A genomic perspective on hybridization and speciation

Historical introgression among the American live oaks and the comparative nature of tests for introgression

(2015) Deren A. R. Eaton et al.   EVOLUTION

The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact

(2015) Dorothea Lindtke et al.   EVOLUTION

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

(2015) Konrad Lohse et al.   EVOLUTION

Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

(2015) Jeffrey M. Good et al.   EVOLUTION

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

(2015) Christopher H. Martin et al.   EVOLUTION

Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent

(2015) K. Lohse et al.   GENETICS

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

Functional Organization of the Genome May Shape the Species Boundary in the House Mouse

(2015) Václav Janoušek et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the occurrence of false positives in tests of migration under an isolation-with-migration model

(2015) Jody Hey et al.   MOLECULAR ECOLOGY

IMa2p - parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model

(2015) Arun Sethuraman et al.   Molecular Ecology Resources

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

(2015) Nathan D. Olson et al.   Frontiers in Genetics

LANDSCAPE GENOMICS OFPOPULUS TRICHOCARPA: THE ROLE OF HYBRIDIZATION, LIMITED GENE FLOW, AND NATURAL SELECTION IN SHAPING PATTERNS OF POPULATION STRUCTURE

(2014) Armando Geraldes et al.   EVOLUTION

HOW COMMON IS HOMOPLOID HYBRID SPECIATION?

(2014) Molly Schumer et al.   EVOLUTION

High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline

(2014) Eric Yi Liu et al.   GENETICS

Chromosomal Evolution and Patterns of Introgression in Helianthus

(2014) J. G. Barb et al.   GENETICS

Genome-Wide Patterns of Differentiation Among House Mouse Subspecies

(2014) Megan Phifer-Rixey et al.   GENETICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

(2014) Konrad Lohse et al.   GENETICS

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

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

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Analyses of Three Malaria Vectors Reveals Extensive Shared Polymorphism but Contrasting Population Histories

(2014) Samantha M. O’Loughlin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

(2014) Jeffrey W. Streicher et al.   MOLECULAR ECOLOGY

ABC inference of multi-population divergence with admixture from unphased population genomic data

(2014) John D. Robinson et al.   MOLECULAR ECOLOGY

Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East AsianSusspecies during the Plio-Pleistocene climatic fluctuations

(2014) Laurent A. F. Frantz 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

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

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

Genomic divergence in a ring species complex

(2014) Miguel Alcaide et al.   NATURE

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interspecific introgressive origin of genomic diversity in the house mouse

(2014) Kevin J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speciation with gene flow in equids despite extensive chromosomal plasticity

(2014) Hákon Jónsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Higher levels of sex chromosome heteromorphism are associated with markedly stronger reproductive isolation

(2014) Thiago G. Lima   Nature Communications

Spatial Localization of Recent Ancestors for Admixed Individuals

(2014) Wen-Yun Yang et al.   G3-Genes Genomes Genetics

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

(2014) Kevin J. Liu et al.   PLoS Computational Biology

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

(2014) Miguel Carneiro et al.   PLoS Genetics

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

(2014) Molly Schumer et al.   eLife

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES

(2013) Rose L. Andrew et al.   EVOLUTION

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

(2013) Samuel M. Flaxman et al.   EVOLUTION

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

(2013) Vitor C. Sousa et al.   GENETICS

Higher Levels of Neanderthal Ancestry in East Asians than in Europeans

(2013) Jeffrey D. Wall et al.   GENETICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

(2013) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

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

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

Analyses of genetic ancestry enable key insights for molecular ecology

(2013) Zachariah Gompert et al.   MOLECULAR ECOLOGY

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

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

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Genomic rearrangements and the evolution of clusters of locally adaptive loci

(2013) S. Yeaman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs

(2013) Frank E. Rheindt et al.   SYSTEMATIC BIOLOGY

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

(2013) Yun Yu et al.   SYSTEMATIC BIOLOGY

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Genomic islands of divergence are not affected by geography of speciation in sunflowers

(2013) S. Renaut et al.   Nature Communications

Alternative forms for genomic clines

(2013) Benjamin M. Fitzpatrick   Ecology and Evolution

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

(2013) Krystyna Nadachowska-Brzyska et al.   PLoS Genetics

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

(2013) Kelley Harris et al.   PLoS Genetics

Does the speciation clock tick more slowly in the absence of heteromorphic sex chromosomes?

(2012) Barret C. Phillips et al.   BIOESSAYS

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

(2012) Zachariah Gompert et al.   EVOLUTION

Population Genetics Models of Local Ancestry

(2012) S. Gravel   GENETICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

A beginners guide to SNP calling from high-throughput DNA-sequencing data

(2012) André Altmann et al.   HUMAN GENETICS

Recent nonhybrid origin of sunflower ecotypes in a novel habitat

(2012) Rose L. Andrew et al.   MOLECULAR ECOLOGY

Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

(2012) I. Keller et al.   MOLECULAR ECOLOGY

Genome-wide patterns of divergence and gene flow across a butterfly radiation

(2012) Nicola J. Nadeau et al.   MOLECULAR ECOLOGY

Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species

(2012) Kai N. Stölting et al.   MOLECULAR ECOLOGY

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

(2012) VÁCLAV JANOUŠEK et al.   MOLECULAR ECOLOGY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

The long wait for hybrid sterility in flowering plants

(2012) Donald A. Levin   NEW PHYTOLOGIST

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

The Date of Interbreeding between Neandertals and Modern Humans

(2012) Sriram Sankararaman et al.   PLoS Genetics

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

(2012) Thomas Mailund et al.   PLoS Genetics

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

Genes versus phenotypes in the study of speciation

(2011) Kerry L. Shaw et al.   GENETICA

Quaternary phylogeography: the roots of hybrid zones

(2011) Godfrey M. Hewitt   GENETICA

A General Method for Calculating Likelihoods Under the Coalescent Process

(2011) K. Lohse et al.   GENETICS

Recombination rate variation in closely related species

(2011) C S Smukowski et al.   HEREDITY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone

(2011) LIUYANG WANG et al.   MOLECULAR ECOLOGY

Bayesian estimation of genomic clines

(2011) ZACHARIAH GOMPERT et al.   MOLECULAR ECOLOGY

Interpreting the estimated timing of migration events between hybridizing species

(2011) JARED L. STRASBURG et al.   MOLECULAR ECOLOGY

On the nonidentifiability of migration time estimates in isolation with migration models

(2011) VITOR C. SOUSA et al.   MOLECULAR ECOLOGY

Recombination rates in admixed individuals identified by ancestry-based inference

(2011) Daniel Wegmann et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

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

Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

(2011) S. Via   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data

(2010) Ziheng Yang   Genome Biology and Evolution

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

(2010) BRET A. PAYSEUR   Molecular Ecology Resources

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

THE EFFICACY OF DIVERGENCE HITCHHIKING IN GENERATING GENOMIC ISLANDS DURING ECOLOGICAL SPECIATION

(2009) Jeffrey L. Feder et al.   EVOLUTION

Estimating Divergence Parameters With Small Samples From a Large Number of Loci

(2009) Y. Wang et al.   GENETICS

Fast model-based estimation of ancestry in unrelated individuals

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

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2009) M A F Noor et al.   HEREDITY

The Divergence of Chimpanzee Species and Subspecies as Revealed in Multipopulation Isolation-with-Migration Analyses

(2009) J. Hey   MOLECULAR BIOLOGY AND EVOLUTION

A powerful regression-based method for admixture mapping of isolation across the genome of hybrids

(2009) ZACHARIAH GOMPERT et al.   MOLECULAR ECOLOGY

Inferring weak population structure with the assistance of sample group information

(2009) MELISSA J. HUBISZ et al.   Molecular Ecology Resources

Spatial patterns of variation due to natural selection in humans

(2009) John Novembre et al.   NATURE REVIEWS GENETICS

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations

(2009) Alkes L. Price 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

Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts

(2008) J. E. Pool et al.   GENETICS

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY