Restoring ancestral phenotypes is a general pattern in gene expression evolution during adaptation to new environments in Tribolium castaneum

Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum

(2020) Eva L. Koch et al.   PLoS Genetics

Genetic gene expression changes during environmental adaptations tend to reverse plastic changes even after the correction for statistical nonindependence

(2019) Wei-Chin Ho et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic redundancy fuels polygenic adaptation in Drosophila

(2019) Neda Barghi et al.   PLOS BIOLOGY

Species’ Range Dynamics Affect the Evolution of Spatial Variation in Plasticity under Environmental Change

(2019) Max Schmid et al.   AMERICAN NATURALIST

Contesting the evidence for non-adaptive plasticity

(2018) François Mallard et al.   NATURE

Sticklebacks adapted to divergent osmotic environments show differences in plasticity for kidney morphology and candidate gene expression

(2017) M. Mehedi Hasan et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Gene expression stasis and plasticity following migration into a foreign environment

(2017) Brian K. Lohman et al.   MOLECULAR ECOLOGY

The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish

(2017) Courtney N. Passow et al.   MOLECULAR ECOLOGY

Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats

(2017) Taylor C. Gibbons et al.   MOLECULAR ECOLOGY

Temperature, energy metabolism, and adaptive divergence in two oyster subspecies

(2017) Ao Li et al.   Ecology and Evolution

Reproduction–Immunity Trade-Offs in Insects

(2016) Robin A. Schwenke et al.   Annual Review of Entomology

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis

(2016) Masaomi Hatakeyama et al.   BMC BIOINFORMATICS

Thermal plasticity inDrosophila melanogasterpopulations from eastern Australia: quantitative traits to transcripts

(2016) A. S. Clemson et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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(2016) Russell V. Lenth   Journal of Statistical Software

Evaluating ‘Plasticity-First’ Evolution in Nature: Key Criteria and Empirical Approaches

(2016) Nicholas A. Levis et al.   TRENDS IN ECOLOGY & EVOLUTION

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

(2016) Yuheng Huang et al.   PLoS Genetics

Transcriptomic response to heat stress among ecologically divergent populations of redband trout

(2015) Shawn R Narum et al.   BMC GENOMICS

Resurrecting complexity: the interplay of plasticity and rapid evolution in the multiple trait response to strong changes in predation pressure in the water fleaDaphnia magna

(2015) Robby Stoks et al.   ECOLOGY LETTERS

Plastic and Evolutionary Gene Expression Responses Are Correlated in European Grayling (Thymallus thymallus) Subpopulations Adapted to Different Thermal Environments

(2015) Hannu Mäkinen et al.   JOURNAL OF HEREDITY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of TwoOryzaSpecies

(2015) Jie Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differences in performance and transcriptome-wide gene expression associated withRhagoletis(Diptera: Tephritidae) larvae feeding in alternate host fruit environments

(2015) Gregory J. Ragland et al.   MOLECULAR ECOLOGY

Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations ofFundulus heteroclitus

(2015) David I. Dayan et al.   MOLECULAR ECOLOGY

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature

(2015) Cameron K. Ghalambor et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia

(2014) Lev Y Yampolsky et al.   BMC GENOMICS

Rethinking phenotypic plasticity and its consequences for individuals, populations and species

(2014) A Forsman   HEREDITY

Natural Selection Canalizes Expression Variation of Environmentally Induced Plasticity-Enabling Genes

(2014) Joseph R. Shaw et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

(2014) Matthew R. J. Morris et al.   MOLECULAR ECOLOGY

Co-Gradient Variation in Growth Rate and Development Time of a Broadly Distributed Butterfly

(2014) Madeleine Barton et al.   PLoS One

Rapid Evolution of Phenotypic Plasticity and Shifting Thresholds of Genetic Assimilation in the Nematode Caenorhabditis remanei

(2014) Kristin L. Sikkink et al.   G3-Genes Genomes Genetics

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Energy-Limited Tolerance to Stress as a Conceptual Framework to Integrate the Effects of Multiple Stressors

(2013) I. M. Sokolova   INTEGRATIVE AND COMPARATIVE BIOLOGY

The Red Flour Beetle as a Model for Bacterial Oral Infections

(2013) Barbara Milutinović et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

PHENOTYPIC PLASTICITY FACILITATES MUTATIONAL VARIANCE, GENETIC VARIANCE, AND EVOLVABILITY ALONG THE MAJOR AXIS OF ENVIRONMENTAL VARIATION

(2012) Jeremy A. Draghi et al.   EVOLUTION

Assessing the Impacts of Phenotypic Plasticity on Evolution

(2012) M. A. Wund   INTEGRATIVE AND COMPARATIVE BIOLOGY

Evolution of gene expression and expression plasticity in long-term experimental populations ofDrosophila melanogastermaintained under constant and variable ethanol stress

(2012) LEV Y. YAMPOLSKY et al.   MOLECULAR ECOLOGY

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Phenotypic Plasticity Influences the Size, Shape and Dynamics of the Geographic Distribution of an Invasive Plant

(2012) Jean-Baptiste Pichancourt et al.   PLoS One

Variation in plastic responses of a globally distributed picoplankton species to ocean acidification

(2012) Elisa Schaum et al.   Nature Climate Change

Higher plasticity in ecophysiological traits enhances the performance and invasion success of Taraxacum officinale (dandelion) in alpine environments

(2011) Marco A. Molina-Montenegro et al.   BIOLOGICAL INVASIONS

HIGH-DIMENSIONAL VARIANCE PARTITIONING REVEALS THE MODULAR GENETIC BASIS OF ADAPTIVE DIVERGENCE IN GENE EXPRESSION DURING REPRODUCTIVE CHARACTER DISPLACEMENT

(2011) Elizabeth A. McGraw et al.   EVOLUTION

A history of phenotypic plasticity accelerates adaptation to a new environment

(2011) J. L. FIERST   JOURNAL OF EVOLUTIONARY BIOLOGY

The role of gene expression in ecological speciation

(2010) Scott A. Pavey et al.   Annals of the New York Academy of Sciences

Whole-Genome Expression Plasticity across Tropical and Temperate Drosophila melanogaster Populations from Eastern Australia

(2010) M. T. Levine et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phenotypic plasticity's impacts on diversification and speciation

(2010) David W. Pfennig et al.   TRENDS IN ECOLOGY & EVOLUTION

Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory

(2010) Luis-Miguel Chevin et al.   PLOS BIOLOGY

The Covariance between Genetic and Environmental Influences across Ecological Gradients

(2009) David O. Conover et al.   Annals of the New York Academy of Sciences

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

ADAPTIVE DIVERGENCE BETWEEN FRESHWATER AND MARINE STICKLEBACKS: INSIGHTS INTO THE ROLE OF PHENOTYPIC PLASTICITY FROM AN INTEGRATED ANALYSIS OF CANDIDATE GENE EXPRESSION

(2009) R. J. Scott McCairns et al.   EVOLUTION

Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation

(2009) R. LANDE   JOURNAL OF EVOLUTIONARY BIOLOGY

Systems genetics of complex traits in Drosophila melanogaster

(2009) Julien F Ayroles et al.   NATURE GENETICS

Evolving gene expression: from G to E to G×E

(2009) Andrea Hodgins-Davis et al.   TRENDS IN ECOLOGY & EVOLUTION

Phenotypic plasticity and experimental evolution

(2008) T. Garland et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

The environmental contribution to gene expression profiles

(2008) Greg Gibson   NATURE REVIEWS GENETICS

Postgenomics of Tribolium: Targeting the endocrine regulation of diuresis

(2008) Yoonseong PARK et al.   ENTOMOLOGICAL RESEARCH