Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures inZostera marina, a globally important seagrass

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

(2016) Jeanine L. Olsen et al.   NATURE

How Useful Are Species Distribution Models for Managing Biodiversity under Future Climates?

(2016) Steve J. Sinclair et al.   ECOLOGY AND SOCIETY

Towards the identification of the loci of adaptive evolution

(2015) Carolina Pardo-Diaz et al.   Methods in Ecology and Evolution

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

HTSeq--a Python framework to work with high-throughput sequencing data

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

(2014) Juha Merilä et al.   Evolutionary Applications

Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types

(2014) Susanne U. Franssen et al.   Marine Genomics

The Geography and Body-Size Dependence of Top-Down Forcing in New England's Lobster-Groundfish Interaction

(2013) Richard A Wahle et al.   BULLETIN OF MARINE SCIENCE

Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants

(2013) Thorsten B. H. Reusch   Evolutionary Applications

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

driftsel: an R package for detecting signals of natural selection in quantitative traits

(2013) M. Karhunen et al.   Molecular Ecology Resources

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

(2013) Luke W. Pembleton et al.   Molecular Ecology Resources

QST–FST comparisons: evolutionary and ecological insights from genomic heterogeneity

(2013) Tuomas Leinonen et al.   NATURE REVIEWS GENETICS

Quantitative PCR Reveals Strong Spatial and Temporal Variation of the Wasting Disease Pathogen, Labyrinthula zosterae in Northern European Eelgrass (Zostera marina) Beds

(2013) Anna-Christina Bockelmann et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation

(2012) Christina L. Richards et al.   ECOLOGY LETTERS

Estimating Population-Level Coancestry Coefficients by an Admixture F Model

(2012) M. Karhunen et al.   GENETICS

Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation contributing to systems robustness

(2012) Jenny Gu et al.   Integrative Biology

ORCAE: online resource for community annotation of eukaryotes

(2012) Lieven Sterck et al.   NATURE METHODS

Epigenetic variation creates potential for evolution of plant phenotypic plasticity

(2012) Yuan-Ye Zhang et al.   NEW PHYTOLOGIST

A New Method to Uncover Signatures of Divergent and Stabilizing Selection in Quantitative Traits

(2011) Otso Ovaskainen et al.   GENETICS

Effects of a simulated heat wave on photophysiology and gene expression of high- and low-latitude populations of Zostera marina

(2011) G Winters et al.   MARINE ECOLOGY PROGRESS SERIES

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

Wasting disease regulates long-term population dynamics in a threatened seagrass

(2011) James C. Bull et al.   OECOLOGIA

Overexpression of the trehalose-6-phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice

(2011) Hao-Wen Li et al.   PLANTA

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species

(2011) S. U. Franssen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biodiversity and Climate Change: Integrating Evolutionary and Ecological Responses of Species and Communities

(2010) Sébastien Lavergne et al.   Annual Review of Ecology Evolution and Systematics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Population-specificity of heat stress gene induction in northern and southern eelgrass Zostera marina populations under simulated global warming

(2010) NINA BERGMANN et al.   MOLECULAR ECOLOGY

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Accelerating loss of seagrasses across the globe threatens coastal ecosystems

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

Starch synthase activity and heat shock protein in relation to thermal tolerance of developing wheat grains

(2008) K. V. Sumesh et al.   BIOLOGIA PLANTARUM

Adaptation, migration or extirpation: climate change outcomes for tree populations

(2008) Sally N. Aitken et al.   Evolutionary Applications

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Effects of salinity and water temperature on the ecological performance of Zostera marina

(2007) Lars Brammer Nejrup et al.   AQUATIC BOTANY

Importance of genetic diversity in eelgrass Zostera marina for its resilience to global warming

(2007) A Ehlers et al.   MARINE ECOLOGY PROGRESS SERIES