Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes

The on-again, off-again relationship between mitochondrial genomes and species boundaries

(2017) Daniel B. Sloan et al.   MOLECULAR ECOLOGY

GppFst: genomic posterior predictive simulations ofFSTanddXYfor identifying outlier loci from population genomic data

(2016) Richard H. Adams et al.   BIOINFORMATICS

Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

(2016) Darren E. Irwin et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

(2016) Bret A. Payseur et al.   MOLECULAR ECOLOGY

minotaur: A platform for the analysis and visualization of multivariate results from genome scans with R Shiny

(2016) Robert Verity et al.   Molecular Ecology Resources

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

The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments

(2015) Anne-Laure Ferchaud et al.   MOLECULAR ECOLOGY

Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox)

(2015) Drew R. Schield et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

(2015) Celine Caseys et al.   Tree Genetics & Genomes

Biased Gene Conversion Skews Allele Frequencies in Human Populations, Increasing the Disease Burden of Recessive Alleles

(2014) Joseph Lachance et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species

(2014) Cassandra N. Trier et al.   PLoS Genetics

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

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

(2013) Samuel M. Flaxman et al.   EVOLUTION

The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

(2013) T. L. Parchman et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Advances in Ecological Speciation: an integrative approach

(2013) Rui Faria et al.   MOLECULAR ECOLOGY

Phylogenetic relationships of the enigmatic longtailed rattlesnakes (Crotalus ericsmithi, C. lannomi, and C. stejnegeri)

(2013) Jacobo Reyes-Velasco et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

(2013) F. J. Vonk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Do highly divergent loci reside in genomic regions affecting reproductive isolation? A test using next-generation sequence data in Timema stick insects

(2012) Patrik Nosil et al.   BMC EVOLUTIONARY BIOLOGY

GENOMIC REGIONS WITH A HISTORY OF DIVERGENT SELECTION AFFECT FITNESS OF HYBRIDS BETWEEN TWO BUTTERFLY SPECIES

(2012) Zachariah Gompert et al.   EVOLUTION

Comparative Genomics Reveals Adaptive Protein Evolution and a Possible Cytonuclear Incompatibility between European and American Eels

(2012) Pierre-Alexandre Gagnaire et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide architecture of reproductive isolation in a naturally occurring hybrid zone betweenMus musculus musculusandM. m. domesticus

(2012) VÁCLAV JANOUŠEK et al.   MOLECULAR ECOLOGY

Forecasting changes in population genetic structure of alpine plants in response to global warming

(2012) FLORA JAY et al.   MOLECULAR ECOLOGY

bgc: Software for Bayesian estimation of genomic clines

(2012) Z. Gompert et al.   Molecular Ecology Resources

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Predation and the Maintenance of Color Polymorphism in a Habitat Specialist Squamate

(2012) Vincent R. Farallo et al.   PLoS One

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Bayesian estimation of genomic clines

(2011) ZACHARIAH GOMPERT et al.   MOLECULAR ECOLOGY

Genomics of isolation in hybrids

(2011) Z. Gompert 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

Evaluation of a Bayesian Coalescent Method of Species Delimitation

(2011) Chi Zhang et al.   SYSTEMATIC BIOLOGY

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

Using differential introgression in hybrid zones to identify genomic regions involved in speciation

(2010) BRET A. PAYSEUR   Molecular Ecology Resources

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

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Genetics and ecological speciation

(2009) D. Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers

(2008) Julianno B. M. Sambatti et al.   ECOLOGY LETTERS

COMPARING CLINES ON MOLECULAR AND PHENOTYPIC TRAITS IN HYBRID ZONES: A WINDOW ON TENSION ZONE MODELS

(2008) Laurène Gay et al.   EVOLUTION

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

(2008) Patrik Nosil et al.   EVOLUTION

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

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

Confounding between recombination and selection, and the Ped/Pop method for detecting selection

(2008) P. F. O'Reilly et al.   GENOME RESEARCH

Hybrid breakdown and mitochondrial dysfunction in hybrids of Nasonia parasitoid wasps

(2008) C. K. ELLISON et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence

(2008) R. J. Kulathinal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA