Genomic reaction norms inform predictions of plastic and adaptive responses to climate change

The genetic architecture of fitness drives population viability during rapid environmental change

(2021) Marty Kardos et al.   AMERICAN NATURALIST

Genomic evidence of past and future climate-linked loss in a migratory Arctic fish

(2021) K. K. S. Layton et al.   Nature Climate Change

Spatial scale in prescribed fire regimes: an understudied aspect in conservation with examples from the southeastern United States

(2021) David S. Mason et al.   Fire Ecology

A framework for understanding gene expression plasticity and its influence on stress tolerance

(2021) Hanny E. Rivera et al.   MOLECULAR ECOLOGY

A single-nucleotide change underlies the genetic assimilation of a plastic trait

(2021) Paul Vigne et al.   Science Advances

Computer Vision, Machine Learning, and the Promise of Phenomics in Ecology and Evolutionary Biology

(2021) Moritz D. Lürig et al.   Frontiers in Ecology and Evolution

Genetic and plastic rewiring of food webs under climate change

(2021) Matthew A. Barbour et al.   JOURNAL OF ANIMAL ECOLOGY

The role of alternative splicing in adaptation and evolution

(2021) Jukka-Pekka Verta et al.   TRENDS IN ECOLOGY & EVOLUTION

A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation

(2020) Claire Mérot et al.   TRENDS IN ECOLOGY & EVOLUTION

Nutrition-responsive gene expression and the developmental evolution of insect polyphenism

(2020) Sofia Casasa et al.   Nature Ecology & Evolution

Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes

(2020) Thibaut Capblancq et al.   Annual Review of Ecology Evolution and Systematics

Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change

(2020) Rebekah A Oomen et al.   JOURNAL OF HEREDITY

Multi-locus interactions and the build-up of reproductive isolation

(2020) I. Satokangas et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Polyphenism of a novel trait integrated rapidly evolving genes into ancestrally plastic networks

(2020) Sofia Casasa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic compensation rather than genetic assimilation drives the evolution of plasticity in response to mild warming across latitudes in a damselfly

(2020) Janne Swaegers et al.   MOLECULAR ECOLOGY

What processes must we understand to forecast regional-scale population dynamics?

(2020) Jesse R. Lasky et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomics of Developmental Plasticity in Animals

(2019) Elvira Lafuente et al.   Frontiers in Genetics

Among‐family variation in survival and gene expression uncovers adaptive genetic variation in a threatened fish

(2019) Avril M. Harder et al.   MOLECULAR ECOLOGY

Ecological genomics predicts climate vulnerability in an endangered southwestern songbird

(2018) Kristen Ruegg et al.   ECOLOGY LETTERS

R(NA)-tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics

(2018) Brenna C. M. Stanford et al.   MOLECULAR ECOLOGY

Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths

(2018) D. M. Leigh et al.   Molecular Ecology Resources

Genomic signals of selection predict climate-driven population declines in a migratory bird

(2018) Rachael A. Bay et al.   SCIENCE

Climate Velocity Can Inform Conservation in a Warming World

(2018) Isaac Brito-Morales et al.   TRENDS IN ECOLOGY & EVOLUTION

Eco-Evolutionary Genomics of Chromosomal Inversions

(2018) Maren Wellenreuther et al.   TRENDS IN ECOLOGY & EVOLUTION

A brief introduction to mixed effects modelling and multi-model inference in ecology

(2018) Xavier A. Harrison et al.   PeerJ

Genomics and conservation units: The genetic basis of adult migration timing in Pacific salmonids

(2018) Robin S. Waples et al.   Evolutionary Applications

Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

(2018) Majid Khansefid et al.   BMC GENOMICS

Developing specific molecular biomarkers for thermal stress in salmonids

(2018) Arash Akbarzadeh et al.   BMC GENOMICS

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Plasticity in gene transcription explains the differential performance of two invasive fish species

(2017) Kyle W. Wellband et al.   Evolutionary Applications

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes

(2017) Luisa Orsini et al.   MOLECULAR ECOLOGY

Phenotypic variation explains food web structural patterns

(2017) Jean P. Gibert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genetics and Demography Unite Ecology and Evolution

(2017) Winsor H. Lowe et al.   TRENDS IN ECOLOGY & EVOLUTION

Harnessing the Power of Genomics to Secure the Future of Seafood

(2017) Louis Bernatchez et al.   TRENDS IN ECOLOGY & EVOLUTION

Developmental plasticity: re-conceiving the genotype

(2017) Sonia E. Sultan   Interface Focus

The ecological importance of intraspecific variation

(2017) Simone Des Roches et al.   Nature Ecology & Evolution

variancePartition: interpreting drivers of variation in complex gene expression studies

(2016) Gabriel E. Hoffman et al.   BMC BIOINFORMATICS

Transgenerational effects persist down the maternal line in marine sticklebacks: gene expression matches physiology in a warming ocean

(2016) Lisa N.S. Shama et al.   Evolutionary Applications

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

(2016) L. Bernatchez   JOURNAL OF FISH BIOLOGY

Gene expression under thermal stress varies across a geographical range expansion front

(2016) Lesley T. Lancaster et al.   MOLECULAR ECOLOGY

Genomics of local adaptation with gene flow

(2016) Anna Tigano et al.   MOLECULAR ECOLOGY

The power and promise of RNA-seq in ecology and evolution

(2016) Erica V. Todd et al.   MOLECULAR ECOLOGY

Genetic architecture of age at maturity can generate divergent and disruptive harvest-induced evolution

(2016) Anna Kuparinen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic specificity of a plant–insect food web: Implications for linking genetic variation to network complexity

(2016) Matthew A. Barbour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic variability in reaction norms in fishes

(2015) Rebekah A. Oomen et al.   ENVIRONMENTAL REVIEWS

Gene Networks in the Wild: Identifying Transcriptional Modules that Mediate Coral Resistance to Experimental Heat Stress

(2015) Noah H. Rose et al.   Genome Biology and Evolution

Common garden experiments in the genomic era: new perspectives and opportunities

(2015) P de Villemereuil et al.   HEREDITY

The effects of temperature on aerobic metabolism: towards a mechanistic understanding of the responses of ectotherms to a changing environment

(2015) P. M. Schulte   JOURNAL OF EXPERIMENTAL BIOLOGY

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

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

(2015) Nicola J. Barson et al.   NATURE

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

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

Genetic variability in reaction norms in fishes

(2015) Rebekah A. Oomen et al.   ENVIRONMENTAL REVIEWS

Molecular processes of transgenerational acclimation to a warming ocean

(2015) Heather D. Veilleux et al.   Nature Climate Change

Assessing species vulnerability to climate change

(2015) Michela Pacifici et al.   Nature Climate Change

Evolutionary Change in Continuous Reaction Norms

(2014) Courtney J. Murren et al.   AMERICAN NATURALIST

Plastic and evolutionary responses to climate change in fish

(2014) Lisa G. Crozier et al.   Evolutionary Applications

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

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

Local Adaptation at the Transcriptome Level in Brown Trout: Evidence from Early Life History Temperature Genomic Reaction Norms

(2014) Kristian Meier et al.   PLoS One

Microgeographic adaptation and the spatial scale of evolution

(2014) Jonathan L. Richardson et al.   TRENDS IN ECOLOGY & EVOLUTION

Grand challenges in evolutionary and population genetics: the importance of integrating epigenetics, genomics, modeling, and experimentation

(2014) Samuel A. Cushman   Frontiers in Genetics

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species

(2013) Steve Smith et al.   BMC GENOMICS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Monitoring adaptive genetic responses to environmental change

(2012) MICHAEL M. HANSEN et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change

(2012) T. G. Evans et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Local and global factors affecting RNA sequencing analysis

(2011) Edward Sendler et al.   ANALYTICAL BIOCHEMISTRY

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

Old wine in new bottles: reaction norms in salmonid fishes

(2011) J A Hutchings   HEREDITY

Thermal Performance Curves, Phenotypic Plasticity, and the Time Scales of Temperature Exposure

(2011) P. M. Schulte et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

Quantifying individual variation in reaction norms: how study design affects the accuracy, precision and power of random regression models

(2011) Martijn van de Pol   Methods in Ecology and Evolution

Geographic variation in phenotypic plasticity in response to dissolved oxygen in an African cichlid fish

(2010) E. CRISPO et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Conservation genomics of Atlantic salmon: variation in gene expression between and within regions of the Bay of Fundy

(2010) WENDY VANDERSTEEN TYMCHUK et al.   MOLECULAR ECOLOGY

Expression of interest: transcriptomics and the designation of conservation units

(2010) MICHAEL M. HANSEN   MOLECULAR ECOLOGY

Temperature and length-dependent modulation of the MH class IIβ gene expression in brook charr (Salvelinus fontinalis) by a cis-acting minisatellite

(2010) Sébastien Croisetière et al.   MOLECULAR IMMUNOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Genomics and the future of conservation genetics

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

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

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

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

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

(2009) R. LANDE   JOURNAL OF EVOLUTIONARY BIOLOGY

Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity

(2009) NADIA AUBIN-HORTH et al.   MOLECULAR ECOLOGY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology

(2009) ANNE C. DALZIEL et al.   MOLECULAR ECOLOGY

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Towards an Integrated Framework for Assessing the Vulnerability of Species to Climate Change

(2008) Stephen E Williams et al.   PLOS BIOLOGY