History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei)

Complementary sex determination, inbreeding depression and inbreeding avoidance in a gregarious sawfly

(2016) K E Harper et al.   HEREDITY

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species

(2016) Tanya N. Phung et al.   PLoS Genetics

Detection and Removal of PCR Duplicates in Population Genomic ddRAD Studies by Addition of a Degenerate Base Region (DBR) in Sequencing Adapters

(2016) Hannah Schweyen et al.   BIOLOGICAL BULLETIN

Computationally Efficient Composite Likelihood Statistics for Demographic Inference

(2015) Alec J. Coffman et al.   MOLECULAR BIOLOGY AND EVOLUTION

The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

(2015) Stefan Laurent et al.   MOLECULAR ECOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Impact of range expansions on current human genomic diversity

(2014) Vitor Sousa et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genome-Wide Congealing and Rapid Transitions across the Speciation Continuum during Speciation with Gene Flow

(2014) Jeffrey L. Feder et al.   JOURNAL OF HEREDITY

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

Isolation by environment

(2014) Ian J. Wang et al.   MOLECULAR ECOLOGY

Theoretical models of the influence of genomic architecture on the dynamics of speciation

(2014) Samuel M. Flaxman et al.   MOLECULAR ECOLOGY

Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation?

(2014) Lewis G. Spurgin et al.   MOLECULAR ECOLOGY

A practical guide to measuring local adaptation

(2013) François Blanquart et al.   ECOLOGY LETTERS

Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology

(2013) Aaron B. A. Shafer et al.   ECOLOGY LETTERS

DISENTANGLING THE EFFECTS OF GEOGRAPHIC AND ECOLOGICAL ISOLATION ON GENETIC DIFFERENTIATION

(2013) Gideon S. Bradburd et al.   EVOLUTION

EXAMINING THE FULL EFFECTS OF LANDSCAPE HETEROGENEITY ON SPATIAL GENETIC VARIATION: A MULTIPLE MATRIX REGRESSION APPROACH FOR QUANTIFYING GEOGRAPHIC AND ECOLOGICAL ISOLATION

(2013) Ian J. Wang   EVOLUTION

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

(2013) Jason P. Sexton et al.   EVOLUTION

GENETIC HITCHHIKING AND THE DYNAMIC BUILDUP OF GENOMIC DIVERGENCE DURING SPECIATION WITH GENE FLOW

(2013) Samuel M. Flaxman et al.   EVOLUTION

Mantel test in population genetics

(2013) José Alexandre F. Diniz-Filho et al.   GENETICS AND MOLECULAR BIOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization

(2013) Luisa Orsini et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Neutral genomic regions refine models of recent rapid human population growth

(2013) E. Gazave et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dismantling the Mantel tests

(2013) Gilles Guillot et al.   Methods in Ecology and Evolution

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

(2013) Kelley Harris et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Quantifying the roles of ecology and geography in spatial genetic divergence

(2012) Ian J. Wang et al.   ECOLOGY LETTERS

GENETIC DIVERGENCE IS DECOUPLED FROM ECOLOGICAL DIVERSIFICATION IN THE HAWAIIAN NESOSYDNE PLANTHOPPERS

(2012) Kari Roesch Goodman et al.   EVOLUTION

LARGE-SCALE CANDIDATE GENE SCAN REVEALS THE ROLE OF CHEMORECEPTOR GENES IN HOST PLANT SPECIALIZATION AND SPECIATION IN THE PEA APHID

(2012) Carole M. Smadja et al.   EVOLUTION

The Role of Background Selection in Shaping Patterns of Molecular Evolution and Variation: Evidence from Variability on the Drosophila X Chromosome

(2012) B. Charlesworth   GENETICS

Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion

(2012) S. Lukic et al.   GENETICS

The trouble with isolation by distance

(2012) PATRICK G. MEIRMANS   MOLECULAR ECOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

LocalizingFSToutliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow

(2012) Sara Via et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers

(2012) Eva-Maria Willing et al.   PLoS One

Subsampling methods for genomic inference

(2011) Peter J. Bickel et al.   Annals of Applied Statistics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Divergent host plant specialization as the critical driving force in speciation between populations of a phytophagous ladybird beetle

(2011) K. W. MATSUBAYASHI et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Isolation by adaptation in Neochlamisus leaf beetles: host-related selection promotes neutral genomic divergence

(2011) DANIEL J. FUNK et al.   MOLECULAR ECOLOGY

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

No evidence for biased co-transmission of speciation islands in Anopheles gambiae

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

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

(2011) Nicola J. Nadeau 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

Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

(2011) Kirk E. Lohmueller et al.   PLoS Genetics

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection

(2010) E. M. Kenny et al.   DNA RESEARCH

Host-associated differentiation and evidence for sexual reproduction in Iranian populations of the cotton aphid,Aphis gossypii

(2010) Jabraeil Razmjou et al.   ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

(2010) L. Chikhi 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

Genomic signals of diversification along ecological gradients in a tropical lizard

(2010) ADAM H. FREEDMAN et al.   MOLECULAR ECOLOGY

When can ecological speciation be detected with neutral loci?

(2010) XAVIER THIBERT-PLANTE et al.   MOLECULAR ECOLOGY

Spurious correlations and inference in landscape genetics

(2010) SAMUEL A. CUSHMAN 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

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Evaluation of Five Methods for Total DNA Extraction from Western Corn Rootworm Beetles

(2010) Hong Chen et al.   PLoS One

Widespread genomic divergence during sympatric speciation

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

A test of the sympatric host race formation hypothesis in Neodiprion (Hymenoptera: Diprionidae)

(2010) C. R. Linnen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

PASSaGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2

(2010) Michael S. Rosenberg et al.   Methods in Ecology and Evolution

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Inferring the past from the present phylogeographic structure of North American forest trees: seeing the forest for the genes

(2009) Juan P. Jaramillo-Correa et al.   CANADIAN JOURNAL OF FOREST RESEARCH

Ecological speciation in phytophagous insects

(2009) Kei W. Matsubayashi et al.   ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA

The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

(2009) T. Stadler et al.   GENETICS

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

(2009) P. D. Keightley et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

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

Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance?

(2009) A. C. Frantz et al.   JOURNAL OF APPLIED ECOLOGY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog

(2009) IAN J. WANG et al.   MOLECULAR ECOLOGY

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Ecologically dependent postmating isolation between sympatric host forms of Neochlamisus bebbianae leaf beetles

(2009) S. P. Egan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

Ecological explanations for (incomplete) speciation

(2009) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

(2009) Graham McVicker et al.   PLoS Genetics

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

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

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

(2008) Thibaut Jombart   BIOINFORMATICS

Why sampling scheme matters: the effect of sampling scheme on landscape genetic results

(2008) Michael K. Schwartz et al.   CONSERVATION GENETICS

Disentangling interactions between adaptive divergence and gene flow when ecology drives diversification

(2008) Katja Räsänen et al.   ECOLOGY LETTERS

HETEROGENEOUS GENOMIC DIFFERENTIATION BETWEEN WALKING-STICK ECOTYPES: "ISOLATION BY ADAPTATION" AND MULTIPLE ROLES FOR DIVERGENT SELECTION

(2008) Patrik Nosil et al.   EVOLUTION

Comparison of Methods for Species-Tree Inference in the Sawfly Genus Neodiprion (Hymenoptera: Diprionidae)

(2008) Catherine R. Linnen et al.   SYSTEMATIC BIOLOGY