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

Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana , Poeciliidae)

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

Contrasting effects of environment and genetics generate a continuum of parallel evolution

(2017) Yoel E. Stuart et al.   Nature Ecology & Evolution

The Evolutionary Ecology of Animals Inhabiting Hydrogen Sulfide–Rich Environments

(2016) Michael Tobler et al.   Annual Review of Ecology Evolution and Systematics

Sulfide exposure results in enhanced sqr transcription through upregulating the expression and activation of HSF1 in echiuran worm Urechis unicinctus

(2016) Xiaolong Liu et al.   AQUATIC TOXICOLOGY

Canalization of gene expression is a major signature of regulatory cold adaptation in temperate Drosophila melanogaster

(2016) Korbinian von Heckel et al.   BMC GENOMICS

Adaptive, but not condition-dependent, body shape differences contribute to assortative mating preferences during ecological speciation

(2016) Ryan Greenway et al.   EVOLUTION

Toxic hydrogen sulphide shapes brain anatomy: a comparative study of sulphide-adapted ecotypes in thePoecilia mexicanacomplex

(2016) T. Schulz-Mirbach et al.   JOURNAL OF ZOOLOGY

Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide–Rich Environments

(2016) Joanna L. Kelley et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analyses of the subgenus Mollienesia ( Poecilia , Poeciliidae, Teleostei) reveal taxonomic inconsistencies, cryptic biodiversity, and spatio-temporal aspects of diversification in Middle America

(2016) Maura Palacios et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

A single generation of domestication heritably alters the expression of hundreds of genes

(2016) Mark R. Christie et al.   Nature Communications

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

(2016) Yuheng Huang et al.   PLoS Genetics

Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis

(2015) Xiaolong Liu et al.   BMC GENOMICS

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

(2015) Shawn R Narum et al.   BMC GENOMICS

Convergent changes in the trophic ecology of extremophile fish along replicated environmental gradients

(2015) Michael Tobler et al.   FRESHWATER BIOLOGY

Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)

(2015) Markus Pfenninger et al.   MOLECULAR ECOLOGY

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

(2015) Cameron K. Ghalambor et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

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

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

Reduction of Energetic Demands through Modification of Body Size and Routine Metabolic Rates in Extremophile Fish

(2015) Courtney N. Passow et al.   PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY

Sulfur as a Signaling Nutrient Through Hydrogen Sulfide

(2014) Omer Kabil et al.   Annual Review of Nutrition

H2S exposure elicits differential expression of candidate genes in fish adapted to sulfidic and non-sulfidic environments

(2014) Michael Tobler et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations

(2014) M. Tobler et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks—Signatures of Selection and Widespread Heritability

(2014) Erica H. Leder et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Parallel evolution of cox genes in H2S-tolerant fish as key adaptation to a toxic environment

(2014) Markus Pfenninger et al.   Nature Communications

Colonisation of toxic environments drives predictable life-history evolution in livebearing fishes (Poeciliidae)

(2013) Rüdiger Riesch et al.   ECOLOGY LETTERS

GENETIC DIFFERENTIATION AND SELECTION AGAINST MIGRANTS IN EVOLUTIONARILY REPLICATED EXTREME ENVIRONMENTS

(2013) Martin Plath et al.   EVOLUTION

Thermal adaptation and acclimation of ectotherms from differing aquatic climates

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

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

The Rediscovery of a Long Described Species Reveals Additional Complexity in Speciation Patterns of Poeciliid Fishes in Sulfide Springs

(2013) Maura Palacios et al.   PLoS One

Gene transcription reflects poor health status of resident European eel chronically exposed to environmental pollutants

(2012) G.E. Maes et al.   AQUATIC TOXICOLOGY

Human Sulfide:Quinone Oxidoreductase Catalyzes the First Step in Hydrogen Sulfide Metabolism and Produces a Sulfane Sulfur Metabolite

(2012) Michael R. Jackson et al.   BIOCHEMISTRY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Balancing noise and plasticity in eukaryotic gene expression

(2012) Djordje Bajić et al.   BMC GENOMICS

Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome

(2012) Joanna L Kelley et al.   BMC GENOMICS

Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

(2012) A. Whitehead   JOURNAL OF EXPERIMENTAL 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

Phylogeny and biogeography of the Poecilia sphenops species complex (Actinopterygii, Poeciliidae) in Central America

(2012) Fernando Alda et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Regulatory changes contribute to the adaptive enhancement of thermogenic capacity in high-altitude deer mice

(2012) Z. A. Cheviron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrogen Sulfide and Cell Signaling

(2011) Ling Li et al.   Annual Review of Pharmacology and Toxicology

Assessment of Chemical Mixtures and Groundwater Effects on Daphnia magna Transcriptomics

(2011) Natàlia Garcia-Reyero et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

PARALLEL AND NONPARALLEL ASPECTS OF ECOLOGICAL, PHENOTYPIC, AND GENETIC DIVERGENCE ACROSS REPLICATE POPULATION PAIRS OF LAKE AND STREAM STICKLEBACK

(2011) Renaud Kaeuffer et al.   EVOLUTION

EVOLUTION IN EXTREME ENVIRONMENTS: REPLICATED PHENOTYPIC DIFFERENTIATION IN LIVEBEARING FISH INHABITING SULFIDIC SPRINGS

(2011) Michael Tobler et al.   EVOLUTION

Response of Sulfide:Quinone Oxidoreductase to Sulfide Exposure in the Echiuran Worm Urechis unicinctus

(2011) Yu-Bin Ma et al.   MARINE BIOTECHNOLOGY

Transcriptomics of environmental acclimatization and survival in wild adult Pacific sockeye salmon (Oncorhynchus nerka) during spawning migration

(2011) TYLER G. EVANS et al.   MOLECULAR ECOLOGY

INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCI

(2010) Jay F. Storz et al.   EVOLUTION

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Effect of pH on Gene Expression and Thermal Tolerance of Early Life History Stages of Red Abalone (Haliotis rufescens)

(2010) MacKenzie L. Zippay et al.   JOURNAL OF SHELLFISH RESEARCH

Comparative transcriptomics implicates mechanisms of evolved pollution tolerance in a killifish population

(2010) A. WHITEHEAD et al.   MOLECULAR ECOLOGY

Phenotypic plasticity facilitates recurrent rapid adaptation to introduced predators

(2010) A. G. Scoville et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC 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

Loss of ETHE1, a mitochondrial dioxygenase, causes fatal sulfide toxicity in ethylmalonic encephalopathy

(2009) Valeria Tiranti et al.   NATURE MEDICINE

The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration

(2009) M. Marcia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions between effects of environmental chemicals and natural stressors: A review

(2009) Martin Holmstrup et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Transgenerational Epigenetic Effects

(2008) Neil A. Youngson et al.   Annual Review of Genomics and Human Genetics

Rhythms of Gene Expression in a Fluctuating Intertidal Environment

(2008) Andrew Y. Gracey et al.   CURRENT BIOLOGY

Three enzymatic activities catalyze the oxidation of sulfide to thiosulfate in mammalian and invertebrate mitochondria

(2008) Tatjana M. Hildebrandt et al.   FEBS Journal

The inhibition of mitochondrial cytochrome oxidase by the gases carbon monoxide, nitric oxide, hydrogen cyanide and hydrogen sulfide: chemical mechanism and physiological significance

(2008) Chris E. Cooper et al.   JOURNAL OF BIOENERGETICS AND BIOMEMBRANES

Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient

(2008) ZACHARY A. CHEVIRON et al.   MOLECULAR ECOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS