The role of plastic and evolved DNA methylation in parallel adaptation of threespine stickleback ( Gasterosteus aculeatus )

Loss of transcriptional plasticity but sustained adaptive capacity after adaptation to global change conditions in a marine copepod

(2022) Reid S. Brennan et al.   Nature Communications

The dynamic response to hypo‐osmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom

(2022) Kala M. Downey et al.   MOLECULAR ECOLOGY

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

(2022) Julia I. Wucherpfennig et al.   Nature Ecology & Evolution

Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

(2021) Melanie Lindner et al.   BMC GENOMICS

An epigenetic clock to estimate the age of living beluga whales

(2021) Eleanor K. Bors et al.   Evolutionary Applications

Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance

(2021) Günter Vogt   JOURNAL OF BIOSCIENCES

Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish

(2021) Arne Jacobs et al.   MOLECULAR ECOLOGY

Nonparallel transcriptional divergence during parallel adaptation

(2021) Eva K. Fischer et al.   MOLECULAR ECOLOGY

Using seasonal genomic changes to understand historical adaptation to new environments: parallel selection on stickleback in highly‐variable estuaries

(2021) Alan Garcia‐Elfring et al.   MOLECULAR ECOLOGY

Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates

(2021) Pedro Andrade et al.   PLoS Genetics

Threespine Stickleback: A Model System For Evolutionary Genomics

(2021) Kerry Reid et al.   Annual Review of Genomics and Human Genetics

Epigenomic modifications induced by hatchery rearing persist in germ line cells of adult salmon after their oceanic migration

(2021) Maeva Leitwein et al.   Evolutionary Applications

Population structure limits parallel evolution in sticklebacks

(2021) Bohao Fang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ageing European lobsters ( Homarus gammarus ) using DNA methylation of evolutionarily conserved ribosomal DNA

(2021) Eleanor A. Fairfield et al.   Evolutionary Applications

Epigenetic inheritance and reproductive mode in plants and animals

(2021) Dafni Anastasiadi et al.   TRENDS IN ECOLOGY & EVOLUTION

Epigenetics and the city: Non‐parallel DNA methylation modifications across pairs of urban‐forest Great tit populations

(2021) Aude E. Caizergues et al.   Evolutionary Applications

Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

(2021) Grégoire Vernaz et al.   Nature Communications

Phenotypic convergence is not mirrored at the protein level in a lizard adaptive radiation

(2020) Russell Corbett-Detig et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs

(2020) Alexandra Weyrich et al.   MAMMALIAN GENOME

Gene duplication in the honeybee: Patterns of DNA methylation, gene expression, and genomic environment

(2020) Carl J Dyson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population transcriptomics reveals weak parallel genetic basis in repeated marine and freshwater divergence in nine‐spined sticklebacks

(2020) Yingnan Wang et al.   MOLECULAR ECOLOGY

Two different epigenetic information channels in wild three-spined sticklebacks are involved in salinity adaptation

(2020) Melanie J. Heckwolf et al.   Science Advances

Phenotypic plasticity as a long-term memory easing readaptations to ancestral environments

(2020) Wei-Chin Ho et al.   Science Advances

On the causes of geographically heterogeneous parallel evolution in sticklebacks

(2020) Bohao Fang et al.   Nature Ecology & Evolution

Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations

(2020) Isabel S. Magalhaes et al.   Nature Ecology & Evolution

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

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

Sparse evidence for selection on phenotypic plasticity in response to temperature

(2019) Pieter A. Arnold et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change

(2019) Rebecca J. Fox et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks

(2019) Jukka-Pekka Verta et al.   eLife

DNA Methylation Changes in the Sperm of Captive-Reared Fish: A Route to Epigenetic Introgression in Wild Populations

(2019) Deiene Rodriguez Barreto et al.   MOLECULAR BIOLOGY AND EVOLUTION

Shared patterns of genome-wide differentiation are more strongly predicted by geography than by ecology

(2019) Diana Jessie Rennison et al.   AMERICAN NATURALIST

Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast

(2019) Hernán E. Morales et al.   Science Advances

The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity

(2018) David C H Metzger et al.   Genome Biology and Evolution

Genome-wide DNA methylation signatures of infection status in Trinidadian guppies (Poecilia reticulata )

(2018) Juntao Hu et al.   MOLECULAR ECOLOGY

The Evolution of Gene Expression in cis and trans

(2018) Sarah A. Signor et al.   TRENDS IN GENETICS

Evolutionary adaptations to new environments generally reverse plastic phenotypic changes

(2018) Wei-Chin Ho et al.   Nature Communications

Convergent evolution of gene expression in two high-toothed stickleback populations

(2018) James C. Hart et al.   PLoS Genetics

(Non)Parallel Evolution

(2018) Daniel I. Bolnick et al.   Annual Review of Ecology Evolution and Systematics

OUP accepted manuscript

(2018)   INTEGRATIVE AND COMPARATIVE BIOLOGY

Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes

(2017) Asano Ishikawa et al.   EVOLUTION

Heritable gene expression differences between lake and stream stickleback include both parallel and antiparallel components

(2017) D Hanson et al.   HEREDITY

Epigenetics in natural animal populations

(2017) J. Hu et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Non-parallel divergence across freshwater and marine three-spined stickleback Gasterosteus aculeatus populations

(2017) J. M. Pujolar et al.   JOURNAL OF FISH BIOLOGY

Genome-Wide DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and Freshwater Conditions

(2017) Artem V. Artemov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon

(2017) Jérémy Le Luyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Epigenetics in ecology and evolution: what we know and what we need to know

(2016) Koen J. F. Verhoeven et al.   MOLECULAR ECOLOGY

Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice

(2015) Luz D. Orozco et al.   Cell Metabolism

Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity

(2015) C J Murren et al.   HEREDITY

Does plasticity enhance or dampen phenotypic parallelism? A test with three lake-stream stickleback pairs

(2015) K. B. Oke et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Transcriptomic responses to environmental temperature in eurythermal and stenothermal fishes

(2015) C. A. Logan et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Genome-Wide DNA Methylation Patterns in Wild Samples of Two Morphotypes of Threespine Stickleback (Gasterosteus aculeatus)

(2015) Gilbert Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Paternal intergenerational epigenetic response to heat exposure in male Wild guinea pigs

(2015) Alexandra Weyrich et al.   MOLECULAR ECOLOGY

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

(2015) Cameron K. Ghalambor et al.   NATURE

DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip

(2015) Denise L Walker et al.   Epigenomics

genomation: a toolkit to summarize, annotate and visualize genomic intervals

(2014) A. Akalin et al.   BIOINFORMATICS

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

(2014) Edith Heard et al.   CELL

Identification of methylation quantitative trait loci (mQTLs) influencing promoter DNA methylation of alcohol dependence risk genes

(2014) Huiping Zhang et al.   HUMAN GENETICS

DNA methylation and evolution of duplicate genes

(2014) T. E. Keller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus

(2014) Nadezhda V. Terekhanova et al.   PLoS Genetics

Parallelism Isn’t Perfect: Could Disease and Flooding Drive a Life-History Anomaly in Trinidadian Guppies?

(2013) Sarah W. Fitzpatrick et al.   AMERICAN NATURALIST

How epigenetic mutations can affect genetic evolution: Model and mechanism

(2013) Filippos D. Klironomos et al.   BIOESSAYS

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Bridging the transgenerational gap with epigenetic memory

(2013) Jana P. Lim et al.   TRENDS IN GENETICS

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Fine-scale local adaptation in life histories along a continuous environmental gradient in Trinidadian guppies

(2012) Julián Torres Dowdall et al.   FUNCTIONAL ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Epigenetics and the environment: emerging patterns and implications

(2012) Robert Feil et al.   NATURE REVIEWS GENETICS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

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

(2012) Elisa Schaum et al.   Nature Climate Change

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution

(2011) D. B. Wake et al.   SCIENCE

DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent Sex Ratio Shifts in the European Sea Bass

(2011) Laia Navarro-Martín et al.   PLoS Genetics

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Covariance between Genetic and Environmental Influences across Ecological Gradients

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

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

(2009) R. LANDE   JOURNAL OF EVOLUTIONARY BIOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Natural Selection on a Major Armor Gene in Threespine Stickleback

(2008) R. D. H. Barrett et al.   SCIENCE