biogeography

Population Graphs and Landscape Genetics

(2015) Rodney J. Dyer   Annual Review of Ecology Evolution and Systematics

Genomics Are Transforming Our Understanding of Responses to Climate Change

(2015) Jonathon H. Stillman et al.   BIOSCIENCE

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up

(2015) Noah Fahlgren et al.   CURRENT OPINION IN PLANT BIOLOGY

Isolation by distance, resistance and/or clusters? Lessons learned from a forest-dwelling carnivore inhabiting a heterogeneous landscape

(2015) Aritz Ruiz-Gonzalez et al.   MOLECULAR ECOLOGY

The fine-scale genetic structure of the British population

(2015) Stephen Leslie et al.   NATURE

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

(2015) Modhumita Ghosh Dasgupta et al.   PLoS One

Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited

(2014) Sean V. Burke et al.   AMERICAN JOURNAL OF BOTANY

Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica

(2014) Jinhuan Chen et al.   BMC GENOMICS

Structural variation and genome complexity: is dispensable really dispensable?

(2014) Fabio Marroni et al.   CURRENT OPINION IN PLANT BIOLOGY

Dispersal under duress: Can stress enhance the performance of a passively dispersed species?

(2014) Brittany J. Teller et al.   ECOLOGY

Frugivores and cheap fruits make fruiting fruitful

(2014) F. Encinas-Viso et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Trade-offs and utility of alternative RADseq methods: Reply to Puritzet al.

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

Demystifying the RAD fad

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

Recent novel approaches for population genomics data analysis

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

Genome-wide scans detect adaptation to aridity in a widespread forest tree species

(2014) Dorothy A. Steane et al.   MOLECULAR ECOLOGY

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

(2014) T.B.K. Reddy et al.   NUCLEIC ACIDS RESEARCH

RNA-seq analysis of Rubus idaeus cv. Nova: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches

(2014) Tae Kyung Hyun et al.   PLANT CELL REPORTS

RNA-Seq Using Two Populations Reveals Genes and Alleles Controlling Wood Traits and Growth in Eucalyptus nitens

(2014) Saravanan Thavamanikumar et al.   PLoS One

Targeted re-sequencing of five Douglas-fir provenances reveals population structure and putative target genes of positive selection

(2014) Thomas Müller et al.   Tree Genetics & Genomes

Association mapping for wood quality and growth traits in Eucalyptus globulus ssp. globulus Labill identifies nine stable marker-trait associations for seven traits

(2014) Saravanan Thavamanikumar et al.   Tree Genetics & Genomes

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Escape from the laboratory: new horizons for plant genetics

(2014) Maurizio Rossetto et al.   TRENDS IN PLANT SCIENCE

Historical Perspective, Development and Applications of Next-Generation Sequencing in Plant Virology

(2014) Marina Barba et al.   Viruses-Basel

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

(2014) Wanneng Yang et al.   Nature Communications

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

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

(2014) Jonathan B. Puritz et al.   PeerJ

INTEGRATING LANDSCAPE GENOMICS AND SPATIALLY EXPLICIT APPROACHES TO DETECT LOCI UNDER SELECTION IN CLINAL POPULATIONS

(2013) Matthew R. Jones et al.   EVOLUTION

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

(2013) Jason P. Sexton et al.   EVOLUTION

Evolutionary and plastic responses to climate change in terrestrial plant populations

(2013) Steven J. Franks et al.   Evolutionary Applications

Imprints of Natural Selection Along Environmental Gradients in Phenology-Related Genes of Quercus petraea

(2013) F. J. Alberto et al.   GENETICS

Evidence of current impact of climate change on life: a walk from genes to the biosphere

(2013) Josep Peñuelas et al.   GLOBAL CHANGE BIOLOGY

Genetic signatures of natural selection in response to air pollution in red spruce (Picea rubens, Pinaceae)

(2013) Stanislav Bashalkhanov et al.   MOLECULAR ECOLOGY

Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population

(2013) Rajiv C. McCoy et al.   MOLECULAR ECOLOGY

Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization

(2013) Luisa Orsini et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

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

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

(2013) Ilga Porth et al.   NEW PHYTOLOGIST

Where am I and why? Synthesizing range biology and the eco-evolutionary dynamics of dispersal

(2013) Alexander Kubisch et al.   OIKOS

Dispersal and species’ responses to climate change

(2013) Justin M. J. Travis et al.   OIKOS

The problem of conifer species migration lag in the Pacific Northwest region since the last glaciation

(2013) Scott A. Elias   QUATERNARY SCIENCE REVIEWS

Functional Extinction of Birds Drives Rapid Evolutionary Changes in Seed Size

(2013) M. Galetti et al.   SCIENCE

Genetic structure and association mapping of adaptive and selective traits in the east Texas loblolly pine (Pinus taeda L.) breeding populations

(2013) Vikram E. Chhatre et al.   Tree Genetics & Genomes

Insights into drought adaptation of two European oak species revealed by nucleotide diversity of candidate genes

(2013) Andreas Homolka 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

Association of loblolly pine xylem development gene expression with single-nucleotide polymorphisms

(2013) S. R. Palle et al.   TREE PHYSIOLOGY

Ten years of landscape genetics

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

Will plant movements keep up with climate change?

(2013) Richard T. Corlett et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary Biology for the 21st Century

(2013) Jonathan B. Losos et al.   PLOS BIOLOGY

Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments

(2013) Miriam L. Gifford et al.   PLoS Genetics

Conservation Genomics of Threatened Animal Species

(2013) Cynthia C. Steiner et al.   Annual Review of Animal Biosciences

ezRAD: a simplified method for genomic genotyping in non-model organisms

(2013) Robert J. Toonen et al.   PeerJ

Designing a transcriptome next-generation sequencing project for a nonmodel plant species1

(2012) Susan R. Strickler et al.   AMERICAN JOURNAL OF BOTANY

Genetic dissection of growth, wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla

(2012) Anand Raj Kullan et al.   BMC GENETICS

A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings

(2012) Thomas Müller et al.   BMC GENOMICS

Long-distance gene flow and adaptation of forest trees to rapid climate change

(2012) Antoine Kremer et al.   ECOLOGY LETTERS

Phenotypic plasticity and evolutionary demographic responses to climate change: taking theory out to the field

(2012) Luis-Miguel Chevin et al.   FUNCTIONAL ECOLOGY

The climate velocity of the contiguous United States during the 20th century

(2012) Solomon Z. Dobrowski et al.   GLOBAL CHANGE BIOLOGY

High-throughput Phenotyping and Genomic Selection: The Frontiers of Crop Breeding ConvergeF

(2012) Llorenç Cabrera-Bosquet et al.   Journal of Integrative Plant Biology

The trouble with isolation by distance

(2012) PATRICK G. MEIRMANS   MOLECULAR ECOLOGY

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

Next-generation phylogenetics takes root

(2012) John E. McCormack 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

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

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

Biodiversity loss and its impact on humanity

(2012) Bradley J. Cardinale et al.   NATURE

2b-RAD: a simple and flexible method for genome-wide genotyping

(2012) Shi Wang et al.   NATURE METHODS

Early Cone Setting in Picea abies acrocona Is Associated with Increased Transcriptional Activity of a MADS Box Transcription Factor

(2012) D. Uddenberg et al.   PLANT PHYSIOLOGY

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change

(2012) J. T. Anderson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Genotyping-by-Sequencing for Plant Breeding and Genetics

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

A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response

(2012) Daniele L. Filiault et al.   PLoS Genetics

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

Costs of dispersal

(2011) Dries Bonte et al.   BIOLOGICAL REVIEWS

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

Genetic Architecture of Flowering-Time Variation inArabidopsis thaliana

(2011) Patrice A. Salomé et al.   GENETICS

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

(2011) Jean Beaulieu et al.   GENETICS

Seed dispersal distance is more strongly correlated with plant height than with seed mass

(2011) Fiona J. Thomson et al.   JOURNAL OF ECOLOGY

Pollination graphs: quantifying pollen pool covariance networks and the influence of intervening landscape on genetic connectivity in the North American understory tree, Cornus florida L.

(2011) Rodney J. Dyer et al.   LANDSCAPE ECOLOGY

Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce

(2011) JULIEN PRUNIER et al.   MOLECULAR ECOLOGY

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

(2011) ARMANDO GERALDES et al.   Molecular Ecology Resources

An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population

(2011) LORENZ HAUSER et al.   Molecular Ecology Resources

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

(2011) J. E. SEEB et al.   Molecular Ecology Resources

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

Forest tree genomics: growing resources and applications

(2011) David B. Neale 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

Leaf-out phenology of temperate woody plants: from trees to ecosystems

(2011) Caroline A. Polgar et al.   NEW PHYTOLOGIST

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

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

Rapid Range Shifts of Species Associated with High Levels of Climate Warming

(2011) I.-C. Chen et al.   SCIENCE

Staying afloat in the sensor data deluge

(2011) John H. Porter et al.   TRENDS IN ECOLOGY & EVOLUTION

Inertia: the discrepancy between individual and common good in dispersal and prospecting behaviour

