Great tits and the city: Distribution of genomic diversity and gene-environment associations along an urbanization gradient

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

(2017) Stephen E. Harris et al.   MOLECULAR ECOLOGY

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

RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al . (2016)

(2017) Garrett J. McKinney et al.   Molecular Ecology Resources

Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations

(2017) Julian M. Catchen et al.   Molecular Ecology Resources

Detecting gene subnetworks under selection in biological pathways

(2017) Alexandre Gouy et al.   NUCLEIC ACIDS RESEARCH

Global urban signatures of phenotypic change in animal and plant populations

(2017) Marina Alberti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent natural selection causes adaptive evolution of an avian polygenic trait

(2017) Mirte Bosse et al.   SCIENCE

Evolution of life in urban environments

(2017) Marc T. J. Johnson et al.   SCIENCE

Genomic Quantitative Genetics to Study Evolution in the Wild

(2017) Phillip Gienapp et al.   TRENDS IN ECOLOGY & EVOLUTION

Environment-Dependent Genotype-Phenotype Associations in Avian Breeding Time

(2017) Phillip Gienapp et al.   Frontiers in Genetics

Transcriptome analysis of a wild bird reveals physiological responses to the urban environment

(2017) Hannah Watson et al.   Scientific Reports

Experimental demonstration of an ecological trap for a wild bird in a human-transformed environment

(2016) Virginie Demeyrier et al.   ANIMAL BEHAVIOUR

Multidimensional environmental predictors of variation in avian forest and city life histories

(2016) Philipp Sprau et al.   BEHAVIORAL ECOLOGY

Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits

(2016) Mélissa Lemoine et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire et al.   Current Zoology

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

Genomics of local adaptation with gene flow

(2016) Anna Tigano et al.   MOLECULAR ECOLOGY

Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits

(2016) M. Szulkin et al.   MOLECULAR ECOLOGY

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

Human influences on evolution, and the ecological and societal consequences

(2016) Andrew P. Hendry et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary signals of selection on cognition from the great tit genome and methylome

(2016) Veronika N. Laine et al.   Nature Communications

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire et al.   Current Zoology

Urbanization affects neophilia and risk-taking at bird-feeders

(2016) Piotr Tryjanowski et al.   Scientific Reports

Local Adaptation by Alleles of Small Effect

(2015) Sam Yeaman   AMERICAN NATURALIST

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

Successful Colonization of a Novel Urban Environment is Associated with an Urban Behavioural Syndrome in a Reed-Nesting Waterbird

(2015) Piotr Minias   ETHOLOGY

Mediterranean blue tits as a case study of local adaptation

(2015) Anne Charmantier et al.   Evolutionary Applications

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation

(2015) Wolfgang Stephan   MOLECULAR ECOLOGY

Eco-evolutionary dynamics in an urbanizing planet

(2015) Marina Alberti   TRENDS IN ECOLOGY & EVOLUTION

Adaptive evolution in urban ecosystems

(2014) Colin M. Donihue et al.   AMBIO

PRSice: Polygenic Risk Score software

(2014) Jack Euesden et al.   BIOINFORMATICS

Anthropopressure gradients and the population genetic structure of Apodemus agrarius

(2014) Tomasz Gortat et al.   CONSERVATION GENETICS

Testing for Hardy–Weinberg Proportions: Have We Lost the Plot?

(2014) Robin S. Waples   JOURNAL OF HEREDITY

A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers

(2014) M. F. J. Aronson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Explaining additional genetic variation in complex traits

(2014) Matthew R. Robinson et al.   TRENDS IN GENETICS

A Population Genetic Signal of Polygenic Adaptation

(2014) Jeremy J. Berg et al.   PLoS Genetics

Urbanization and its effects on personality traits: a result of microevolution or phenotypic plasticity?

(2013) Ana Catarina Miranda et al.   GLOBAL CHANGE BIOLOGY

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub 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

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

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

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

Candidate gene polymorphisms for behavioural adaptations during urbanization in blackbirds

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

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

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

Conservation genetics of extremely isolated urban populations of the northern dusky salamander (Desmognathus fuscus) in New York City

(2013) Jason Munshi-South et al.   PeerJ

Boldness behavior and stress physiology in a novel urban environment suggest rapid correlated evolutionary adaptation

(2012) Jonathan W. Atwell et al.   BEHAVIORAL ECOLOGY

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Genetic structure in urban and rural populations of Apodemus agrarius in Poland

(2012) Tomasz Gortat et al.   MAMMALIAN BIOLOGY

The design and cross-population application of a genome-wide SNP chip for the great tit Parus major

(2012) NIKKIE E. M. Van BERS et al.   Molecular Ecology Resources

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

High urban population density of birds reflects their timing of urbanization

(2012) Anders Pape Møller et al.   OECOLOGIA

Non-random gene flow: an underappreciated force in evolution and ecology

(2012) Pim Edelaar et al.   TRENDS IN ECOLOGY & EVOLUTION

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Metal pollution indirectly increases oxidative stress in great tit (Parus major) nestlings

(2011) Miia J. Koivula et al.   ENVIRONMENTAL RESEARCH

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

Genetic erosion impedes adaptive responses to stressful environments

(2011) R. Bijlsma et al.   Evolutionary Applications

Condition-dependent clutch desertion in Great Tit (Parus major) females subjected to human disturbance

(2011) Anna Dubiec   JOURNAL OF ORNITHOLOGY

Local adaptation and matching habitat choice in female barn owls with respect to melanic coloration

(2011) A. N. DREISS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Effects of urban matrix on reproductive performance of Great Tit (Parus major) in urban woodlands

(2011) Marcus Hedblom et al.   URBAN ECOSYSTEMS

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

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

Sensory Ecology: Night Lights Alter Reproductive Behavior of Blue Tits

(2010) Travis Longcore   CURRENT BIOLOGY

Contrasting genetic structure of urban and rural populations of the wild rodent Calomys musculinus (Cricetidae, Sigmodontinae)

(2010) Marina B. Chiappero et al.   MAMMALIAN 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

Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient

(2010) VERA L. NUNES et al.   MOLECULAR ECOLOGY

Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data

(2010) PIERRE LEGENDRE et al.   Molecular Ecology Resources

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genetic differentiation in the urban habitat: the great tits (Parus major) of the parks of Barcelona city

(2009) MATS BJÖRKLUND et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

(2009) Einar E Nielsen et al.   BMC EVOLUTIONARY BIOLOGY

Independent colonization of multiple urban centres by a formerly forest specialist bird species

(2009) K. L. Evans et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

(2008) K. Strimmer   BIOINFORMATICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Dispersal as a means of inbreeding avoidance in a wild bird population

(2008) M. Szulkin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES