Demographic history and genomics of local adaptation in blue tit populations

Going beyond SNPs: the role of structural genomic variants in adaptive evolution and species diversification

(2019) Maren Wellenreuther et al.   MOLECULAR ECOLOGY

The genomic complexity of a large inversion in great tits

(2019) Vinicius H da Silva et al.   Genome Biology and Evolution

Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations

(2018) Brenna R. Forester et al.   MOLECULAR ECOLOGY

Heritability estimates from genomewide relatedness matrices in wild populations: Application to a passerine, using a small sample size

(2018) C. Perrier et al.   Molecular Ecology Resources

Contrasting results from GWAS and QTL mapping on wing length in great reed warblers

(2018) Bengt Hansson et al.   Molecular Ecology Resources

Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata

(2018) Pierre-Alexandre Gagnaire et al.   Genome Biology and Evolution

Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review

(2018) Hugo Cayuela et al.   MOLECULAR ECOLOGY

Inferences of genetic architecture of bill morphology in house sparrow using a high-density SNP array point to a polygenic basis

(2018) Sarah L. Lundregan et al.   MOLECULAR ECOLOGY

Local PCA Shows How the Effect of Population Structure Differs Along the Genome

(2018) Han Li et al.   GENETICS

Conserved G-matrices of morphological and life-history traits among continental and island blue tit populations

(2017) B Delahaie et al.   HEREDITY

Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish

(2017) Charles Perrier et al.   MOLECULAR ECOLOGY

Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic

(2017) Marion Sinclair-Waters et al.   MOLECULAR ECOLOGY

Responsible RAD: Striving for best practices in population genomic studies of adaptation

(2017) David B. Lowry et al.   Molecular Ecology Resources

Deriving genotypes from RAD-seq short-read data using Stacks

(2017) Nicolas C Rochette et al.   Nature Protocols

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

(2017) Jessica Stapley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recent natural selection causes adaptive evolution of an avian polygenic trait

(2017) Mirte Bosse et al.   SCIENCE

A sex-chromosome inversion causes strong overdominance for sperm traits that affect siring success

(2017) Ulrich Knief et al.   Nature Ecology & Evolution

A sex-linked supergene controls sperm morphology and swimming speed in a songbird

(2017) Kang-Wook Kim 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

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

(2016) Elaina M. Tuttle et al.   CURRENT BIOLOGY

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

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

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

(2016) D. R. Schrider et al.   GENETICS

Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

(2016) Quentin Rougemont et al.   MOLECULAR ECOLOGY

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

(2016) M. Szulkin et al.   MOLECULAR ECOLOGY

A beak size locus in Darwins finches facilitated character displacement during a drought

(2016) S. Lamichhaney et al.   SCIENCE

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

(2016) N. M. Reid et al.   SCIENCE

Detecting Polygenic Evolution: Problems, Pitfalls, and Promises

(2016) Maren Wellenreuther et al.   TRENDS IN GENETICS

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

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

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

(2016) Camille Roux et al.   PLOS BIOLOGY

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

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

Local Adaptation by Alleles of Small Effect

(2015) Sam Yeaman   AMERICAN NATURALIST

Genome-wide tests for introgression between cactophilicDrosophilaimplicate a role of inversions during speciation

(2015) Konrad Lohse et al.   EVOLUTION

Mediterranean blue tits as a case study of local adaptation

(2015) Anne Charmantier et al.   Evolutionary Applications

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Sympatric divergence and clinal variation in multiple coloration traits ofFicedulaflycatchers

(2015) T. Laaksonen et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The consequences of not accounting for background selection in demographic inference

(2015) Gregory B. Ewing et al.   MOLECULAR ECOLOGY

Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes

(2015) Brenna R. Forester et al.   MOLECULAR ECOLOGY

Genomic resources and their influence on the detection of the signal of positive selection in genome scans

(2015) S. Manel 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

SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

(2015) Mario Barbato et al.   Frontiers in Genetics

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Isolation by environment

(2014) Ian J. Wang 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

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Assessing Multivariate Constraints to Evolution across Ten Long-Term Avian Studies

(2014) Celine Teplitsky et al.   PLoS One

Advances and limits of using population genetics to understand local adaptation

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

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

A practical guide to measuring local adaptation

(2013) François Blanquart et al.   ECOLOGY LETTERS

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

(2013) Vitor C. Sousa et al.   GENETICS

Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

(2013) Camille Roux 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

Pervasive selection or is it…? why areFSToutliers sometimes so frequent?

(2013) Nicolas Bierne et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

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

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Examining the Role of Effective Population Size on Mitochondrial and Multilocus Divergence Time Discordance in a Songbird

(2013) Brian Tilston Smith et al.   PLoS One

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

(2012) X. Zheng et al.   BIOINFORMATICS

Habitat-Linked Population Genetic Differentiation in the Blue Tit Cyanistes caeruleus

(2012) Melody Porlier et al.   JOURNAL OF HEREDITY

A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities?

(2012) Ronald S. Burton et al.   MOLECULAR ECOLOGY

Investigation of Inversion Polymorphisms in the Human Genome Using Principal Components Analysis

(2012) Jianzhong Ma et al.   PLoS One

Genetic structure reflects natal dispersal movements at different spatial scales in the blue tit, Cyanistes caeruleus

(2011) Joaquín Ortego et al.   ANIMAL BEHAVIOUR

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

(2011) Anna W Santure et al.   BMC GENOMICS

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

(2011) Matthew V. Rockman   EVOLUTION

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

A multi-gene approach reveals a complex evolutionary history in the Cyanistes species group

(2011) JUAN CARLOS ILLERA et al.   MOLECULAR ECOLOGY

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

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Comparison ofFSToutlier tests for SNP loci under selection

(2011) SHAWN R. NARUM et al.   Molecular Ecology Resources

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The complex analytical landscape of gene flow inference

(2011) Peter B. Marko et al.   TRENDS IN ECOLOGY & EVOLUTION

Divergence with Gene Flow: Models and Data

(2010) Catarina Pinho et al.   Annual Review of Ecology Evolution and Systematics

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

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

(2010) David B. Lowry et al.   PLOS BIOLOGY

How and Why Chromosome Inversions Evolve

(2010) Mark Kirkpatrick   PLOS BIOLOGY

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

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

Local adaptation of timing of reproduction: females are in the driver's seat

(2008) Samuel P. Caro et al.   FUNCTIONAL ECOLOGY

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

(2008) M. Foll et al.   GENETICS

A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution

(2008) N. Backstrom et al.   GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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