Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus )

Trapped within the city: integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization

(2017) André Lourenço et al.   MOLECULAR ECOLOGY

Peromyscus transcriptomics: Understanding adaptation and gene expression plasticity within and between species of deer mice

(2017) Jason Munshi-South et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Dietary adaptation of FADS genes in Europe varied across time and geography

(2017) Kaixiong Ye et al.   Nature Ecology & Evolution

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Urbanization shapes the demographic history of a native rodent (the white-footed mouse,Peromyscus leucopus) in New York City

(2016) Stephen E. Harris et al.   Biology Letters

Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

(2016) Jason Munshi-South et al.   Evolutionary Applications

Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri

(2016) C Rellstab et al.   HEREDITY

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Urbanization drives the evolution of parallel clines in plant populations

(2016) Ken A. Thompson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

(2016) N. M. Reid et al.   SCIENCE

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Inference of Gorilla Demographic and Selective History from Whole-Genome Sequence Data

(2015) Kimberly F. McManus et al.   MOLECULAR BIOLOGY AND EVOLUTION

A practical guide to environmental association analysis in landscape genomics

(2015) Christian Rellstab et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

Adaptive evolution in urban ecosystems

(2014) Colin M. Donihue et al.   AMBIO

Disease and freeways drive genetic change in urban bobcat populations

(2014) Laurel E. K. Serieys et al.   Evolutionary Applications

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

(2014) Juha Merilä et al.   Evolutionary Applications

Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree speciesAlnus glutinosa

(2014) Hanne De Kort et al.   MOLECULAR ECOLOGY

Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

(2014) L. Zhou et al.   MOLECULAR ECOLOGY

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Genome scan methods against more complex models: when and how much should we trust them?

(2014) Pierre de Villemereuil et al.   MOLECULAR ECOLOGY

Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

(2014) Stephen E. Harris et al.   Molecular Ecology Resources

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

Advances and limits of using population genetics to understand local adaptation

(2014) Peter Tiffin et al.   TRENDS IN ECOLOGY & EVOLUTION

Insulin Receptor Signaling in Normal and Insulin-Resistant States

(2014) J. Boucher et al.   Cold Spring Harbor Perspectives in Biology

Urban park characteristics, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus) populations in New York City

(2014) Jason Munshi-South et al.   PeerJ

Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mousePeromyscus eremicus

(2014) Matthew D. MacManes et al.   PeerJ

Glycine metabolism in animals and humans: implications for nutrition and health

(2013) Weiwei Wang et al.   AMINO ACIDS

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Cranial size has increased over 133 years in a common bat,Pipistrellus kuhlii: a response to changing climate or urbanization?

(2013) Alessandra Tomassini et al.   JOURNAL OF BIOGEOGRAPHY

Genomic Divergence during Speciation Driven by Adaptation to Altitude

(2013) Mark A. Chapman et al.   MOLECULAR BIOLOGY AND EVOLUTION

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Candidate gene polymorphisms for behavioural adaptations during urbanization in blackbirds

(2013) J. C. Mueller et al.   MOLECULAR ECOLOGY

Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice

(2013) Jesse N. Weber et al.   NATURE

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area

(2013) Stephen E. Harris et al.   PLoS One

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

(2013) C. Natarajan 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

Adaptive divergence along environmental gradients in a climate-change-sensitive mammal

(2013) P. Henry et al.   Ecology and Evolution

Genetic structure of the white-footed mouse in the context of the emergence of Lyme disease in southern Québec

(2013) Anita Rogic et al.   Ecology and Evolution

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

(2012) MORTEN T. LIMBORG et al.   MOLECULAR ECOLOGY

Urban landscape genetics: canopy cover predicts gene flow between white-footed mouse (Peromyscus leucopus) populations in New York City

(2012) JASON MUNSHI-SOUTH   MOLECULAR ECOLOGY

Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

(2012) Pierre De Wit et al.   MOLECULAR ECOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Matthew V. Rockman   EVOLUTION

Newly rare or newly common: evolutionary feedbacks through changes in population density and relative species abundance, and their management implications

(2011) Richard A. Lankau et al.   Evolutionary Applications

Evolution and behavioural responses to human-induced rapid environmental change

(2011) Andrew Sih et al.   Evolutionary Applications

Joint analysis of demography and selection in population genetics: where do we stand and where could we go?

(2011) JUNRUI LI et al.   MOLECULAR ECOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

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

Mechanistic Basis of Resistance to PCBs in Atlantic Tomcod from the Hudson River

(2011) I. Wirgin et al.   SCIENCE

Urban conservation genetics: Study of a terrestrial salamander in the city

(2010) Sarah Noël et al.   BIOLOGICAL CONSERVATION

Searching for Footprints of Positive Selection in Whole-Genome SNP Data From Nonequilibrium Populations

(2010) P. Pavlidis et al.   GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations

(2010)   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Comparing three different methods to detect selective loci using dominant markers

(2010) A. PÉREZ-FIGUEROA et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genetic differences in hemoglobin function between highland and lowland deer mice

(2010) J. F. Storz et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Rapid, pervasive genetic differentiation of urban white-footed mouse (Peromyscus leucopus) populations in New York City

(2010) JASON MUNSHI-SOUTH et al.   MOLECULAR ECOLOGY

Comparative transcriptomics implicates mechanisms of evolved pollution tolerance in a killifish population

(2010) A. WHITEHEAD et al.   MOLECULAR ECOLOGY

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

(2010) S. R. Grossman et al.   SCIENCE

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

Obesity and nonalcoholic fatty liver disease: Biochemical, metabolic, and clinical implications

(2009) Elisa Fabbrini et al.   HEPATOLOGY

Who believes in whole-genome scans for selection?

(2009) J Hermisson   HEREDITY

The worm in the fruit of the mitochondrial DNA tree

(2009) F Balloux   HEREDITY

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

Genome-wide scans for footprints of natural selection

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

Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin

(2009) J. F. Storz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the Origin and Spread of an Adaptive Allele in Deer Mice

(2009) C. R. Linnen et al.   SCIENCE

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

NATURAL SELECTION ALONG AN ENVIRONMENTAL GRADIENT: A CLASSIC CLINE IN MOUSE PIGMENTATION

(2008) Lynne M. Mullen et al.   EVOLUTION

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

(2008) M. Foll et al.   GENETICS

Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae)

(2008) D. C. S. G. Oliveira et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genomics: a new generation of genome scans to bridge the gap with functional genomics

(2008) AURÉLIE BONIN   MOLECULAR ECOLOGY

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Rapid evolution of seed dispersal in an urban environment in the weed Crepis sancta

(2008) P.-O. Cheptou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid morphological and genetic change in Chicago-areaPeromyscus

(2007) OLIVER R. W. PERGAMS et al.   MOLECULAR ECOLOGY

Adaptation from standing genetic variation

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