Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism

Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas

(2021) Haigang Qi et al.   Molecular Ecology Resources

Adaptation to climate change through genetic accommodation and assimilation of plastic phenotypes

(2019) Morgan Kelly   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary trade-offs between baseline and plastic gene expression in two congeneric oyster species

(2019) Ao Li et al.   Biology Letters

Thermotolerance Divergence Revealed by the Physiological and Molecular Responses in Two Oyster Subspecies of Crassostrea gigas in China

(2019) Hamze Ghaffari et al.   Frontiers in Physiology

Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata

(2018) Pierre-Alexandre Gagnaire et al.   Genome Biology and Evolution

Transcriptomics and Fitness Data Reveal Adaptive Plasticity of Thermal Tolerance in Oysters Inhabiting Different Tidal Zones

(2018) Ao Li et al.   Frontiers in Physiology

Divergence and plasticity shape adaptive potential of the Pacific oyster

(2018) Li Li et al.   Nature Ecology & Evolution

Diversity and Evolution of Living Oysters

(2018) Ximing Guo et al.   JOURNAL OF SHELLFISH RESEARCH

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

(2017) Ao Li et al.   Ecology and Evolution

Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod

(2016) Morgan W. Kelly et al.   FUNCTIONAL ECOLOGY

Can a Network Approach Resolve How Adaptive vs Nonadaptive Plasticity Impacts Evolutionary Trajectories?

(2016) Eva K. Fischer et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Oyster reproduction is affected by exposure to polystyrene microplastics

(2016) Rossana Sussarellu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters ( Crassostrea gigas × Crassostrea angulata ) Using Genotyping-by-Sequencing

(2016) Jinpeng Wang et al.   G3-Genes Genomes Genetics

Molecular Basis for Adaptation of Oysters to Stressful Marine Intertidal Environments

(2016) Guofan Zhang et al.   Annual Review of Animal Biosciences

Gene expression plasticity as a mechanism of coral adaptation to a variable environment

(2016) Carly D. Kenkel et al.   Nature Ecology & Evolution

Selection on oxidative phosphorylation and ribosomal structure as a multigenerational response to ocean acidification in the common copepodPseudocalanus acuspes

(2015) Pierre De Wit et al.   Evolutionary Applications

Immune and stress responses in oysters with insights on adaptation

(2015) Ximing Guo et al.   FISH & SHELLFISH IMMUNOLOGY

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

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

Reef-Specific Patterns of Gene Expression Plasticity in Eastern Oysters (Crassostrea virginica)

(2015) Laura E. Eierman et al.   JOURNAL OF HEREDITY

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

(2015) Cameron K. Ghalambor et al.   NATURE

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Proteomics to study adaptations in marine organisms to environmental stress

(2014) Lars Tomanek   Journal of Proteomics

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides ) from different thermal environments

(2013) C. D. Kenkel et al.   MOLECULAR ECOLOGY

The genomic determinants of genotype × environment interactions in gene expression

(2013) Vladislav Grishkevich et al.   TRENDS IN GENETICS

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

(2012) Pablo Cingolani et al.   FLY

Energy homeostasis as an integrative tool for assessing limits of environmental stress tolerance in aquatic invertebrates

(2012) Inna M. Sokolova et al.   MARINE ENVIRONMENTAL RESEARCH

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

The Physiology of Global Change: Linking Patterns to Mechanisms

(2011) George N. Somero   Annual Review of Marine Science

Growth and reproductive simulation of candidate shellfish species at fish cages in the Southern Mediterranean: Dynamic Energy Budget (DEB) modelling for integrated multi-trophic aquaculture

(2011) G. Sarà et al.   AQUACULTURE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia

(2011) Jianfeng Ren et al.   BMC EVOLUTIONARY BIOLOGY

Classification of a Common Cupped Oyster from Southern China

(2011) Haiyan Wang et al.   JOURNAL OF SHELLFISH RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Local Adaptation in Marine Invertebrates

(2010) Eric Sanford et al.   Annual Review of Marine Science

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Temperature tolerance and energetics: a dynamic energy budget-based comparison of North Atlantic marine species

(2010) V. Freitas et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Rhythms of Gene Expression in a Fluctuating Intertidal Environment

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

Classification of Common Oysters from North China

(2008) Haiyan Wang et al.   JOURNAL OF SHELLFISH RESEARCH

Climate change and evolution: disentangling environmental and genetic responses

(2007) P. GIENAPP et al.   MOLECULAR ECOLOGY