Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod

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

Rapid evolution generates synergism between multiple stressors: Linking theory and an evolution experiment

(2021) James A. Orr et al.   GLOBAL CHANGE BIOLOGY

Selection Experiments in the Sea: What Can Experimental Evolution Tell Us About How Marine Life Will Respond to Climate Change?

(2021) Morgan W. Kelly et al.   BIOLOGICAL BULLETIN

Global patterns in copepod thermal tolerance

(2021) Matthew Sasaki et al.   JOURNAL OF PLANKTON RESEARCH

Rapid, but limited, zooplankton adaptation to simultaneous warming and acidification

(2021) Hans G. Dam et al.   Nature Climate Change

The Importance of Genetic Redundancy in Evolution

(2020) Áki J. Láruson et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogeography of Acartia tonsa Dana, 1849 (Calanoida: Copepoda) and phylogenetic reconstruction of the genus Acartia Dana, 1846

(2020) Nicole J. Figueroa et al.   Marine Biodiversity

Polygenic adaptation: a unifying framework to understand positive selection

(2020) Neda Barghi et al.   NATURE REVIEWS GENETICS

Estimating the genome-wide contribution of selection to temporal allele frequency change

(2020) Vince Buffalo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary origins of genomic adaptations in an invasive copepod

(2020) David Ben Stern et al.   Nature Ecology & Evolution

Meta‐analysis of multiple driver effects on marine phytoplankton highlights modulating role of p CO 2

(2020) Miriam Seifert et al.   GLOBAL CHANGE BIOLOGY

Variation in Thermal Tolerance and Its Relationship to Mitochondrial Function Across Populations of Tigriopus californicus

(2019) Alice E. Harada et al.   Frontiers in Physiology

Polygenic adaptation: From sweeps to subtle frequency shifts

(2019) Ilse Höllinger et al.   PLoS Genetics

Genetic redundancy fuels polygenic adaptation in Drosophila

(2019) Neda Barghi et al.   PLOS BIOLOGY

The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution

(2019) Tue Sparholt Jørgensen et al.   Genome Biology and Evolution

Acclimation and adaptation of the coastal calanoid copepod Acartia tonsa to ocean acidification: a long-term laboratory investigation

(2019) JAF Langer et al.   MARINE ECOLOGY PROGRESS SERIES

Rare genetic variation and balanced polymorphisms are important for survival in global change conditions

(2019) Reid S. Brennan et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

(2019) Nina O. Therkildsen et al.   SCIENCE

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

(2019) João PL Castro et al.   eLife

The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data

(2019) Vince Buffalo et al.   GENETICS

The DEAD-box RNA helicase Ddx39ab is essential for myocyte and lens development in zebrafish

(2018) Linlin Zhang et al.   DEVELOPMENT

Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-A review

(2018) Philip W. Boyd et al.   GLOBAL CHANGE BIOLOGY

Reproductive isolation and morphological divergence between cryptic lineages of the copepod Acartia tonsa in Chesapeake Bay

(2018) LV Plough et al.   MARINE ECOLOGY PROGRESS SERIES

Multiple modes of adaptation: regulatory and structural evolution in a small heat shock protein gene

(2018) Sumaetee Tangwancharoen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reproductive isolation and morphological divergence between cryptic lineages of the copepod Acartia tonsa in Chesapeake Bay

(2018) LV Plough et al.   MARINE ECOLOGY PROGRESS SERIES

Hurricane-induced selection on the morphology of an island lizard

(2018) Colin M. Donihue et al.   NATURE

Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans

(2018) John K. Kelly et al.   GENETICS

Quantifying Metabolically Driven pH and Oxygen Fluctuations in US Nearshore Habitats at Diel to Interannual Time Scales

(2017) Hannes Baumann et al.   Estuaries and Coasts

Quantifying Selection with Pool-Seq Time Series Data

(2017) Thomas Taus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary consequences of multidriver environmental change in an aquatic primary producer

(2017) Georgina L. Brennan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard

(2017) Shane C. Campbell-Staton et al.   SCIENCE

Multiple Stressors in a Changing World: The Need for an Improved Perspective on Physiological Responses to the Dynamic Marine Environment

(2016) Alex R. Gunderson et al.   Annual Review of Marine Science

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

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

Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

(2016) A. Jonas et al.   GENETICS

Can Population Genetics Adapt to Rapid Evolution?

(2016) Philipp W. Messer et al.   TRENDS IN GENETICS

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

Transgenerational effects alleviate severe fecundity loss during ocean acidification in a ubiquitous planktonic copepod

(2015) Peter Thor et al.   GLOBAL CHANGE BIOLOGY

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

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Efficient Test and Visualization of Multi-Set Intersections

(2015) Minghui Wang et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Selection for complex traits leaves little or no classic signatures of selection

(2014) Kathryn E Kemper et al.   BMC GENOMICS

Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation

(2014) C Schlötterer et al.   HEREDITY

Forensic genomics as a novel tool for identifying the causes of mass mortality events

(2014) Pierre De Wit et al.   Nature Communications

Genome-wide evolutionary response to a heat wave in Drosophila

(2013) F. Rodriguez-Trelles et al.   Biology Letters

A Guide for the Design of Evolve and Resequencing Studies

(2013) Robert Kofler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments

(2013) Ray Tobler et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Meta-analysis reveals complex marine biological responses to the interactive effects of ocean acidification and warming

(2013) Ben P. Harvey et al.   Ecology and Evolution

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data

(2012) Alison F. Feder et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

PUMPING IONS: RAPID PARALLEL EVOLUTION OF IONIC REGULATION FOLLOWING HABITAT INVASIONS

(2011) Carol Eunmi Lee et al.   EVOLUTION

Cryptic diversity and comparative phylogeography of the estuarine copepod Acartia tonsa on the US Atlantic coast

(2011) GANG CHEN et al.   MOLECULAR ECOLOGY

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Limited potential for adaptation to climate change in a broadly distributed marine crustacean

(2011) M. W. Kelly et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

(2011) Thomas L. Turner et al.   PLoS Genetics

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

Paleo-perspectives on ocean acidification

(2010) Carles Pelejero et al.   TRENDS IN ECOLOGY & EVOLUTION

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

RNA helicase Ddx39 is expressed in the developing central nervous system, limb, otic vesicle, branchial arches and facial mesenchyme of Xenopus laevis

(2009) Jonathan M. Wilson et al.   GENE EXPRESSION PATTERNS

Ocean Acidification: The Other CO2Problem

(2008) Scott C. Doney et al.   Annual Review of Marine Science

Effects of climate and overfishing on zooplankton dynamics and ecosystem structure: regime shifts, trophic cascade, and feedback loops in a simple ecosystem

(2008) C. Mollmann et al.   ICES JOURNAL OF MARINE SCIENCE

Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa

(2008) GANG CHEN et al.   MOLECULAR ECOLOGY

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION