Pooled ecotype sequencing reveals candidate genetic mechanisms for adaptive differentiation and reproductive isolation

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

Genetic loci with parent-of-origin effects cause hybrid seed lethality in crosses between Mimulus species

(2016) Austin G. Garner et al.   NEW PHYTOLOGIST

Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion

(2015) Alex D. Twyford et al.   EVOLUTION

A practical guide to environmental association analysis in landscape genomics

(2015) Christian Rellstab et al.   MOLECULAR ECOLOGY

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

(2015) Sangeet Lamichhaney et al.   NATURE

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

Salinity Is an Agent of Divergent Selection Driving Local Adaptation of Arabidopsis to Coastal Habitats

(2015) Silvia Busoms et al.   PLANT PHYSIOLOGY

Revisiting classic clines in Drosophila melanogaster in the age of genomics

(2015) Jeffrey R. Adrion et al.   TRENDS IN GENETICS

Adaptations between Ecotypes and along Environmental Gradients in Panicum virgatum

(2014) David B. Lowry et al.   AMERICAN NATURALIST

Western corn rootworm (Diabrotica virgifera virgifera) transcriptome assembly and genomic analysis of population structure

(2014) Lex E Flagel et al.   BMC GENOMICS

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

UNIFICATION OF METHODS FOR ESTIMATING THE STRENGTH OF REPRODUCTIVE ISOLATION

(2014) James M. Sobel et al.   EVOLUTION

Evidence of Natural Selection Acting on a Polymorphic Hybrid Incompatibility Locus in Mimulus

(2014) Andrea L. Sweigart et al.   GENETICS

Population-Genetic Inference from Pooled-Sequencing Data

(2014) Michael Lynch et al.   Genome Biology and Evolution

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

Genetic Determinants and Epistasis for Life History Trait Differences in the Common Monkeyflower,Mimulus guttatus

(2014) Jannice Friedman   JOURNAL OF HEREDITY

Selection on Meiosis Genes in Diploid and Tetraploid Arabidopsis arenosa

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

The extent and genetic basis of phenotypic divergence in life history traits inMimulus guttatus

(2014) Jannice Friedman et al.   MOLECULAR ECOLOGY

Divergent population structure and climate associations of a chromosomal inversion polymorphism across theMimulus guttatusspecies complex

(2014) Elen Oneal 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

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

Variation in MPK12 affects water use efficiency in Arabidopsis and reveals a pleiotropic link between guard cell size and ABA response

(2014) D. L. Des Marais et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Advances and limits of using population genetics to understand local adaptation

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

Plant salt-tolerance mechanisms

(2014) Ulrich Deinlein et al.   TRENDS IN PLANT SCIENCE

A High-Resolution Genetic Map of Yellow Monkeyflower Identifies Chemical Defense QTLs and Recombination Rate Variation

(2014) Liza M. Holeski et al.   G3-Genes Genomes Genetics

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

Adaptation through chromosomal inversions in Anopheles

(2014) Diego Ayala et al.   Frontiers in Genetics

Natural variation and genetic constraints on drought tolerance

(2013) Thomas E Juenger   CURRENT OPINION IN PLANT BIOLOGY

The Standing Pool of Genomic Structural Variation in a Natural Population of Mimulus guttatus

(2013) Lex E. Flagel et al.   Genome Biology and Evolution

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Major QTLs for critical photoperiod and vernalization underlie extensive variation in flowering in theMimulus guttatusspecies complex

(2013) Jannice Friedman et al.   NEW PHYTOLOGIST

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

(2013) U. Hellsten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geographically multifarious phenotypic divergence during speciation

(2013) Zachariah Gompert et al.   Ecology and Evolution

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

(2013) Fei Lu et al.   PLoS Genetics

Ecotypes and the controversy over stages in the formation of new species

(2012) DAVID B. LOWRY   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

SNP calling by sequencing pooled samples

(2012) Emanuele Raineri et al.   BMC BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Recent nonhybrid origin of sunflower ecotypes in a novel habitat

(2012) Rose L. Andrew et al.   MOLECULAR ECOLOGY

Genome-wide patterns of latitudinal differentiation among populations ofDrosophila melanogasterfrom North America

(2012) Daniel K. Fabian et al.   MOLECULAR ECOLOGY

Patterns of shoot architecture in locally adapted populations are linked to intraspecific differences in gene regulation

(2012) Robert L. Baker et al.   NEW PHYTOLOGIST

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

Node-specific branching and heterochronic changes underlie population-level differences in Mimulus guttatus (Phrymaceae) shoot architecture

(2011) Robert L. Baker et al.   AMERICAN JOURNAL OF BOTANY

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

Ecological Genomics of Anopheles gambiae Along a Latitudinal Cline: A Population-Resequencing Approach

(2011) C. Cheng et al.   GENETICS

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

(2011) Paul M. Magwene et al.   PLoS Computational Biology

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

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

Is local adaptation in Mimulus guttatus caused by trade-offs at individual loci?

(2010) M. C. HALL et al.   MOLECULAR ECOLOGY

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

(2010) David B. Lowry et al.   PLOS BIOLOGY

A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1

(2010) Ivan Baxter 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

THE BIOLOGY OF SPECIATION

(2009) James M. Sobel et al.   EVOLUTION

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2009) M A F Noor et al.   HEREDITY

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

Genetic and physiological basis of adaptive salt tolerance divergence between coastal and inlandMimulus guttatus

(2009) David B. Lowry et al.   NEW PHYTOLOGIST

Three SnRK2 Protein Kinases are the Main Positive Regulators of Abscisic Acid Signaling in Response to Water Stress in Arabidopsis

(2009) Yasunari Fujita et al.   PLANT AND CELL PHYSIOLOGY

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

Ecological explanations for (incomplete) speciation

(2009) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

The Role of Geography in Human Adaptation

(2009) Graham Coop et al.   PLoS Genetics

GENETICS OF DROUGHT ADAPTATION INARABIDOPSIS THALIANAII. QTL ANALYSIS OF A NEW MAPPING POPULATION, KAS-1 × TSU-1

(2008) John K. McKay et al.   EVOLUTION

ECOLOGICAL REPRODUCTIVE ISOLATION OF COAST AND INLAND RACES OFMIMULUS GUTTATUS

(2008) David B. Lowry et al.   EVOLUTION

Releasing the brakes of plant growth: how GAs shutdown DELLA proteins

(2008) P. Achard et al.   JOURNAL OF EXPERIMENTAL BOTANY

The strength and genetic basis of reproductive isolating barriers in flowering plants

(2008) D. B Lowry et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES