Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish

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Revisiting Adaptive Potential, Population Size, and Conservation

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A novel holistic framework for genetic-based captive-breeding and reintroduction programs

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Range-wide fragmentation in a threatened fish associated with post-European settlement modification in the Murray–Darling Basin, Australia

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Genomic Flatlining in the Endangered Island Fox

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The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes

(2016) R. J. Scott McCairns et al.   Evolutionary Applications

Are heritability and selection related to population size in nature? Meta-analysis and conservation implications

(2016) Jacquelyn L. A. Wood et al.   Evolutionary Applications

Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin

(2016) Chris J. Brauer et al.   MOLECULAR ECOLOGY

Divergence in gene expression within and between two closely related flycatcher species

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Similar plastic responses to elevated temperature among different-sized brook trout populations

(2015) Jacquelyn L. A. Wood et al.   ECOLOGY

Integrated assessment of wastewater treatment plant effluent estrogenicity in the Upper Murray River, Australia, using the native Murray rainbowfish(Melanotaenia fluviatilis)

(2015) Alan M. Vajda et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish

(2015) Jacquelyn L. A. Wood et al.   EVOLUTION

Environmental heterogeneity leads to higher plasticity in dry-edge populations of a semi-arid Chilean shrub: insights into climate change responses

(2015) Ana Lázaro-Nogal et al.   JOURNAL OF ECOLOGY

Plastic and Evolved Responses to Global Change: What Can We Learn from Comparative Transcriptomics?: Table 1.

(2015) Melissa B. DeBiasse et al.   JOURNAL OF HEREDITY

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

Ensembl 2016

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Climate change and pollution speed declines in zebrafish populations

(2015) A. Ross Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution

(2015) Rori V. Rohlfs et al.   SYSTEMATIC BIOLOGY

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change

(2014) Fernando Valladares et al.   ECOLOGY LETTERS

Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels

(2014) Lucie Baillon et al.   ECOTOXICOLOGY

Using genomics to characterize evolutionary potential for conservation of wild populations

(2014) Katherine A. Harrisson et al.   Evolutionary Applications

Climate change, adaptation, and phenotypic plasticity: the problem and the evidence

(2014) Juha Merilä et al.   Evolutionary Applications

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

UniProt: a hub for protein information

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Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish

(2014) D. J. Fraser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2013) Steve Smith et al.   BMC GENOMICS

Phylogenetic Analysis of Gene Expression

(2013) C. W. Dunn et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Freshwater fish conservation in the face of critical water shortages in the southern Murray?Darling Basin, Australia

(2013) Michael P. Hammer et al.   MARINE AND FRESHWATER RESEARCH

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

(2013) C. R. Primmer et al.   MOLECULAR ECOLOGY

Intraspecific variation in the growth and survival of juvenile fish exposed toEucalyptusleachate

(2013) John R. Morrongiello et al.   Ecology and Evolution

Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel

(2012) Jose Pujolar et al.   BMC GENOMICS

Generalists and specialists along a latitudinal transect: patterns of thermal adaptation in six species of damselflies

(2012) Viktor Nilsson-Örtman et al.   ECOLOGY

Spatial variation in egg size and egg number reflects trade-offs and bet-hedging in a freshwater fish

(2012) John R. Morrongiello et al.   JOURNAL OF ANIMAL ECOLOGY

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

(2012) A. Whitehead   JOURNAL OF EXPERIMENTAL BIOLOGY

Comparative studies of gene expression and the evolution of gene regulation

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Phenotypic plasticity in evolutionary rescue experiments

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What is needed for next-generation ecological and evolutionary genomics?

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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Genetic erosion impedes adaptive responses to stressful environments

(2011) R. Bijlsma et al.   Evolutionary Applications

Eucalyptus leachate inhibits reproduction in a freshwater fish

(2011) JOHN R. MORRONGIELLO et al.   FRESHWATER BIOLOGY

Fluctuations in population composition dampen the impact of phenotypic plasticity on trait dynamics in superb fairy-wrens

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Adaptation to marginal habitats by evolution of increased phenotypic plasticity

(2011) L.-M. CHEVIN et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

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A Phylogenetic Analysis of Pygmy Perches (Teleostei: Percichthyidae) with an Assessment of the Major Historical Influences on Aquatic Biogeography in Southern Australia

(2011) Peter J. Unmack et al.   SYSTEMATIC BIOLOGY

Genomic approaches with natural fish populations from polluted environments

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Building evolutionary resilience for conserving biodiversity under climate change

(2010) Carla M. Sgrò et al.   Evolutionary Applications

Nuptial coloration varies with ambient light environment in a freshwater fish

(2010) J. R. MORRONGIELLO et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Functional Genomics of Physiological Plasticity and Local Adaptation in Killifish

(2010) A. Whitehead et al.   JOURNAL OF HEREDITY

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

(2010) A. WHITEHEAD et al.   MOLECULAR ECOLOGY

Phenomics: the next challenge

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

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

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

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

Physiological changes in reproductively active rainbowfish (Melanotaenia fluviatilis) following exposure to naphthalene

(2009) Carmel A. Pollino et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Changes in gene expression due to chronic exposure to environmental pollutants

(2008) Marjorie F. Oleksiak   AQUATIC TOXICOLOGY

Adaptive Phenotypic Plasticity in Response to Climate Change in a Wild Bird Population

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Climate change and evolution: disentangling environmental and genetic responses

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