(2010) María del Mar Delgado et al.   BIOLOGICAL REVIEWS

Climate, climate change and range boundaries

(2010) Chris D. Thomas   DIVERSITY AND DISTRIBUTIONS

The ecological significance of phenology in four different tree species: effects of light and temperature on bud burst

(2010) Amelia Caffarra et al.   INTERNATIONAL JOURNAL OF BIOMETEOROLOGY

Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

(2010) BÉNÉDICTE N. PONCET et al.   MOLECULAR ECOLOGY

INTRODUCTION: Contributions of landscape genetics - approaches, insights, and future potential

(2010) VICTORIA L. SORK et al.   MOLECULAR ECOLOGY

Landscape genetics: where are we now?

(2010) ANDREW STORFER et al.   MOLECULAR ECOLOGY

Using differential introgression in hybrid zones to identify genomic regions involved in speciation

(2010) BRET A. PAYSEUR   Molecular Ecology Resources

Genomics and the future of conservation genetics

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

Association genetics of complex traits in plants

(2010) Pär K. Ingvarsson et al.   NEW PHYTOLOGIST

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

The effects of phenological mismatches on demography

(2010) A. J. Miller-Rushing et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptation and extinction in experimentally fragmented landscapes

(2010) S. Fakheran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phenology Under Global Warming

(2010) C. Korner et al.   SCIENCE

Global Biodiversity: Indicators of Recent Declines

(2010) S. H. M. Butchart et al.   SCIENCE

Scenarios for Global Biodiversity in the 21st Century

(2010) H. M. Pereira et al.   SCIENCE

Adaptation genomics: the next generation

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

Landscape genetics of plants

(2010) Rolf Holderegger et al.   TRENDS IN PLANT SCIENCE

Plant phenotypic plasticity in a changing climate

(2010) A.B. Nicotra et al.   TRENDS IN PLANT SCIENCE

Understanding the consequences of seed dispersal in a heterogeneous environment

(2009) Brooke S. Baythavong et al.   ECOLOGY

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

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

(2009) Andrew J. Eckert et al.   GENETICS

Leaf phenology in 22 North American tree species during the 21st century

(2009) XAVIER MORIN et al.   GLOBAL CHANGE BIOLOGY

A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator)

(2009) Falko Roeding et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The velocity of climate change

(2009) Scott R. Loarie et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Characterization of a MADS FLOWERING LOCUS C-LIKE (MFL ) sequence in Cichorium intybus : a comparative study of CiMFL and AtFLC reveals homologies and divergences in gene function

(2009) A. Locascio et al.   NEW PHYTOLOGIST

With ‘Phenomics,’ Plant Scientists Hope to Shift Breeding Into Overdrive

(2009) Elizabeth Finkel   SCIENCE

EFFECTS OF CLIMATE CHANGE ON PHENOLOGY, FROST DAMAGE, AND FLORAL ABUNDANCE OF MONTANE WILDFLOWERS

(2008) David W. Inouye   ECOLOGY

USING CIRCUIT THEORY TO MODEL CONNECTIVITY IN ECOLOGY, EVOLUTION, AND CONSERVATION

(2008) Brad H. McRae et al.   ECOLOGY

HETEROGENEOUS GENOMIC DIFFERENTIATION BETWEEN WALKING-STICK ECOTYPES: "ISOLATION BY ADAPTATION" AND MULTIPLE ROLES FOR DIVERGENT SELECTION

(2008) Patrik Nosil et al.   EVOLUTION

Applications of graph theory to landscape genetics

(2008) Colin J. Garroway et al.   Evolutionary Applications

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

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

Microrefugia

(2008) Valentí Rull   JOURNAL OF BIOGEOGRAPHY

A change in climate causes rapid evolution of multiple life-history traits and their interactions in an annual plant

(2008) S. J. FRANKS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce

(2008) MARIE-CLAIRE NAMROUD et al.   MOLECULAR ECOLOGY

Next-generation genetics in plants

(2008) Magnus Nordborg et al.   NATURE

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis)

(2008) Jason A. Holliday et al.   NEW PHYTOLOGIST

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Opposing plant community responses to warming with and without herbivores

(2008) E. Post et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid evolution of seed dispersal in an urban environment in the weed Crepis sancta

(2008) P.-O. Cheptou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS

Climate change and evolution: disentangling environmental and genetic responses

(2007) P. GIENAPP et al.   MOLECULAR ECOLOGY