Using genomics to characterize evolutionary potential for conservation of wild populations

Genome-wide evolutionary response to a heat wave in Drosophila

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

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

(2013) Steve Smith et al.   BMC GENOMICS

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

(2013) Michele Vidotto et al.   BMC GENOMICS

Identifying Recent Adaptations in Large-Scale Genomic Data

(2013) Sharon R. Grossman et al.   CELL

Predicting evolutionary responses to climate change in the sea

(2013) Philip L. Munday et al.   ECOLOGY LETTERS

Analysis of the Elodea nuttallii Transcriptome in Response to Mercury and Cadmium Pollution: Development of Sensitive Tools for Rapid Ecotoxicological Testing

(2013) Nicole Regier et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

(2013) A. J. Eckert et al.   GENETICS

Allelic Diversity and Its Implications for the Rate of Adaptation

(2013) A. Caballero et al.   GENETICS

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Gene expression drives local adaptation in humans

(2013) H. B. Fraser   GENOME RESEARCH

Functional transcriptomics in the post-ENCODE era

(2013) J. M. Mudge et al.   GENOME RESEARCH

Key questions in the genetics and genomics of eco-evolutionary dynamics

(2013) A P Hendry   HEREDITY

Ecological Epigenetics: Beyond MS-AFLP

(2013) A. W. Schrey et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Patterns of DNA Methylation Throughout a Range Expansion of an Introduced Songbird

(2013) A. L. Liebl et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

The Role of Methylation of DNA in Environmental Adaptation

(2013) K. B. Flores et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Ecological Epigenetics: An Introduction to the Symposium

(2013) C. C. Ledon-Rettig   INTEGRATIVE AND COMPARATIVE BIOLOGY

Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria

(2013) Ronald C. Taylor et al.   Integrative Biology

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub 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

Gene Coexpression Networks Reveal Key Drivers of Phenotypic Divergence in Lake Whitefish

(2013) Marie Filteau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population

(2013) Anna W. Santure et al.   MOLECULAR ECOLOGY

Next-generation QTL mapping: crowdsourcing SNPs, without pedigrees

(2013) Scott V. Edwards   MOLECULAR ECOLOGY

Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon

(2013) Charles Perrier et al.   MOLECULAR ECOLOGY

Partitioning of genetic variation across the genome using multimarker methods in a wild bird population

(2013) Matthew R. Robinson et al.   MOLECULAR ECOLOGY

Using genomic tools to maintain diversity and fitness in conservation programmes

(2013) María Ángeles Rodríguez de Cara et al.   MOLECULAR ECOLOGY

Crouching variation revealed

(2013) Mark L. Siegal   MOLECULAR ECOLOGY

DNA: Celebrate the unknowns

(2013) Philip Ball   NATURE

Pedigree-Free Estimates of Heritability in the Wild: Promising Prospects for Selfing Populations

(2013) Laurene Gay et al.   PLoS One

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer

(2013) H. V. Siddle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate

(2013) V. L. Sork et al.   Tree Genetics & Genomes

Estimating heritability using genomic data

(2013) John Stanton-Geddes et al.   Methods in Ecology and Evolution

Ubiquitous Polygenicity of Human Complex Traits: Genome-Wide Analysis of 49 Traits in Koreans

(2013) Jian Yang et al.   PLoS Genetics

Accelerating Improvement of Livestock with Genomic Selection

(2013) Theo Meuwissen et al.   Annual Review of Animal Biosciences

Hsp90 is important for fecundity, longevity, and buffering of cryptic deleterious variation in wild fly populations

(2012) Bing Chen et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Quantitative Genetics in the Genomics Era

(2012) William G. Hill   CURRENT GENOMICS

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

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

Impacts of climate change on the future of biodiversity

(2012) Céline Bellard et al.   ECOLOGY LETTERS

ISOLATION BREEDS NAIVETY: ISLAND LIVING ROBS AUSTRALIAN VARANID LIZARDS OF TOAD-TOXIN IMMUNITY VIA FOUR-BASE-PAIR MUTATION

(2012) Beata Ujvari et al.   EVOLUTION

LOST IN THE MAP

(2012) Michael Travisano et al.   EVOLUTION

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity

(2012) H. B. Fraser et al.   GENOME RESEARCH

Personal and population genomics of human regulatory variation

(2012) B. Vernot et al.   GENOME RESEARCH

Environmental Adaptation Contributes to Gene Polymorphism across the Arabidopsis thaliana Genome

(2012) Cheng-Ruei Lee et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

(2012) Tereza Manousaki et al.   MOLECULAR ECOLOGY

Temperature treatments during larval development reveal extensive heritable and plastic variation in gene expression and life history traits

(2012) JOUNI KVIST et al.   MOLECULAR ECOLOGY

Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis

(2012) Tobias L. Lenz et al.   MOLECULAR ECOLOGY

Monitoring adaptive genetic responses to environmental change

(2012) MICHAEL M. HANSEN et al.   MOLECULAR ECOLOGY

Multiple capacitors for natural genetic variation inDrosophila melanogaster

(2012) Kazuo H. Takahashi   MOLECULAR ECOLOGY

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Evidence of widespread selection on standing variation in Europe at height-associated SNPs

(2012) Michael C Turchin et al.   NATURE GENETICS

Predicting demographically sustainable rates of adaptation: can great tit breeding time keep pace with climate change?

(2012) P. Gienapp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary rescue in vertebrates: evidence, applications and uncertainty

(2012) E. Vander Wal et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New Insights into the Role of MHC Diversity in Devil Facial Tumour Disease

(2012) Amanda Lane et al.   PLoS One

Combining Next-Generation Sequencing and Microarray Technology into a Transcriptomics Approach for the Non-Model Organism Chironomus riparius

(2012) Marino Marinković et al.   PLoS One

Dispersal will limit ability of mammals to track climate change in the Western Hemisphere

(2012) C. A. Schloss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomics of adaptation

(2012) J. Radwan et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The role of robustness in phenotypic adaptation and innovation

(2012) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Experimental evolution

(2012) Tadeusz J. Kawecki et al.   TRENDS IN ECOLOGY & EVOLUTION

RNA-Seq Assembly – Are We There Yet?

(2012) Simon Schliesky et al.   Frontiers in Plant Science

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

Predicting the Probability of Outbreeding Depression

(2011) RICHARD FRANKHAM et al.   CONSERVATION BIOLOGY

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

Genomic toolboxes for conservation biologists

(2011) Francesco Angeloni et al.   Evolutionary Applications

Genetic erosion impedes adaptive responses to stressful environments

(2011) R. Bijlsma et al.   Evolutionary Applications

Assessing the benefits and risks of translocations in changing environments: a genetic perspective

(2011) Andrew R. Weeks et al.   Evolutionary Applications

Evolutionary principles and their practical application

(2011) Andrew P. Hendry et al.   Evolutionary Applications

The implications of nongenetic inheritance for evolution in changing environments

(2011) Russell Bonduriansky et al.   Evolutionary Applications

Heritability is not Evolvability

(2011) Thomas F. Hansen et al.   Evolutionary Biology

Genetic Architecture of Flowering-Time Variation inArabidopsis thaliana

(2011) Patrice A. Salomé et al.   GENETICS

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

(2011) M. F. Lin et al.   GENOME RESEARCH

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

Interactions between climate and habitat loss effects on biodiversity: a systematic review and meta-analysis

(2011) Chrystal S. Mantyka-pringle et al.   GLOBAL CHANGE BIOLOGY

Functional genomics of life history variation in a butterfly metapopulation

(2011) CHRISTOPHER W. WHEAT et al.   MOLECULAR ECOLOGY

On statistical methods for estimating heritability in wild populations

(2011) MIKKO J. SILLANPÄÄ   MOLECULAR ECOLOGY

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast

(2011) C. M. HERRERA et al.   MOLECULAR ECOLOGY

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

(2011) Eric J. Hayden et al.   NATURE

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

MHC genotypes associate with resistance to a frog-killing fungus

(2011) A. E. Savage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolution of gene expression and the transcriptome–phenotype relationship

(2011) Peter W. Harrison et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Genotype networks shed light on evolutionary constraints

(2011) Andreas Wagner   TRENDS IN ECOLOGY & EVOLUTION

Systematic Detection of Polygenic cis-Regulatory Evolution

(2011) Hunter B. Fraser et al.   PLoS Genetics

Parallel Adaptive Divergence among Geographically Diverse Human Populations

(2011) Jacob A. Tennessen et al.   PLoS Genetics

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

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The role of gene expression in ecological speciation

(2010) Scott A. Pavey et al.   Annals of the New York Academy of Sciences

What Animal Breeding Has Taught Us about Evolution

(2010) William G. Hill et al.   Annual Review of Ecology Evolution and Systematics

Digital gene expression analysis of the zebra finch genome

(2010) Robert Ekblom et al.   BMC GENOMICS

Interacting Effects of Phenotypic Plasticity and Evolution on Population Persistence in a Changing Climate

(2010) THOMAS E. REED et al.   CONSERVATION BIOLOGY

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

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

Building evolutionary resilience for conserving biodiversity under climate change

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

Genetic Differentiation, Clinal Variation and Phenotypic Associations With Growth Cessation Across the Populus tremula Photoperiodic Pathway

(2010) X.-F. Ma et al.   GENETICS

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

(2010) B. E. Stranger et al.   GENETICS

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

(2010) Robert Ekblom et al.   Genome Biology and Evolution

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

(2010) D. L. Goode et al.   GENOME RESEARCH

Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. Salmonidae)

(2010) S Renaut et al.   HEREDITY

Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonusspp. Salmonidae)

(2010) SÉBASTIEN RENAUT et al.   MOLECULAR ECOLOGY

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Phenomics: the next challenge

(2010) David Houle et al.   NATURE REVIEWS GENETICS

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Understanding natural epigenetic variation

(2010) Christina L. Richards et al.   NEW PHYTOLOGIST

On the origin of species: insights from the ecological genomics of lake whitefish

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

Adaptations to new environments in humans: the role of subtle allele frequency shifts

(2010) A. M. Hancock et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gene expression of DAM5 and DAM6 is suppressed by chilling temperatures and inversely correlated with bud break rate

(2010) S. Jiménez et al.   PLANT MOLECULAR BIOLOGY

Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency

(2010) A. M. Hancock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biodiversity Conservation: Challenges Beyond 2010

(2010) Michael R. W. Rands et al.   SCIENCE

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

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

Population-level declines in Australian predators caused by an invasive species

(2009) J. S. Doody et al.   ANIMAL CONSERVATION

Evolutionary rescue can prevent extinction following environmental change

(2009) Graham Bell et al.   ECOLOGY LETTERS

An ecologist’s guide to the animal model

(2009) Alastair J. Wilson et al.   JOURNAL OF ANIMAL ECOLOGY

Phenotypic correlates ofClockgene variation in a wild blue tit population: evidence for a role in seasonal timing of reproduction

(2009) MIRIAM LIEDVOGEL et al.   MOLECULAR ECOLOGY

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Intense Habitat-Specific Fisheries-Induced Selection at the Molecular Pan I Locus Predicts Imminent Collapse of a Major Cod Fishery

(2009) Einar Árnason et al.   PLoS One

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is Genetic Evolution Predictable?

(2009) D. L. Stern et al.   SCIENCE

Evolutionary consequences of cryptic genetic variation

(2009) Katrina McGuigan et al.   TRENDS IN ECOLOGY & EVOLUTION

The Role of Geography in Human Adaptation

(2009) Graham Coop et al.   PLoS Genetics

New Answers for Old Questions: The Evolutionary Quantitative Genetics of Wild Animal Populations

(2008) Loeske E.B. Kruuk et al.   Annual Review of Ecology Evolution and Systematics

Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

(2008) Luis-Miguel Chevin et al.   GENETICS

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Heritability in the genomics era — concepts and misconceptions

(2008) Peter M. Visscher et al.   NATURE REVIEWS GENETICS

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

Evolutionary potential of hidden genetic variation

(2008) A LEROUZIC et al.   TRENDS IN ECOLOGY & EVOLUTION

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics