A genomic perspective on hybridization and speciation

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Molecular Ecology

• Publication date

  2016-06-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1111/mec.13557PMID 26836441PMCID PMC4915564
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Chromosome Inversions, Local Adaptation and Speciation

  2017cited by this paper
• The genomic landscape of Neanderthal ancestry in present-day humans.

  2016cited by this paper
• IMa2p – parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model

  2016cited by this paper
• Best practices for evaluating single nucleotide variant calling methods for microbial genomics

  2015cited by this paper
• Inference of complex population histories using whole-genome sequences from multiple populations

  2015cited by this paper
• Historical introgression among the American live oaks and the comparative nature of tests for introgression

  2015cited by this paper
• Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

  2015cited by this paper
• Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

  2015cited by this paper
• Extensive introgression in a malaria vector species complex revealed by phylogenomics

  2015cited by this paper
• Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

  2015cited by this paper
• Genome‐wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

  2015cited by this paper
• On the occurrence of false positives in tests of migration under an isolation‐with‐migration model

  2015cited by this paper
• Functional Organization of the Genome May Shape the Species Boundary in the House Mouse

  2015cited by this paper
• The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact

  2015cited by this paper
• Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent

  2015cited by this paper
• The landscape of Neandertal ancestry in present-day humans

  2014cited by this paper
• Genomic Analyses of Three Malaria Vectors Reveals Extensive Shared Polymorphism but Contrasting Population Histories

  2014cited by this paper
• Genomic divergence in a ring species complex

  2014cited by this paper
• Spatial Localization of Recent Ancestors for Admixed Individuals

  2014cited by this paper
• HOW COMMON IS HOMOPLOID HYBRID SPECIATION?

  2014cited by this paper
• Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

  2014cited by this paper
• Maximum likelihood inference of reticulate evolutionary histories

  2014cited by this paper
• Genomics and the origin of species

  2014influential reference
• Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

  2014influential reference
• LANDSCAPE GENOMICS OF POPULUS TRICHOCARPA: THE ROLE OF HYBRIDIZATION, LIMITED GENE FLOW, AND NATURAL SELECTION IN SHAPING PATTERNS OF POPULATION STRUCTURE

  2014cited by this paper
• Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs.

  2014cited by this paper
• Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East Asian Sus species during the Plio-Pleistocene climatic fluctuations

  2014cited by this paper
• High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline

  2014cited by this paper
• Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

  2014cited by this paper
• ABC inference of multi-population divergence with admixture from unphased population genomic data

  2014cited by this paper
• Chromosomal Evolution and Patterns of Introgression in Helianthus

  2014cited by this paper
• High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

  2014cited by this paper
• Speciation with gene flow in equids despite extensive chromosomal plasticity

  2014cited by this paper
• fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

  2014cited by this paper
• Genome-Wide Patterns of Differentiation Among House Mouse Subspecies

  2014cited by this paper
• Detection and Polarization of Introgression in a Five-taxon Phylogeny

  2014cited by this paper
• Genome-wide congealing and rapid transitions across the speciation continuum during speciation with gene flow.

  2014cited by this paper
• The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

  2014cited by this paper
• Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

  2014cited by this paper
• Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

  2014cited by this paper
• Genome-Wide Congealing and Rapid Transitions across the Speciation Continuum during Speciation with Gene Flow.

  2014cited by this paper
• Theoretical models of the influence of genomic architecture on the dynamics of speciation

  2014cited by this paper
• Higher levels of sex chromosome heteromorphism are associated with markedly stronger reproductive isolation

  2014cited by this paper
• Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

  2013cited by this paper
• Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

  2013cited by this paper
• Genomic islands of divergence are not affected by geography of speciation in sunflowers

  2013cited by this paper
• DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES

  2013cited by this paper
• Interspecific introgressive origin of genomic diversity in the house mouse

  2013cited by this paper
• Parsimonious inference of hybridization in the presence of incomplete lineage sorting.

  2013cited by this paper
• Recent nonhybrid origin of sunflower ecotypes in a novel habitat

  2013cited by this paper
• Alternative forms for genomic clines

  2013cited by this paper
• RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

  2013cited by this paper
• Analyses of genetic ancestry enable key insights for molecular ecology

  2013cited by this paper
• The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

  2013cited by this paper
• Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

  2013cited by this paper
• An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

  2013cited by this paper
• Higher Levels of Neanderthal Ancestry in East Asians than in Europeans

  2013cited by this paper
• Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired‐end RAD sequencing

  2013cited by this paper
• Population genomics based on low coverage sequencing: how low should we go?

  2013cited by this paper
• Genomic rearrangements and the evolution of clusters of locally adaptive loci

  2013cited by this paper
• Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

  2013cited by this paper
• Genome-wide evidence for speciation with gene flow in Heliconius butterflies

  2013cited by this paper
• Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

  2013cited by this paper
• Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species

  2013cited by this paper
• Next-generation sequencing platforms.

  2013cited by this paper
• GENETIC HITCHHIKING AND THE DYNAMIC BUILDUP OF GENOMIC DIVERGENCE DURING SPECIATION WITH GENE FLOW

  2013cited by this paper
• Genotyping‐by‐sequencing in ecological and conservation genomics

  2013cited by this paper
• The complete genome sequence of a Neandertal from the Altai Mountains

  2013cited by this paper
• Genome‐wide patterns of divergence and gene flow across a butterfly radiation

  2013cited by this paper
• Understanding the origin of species with genome-scale data: modelling gene flow

  2013cited by this paper
• The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

  2012cited by this paper
• The genomic landscape of species divergence in Ficedula flycatchers

  2012cited by this paper
• The Many Landscapes of Recombination in Drosophila melanogaster

  2012cited by this paper
• A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

  2012cited by this paper
• Genome‐wide architecture of reproductive isolation in a naturally occurring hybrid zone between Mus musculus musculus and M. m. domesticus

  2012cited by this paper
• The long wait for hybrid sterility in flowering plants.

  2012cited by this paper
• Ancient Admixture in Human History

  2012cited by this paper
• Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

  2012cited by this paper
• A beginners guide to SNP calling from high-throughput DNA-sequencing data

  2012cited by this paper
• Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

  2012cited by this paper
• Does the speciation clock tick more slowly in the absence of heteromorphic sex chromosomes?

  2012cited by this paper
• Inference of Population Structure using Dense Haplotype Data

  2012cited by this paper
• GENOMIC REGIONS WITH A HISTORY OF DIVERGENT SELECTION AFFECT FITNESS OF HYBRIDS BETWEEN TWO BUTTERFLY SPECIES

  2012cited by this paper
• The Date of Interbreeding between Neandertals and Modern Humans

  2012cited by this paper
• Population Genetics Models of Local Ancestry

  2012cited by this paper
• Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

  2012cited by this paper
• Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

  2012cited by this paper
• Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

  2012cited by this paper
• Genome sequencing reveals complex speciation in the Drosophila simulans clade

  2012cited by this paper
• Recombination rate variation in closely related species

  2011cited by this paper
• On the nonidentifiability of migration time estimates in isolation with migration models

  2011cited by this paper
• Bayesian estimation of genomic clines

  2011cited by this paper
• Quaternary phylogeography: the roots of hybrid zones

  2011influential reference
• Genes versus phenotypes in the study of speciation

  2011cited by this paper
• Interpreting the estimated timing of migration events between hybridizing species

  2011cited by this paper
• Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone

  2011cited by this paper
• Genotype and SNP calling from next-generation sequencing data

  2011cited by this paper
• Recombination rates in admixed individuals identified by ancestry-based inference

  2011cited by this paper
• A General Method for Calculating Likelihoods Under the Coalescent Process

  2011cited by this paper
• Testing for ancient admixture between closely related populations.

  2011cited by this paper

• Speciation with gene flow

  2026cites this paper
• Vertebral morphological changes driven by rflna lead to body shape differentiation in carp.

  2026cites this paper
• Bayesian test of gene flow between sister lineages using genomic data

  2026cites this paper
• Genetics and Analysis of Quantitative Traits

  2025cites this paper
• A systematic review of interspecific breeding in woodpeckers

  2025cites this paper
• Phylogenomic insights into incomplete lineage sorting and hybridization in early-diverging eudicots.

  2025cites this paper
• Hybridization contributes to reproductive isolation

  2025cites this paper
• Homoploid hybrid speciation: advancements and challenges

  2025cites this paper
• Homoploid hybrid speciation and recurrent hybridization along the northwestern Iberian mountain chains

  2025cites this paper
• Species boundaries, hybridization and gene flow

  2025cites this paper
• Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata)

  2025cites this paper
• Pangenome graphs and their applications in biodiversity genomics

  2025cites this paper
• Massive inter-species introgression overwhelms phylogenomic relationships among jaguar, lion, and leopard.

  2025cites this paper
• Effects of hybridization and gene flow on gene co-expression networks.

  2025cites this paper
• Bypassing the Batch Effects to Improve the Reusability of RAD-seq Data: A Case Study of Recurrent Hybridization in the Japanese Torreya Species Complex

  2025cites this paper
• Reconciling Gene Tree Discordance and Biogeography in European Crows

  2025cites this paper
• The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression

  2025cites this paper
• Genome-wide SNVs revealed reticulate evolutionary history of an Eurasia-African songbird radiation

  2025influential citation
• Synergies between speciation and conservation science yield novel insights for mitigating the biodiversity crisis of the Anthropocene

  2025cites this paper
• Genomic insights into the reticulate evolution of viviparous Phrynocephalus lizards on the Qinghai-Tibetan Plateau.

  2025cites this paper
• Evidence for ancient selective sweeps followed by differentiation among three species of Sphyrapicus sapsuckers

  2025cites this paper
• Interploidy gene flow does not prevent adaptive genetic differentiation in sympatric populations of Epidendrum fulgens and E. puniceoluteum (Orchidaceae)

  2025cites this paper
• Genomic Insights Into Introgression Between Quercus aquifolioides and Its Sympatric Relatives Across Elevational Gradients

  2025cites this paper
• Deforestation-induced Hybridization in Philippine Frogs Creates a Distinct Phenotype With an Inviable Genotype

  2025cites this paper
• Interactions between mechanisms of reproductive isolation

  2025cites this paper
• Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes.

  2025cites this paper
• Conservation genomics of the critically endangered sea lavender Limonium estevei: a recent bottleneck and low introgression from a widespread congener

  2025cites this paper
• Life as a Categorical Information-Handling System: An Evolutionary Information-Theoretic Model of the Holobiont

  2025cites this paper
• Comparative Genomics of the Testacea Group of Drosophila Reveals Introgression and Variation in Chromosome Size and Structure

  2025cites this paper
• From genome to gene expression: the genomic landscape of a hybrid species of Eucalyptus urophylla × Eucalyptus grandis and its divergence from parental species hybrid

  2025cites this paper
• Ancient hybridization and combinatorial mechanism: drivers of adaptive evolution in Clematis sect. Fruticella (Ranunculaceae).

  2025cites this paper
• Towards a Research Programme Aiming at Causes and Consequences of Reticulate Evolution

  2025cites this paper
• Phylogenetic reconstruction of African weakly electric fish (Campylomormyrus spp.) is suggestive of ancient introgression events.

  2025cites this paper
• Host associations, host switching, geographic location, and potential reticulate evolution shape the systematics of sucking lice (Psocodea: Anoplura) belonging to the genera Hoplopleura and Polyplax

  2025cites this paper
• Comparative Analysis of Artemisia Plastomes, with Implications for Revealing Phylogenetic Incongruence and Evidence of Hybridization

  2025cites this paper
• Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages

  2025cites this paper
• Mixed, not stirred: Genomic data confirm the first case of interspecific hybridization in planarian triclads (Platyhelminthes: Tricladida) and raise questions about a possibly novel form of hybrid speciation.

  2025cites this paper
• Sleep disruption as a potential mechanism contributing to post‐zygotic reproductive isolation in hybrids

  2025cites this paper
• Replicate geographic transects across a hybrid zone reveal parallelism and differences in the genetic architecture of reproductive isolation

  2025cites this paper
• Leaping between branches: Hybridisation and the tangled evolutionary history of true lemurs.

  2025cites this paper
• Exploring the patterns of evolution: Core thoughts and focus on the saltational model

  2024cites this paper
• Do Genetic Loci that Cause Reproductive Isolation in the Lab Inhibit Gene Flow in Nature?

  2024cites this paper
• The Complex Genetic Legacy of Hybridization and Introgression between the Rare Ocotea loxensis van der Werff and the Widespread O. infrafoveolata van der Werff (Lauraceae)

  2024cites this paper
• Population genetics and origin of horticultural germplasm in Clematis via genotyping-by-sequencing

  2024cites this paper
• Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance

  2024cites this paper
• Genetic divergence and ecological adaptation of an eastern North American spring ephemeral Sanguinaria canadensis

  2024cites this paper
• A yeast love triangle: multiple hybridizations shape genome evolution in the Pichia cactophila species complex

  2024cites this paper
• Admixture in the fungal pathogen Blastomyces.

  2024cites this paper
• Trans‐Specific Polymorphisms Between Cryptic Daphnia Species Affect Fitness and Behavior

  2024cites this paper
• The Fate of a Polygenic Phenotype Within the Genomic Landscapes of Introgression in the European Seabass Hybrid Zone

  2024cites this paper
• The phenotype, sex ratio and gonadal development in triploid hybrids of rainbow trout (Oncorhynchus mykiss) ♀ and brook trout (Salvelinus fontinalis) ♂.

  2024cites this paper
• Genomic data support reticulate evolution in whiptail lizards from the Brazilian Caatinga.

  2024cites this paper
• Inferring complex evolutionary history of the closely related East Asian wild roses in Rosa sect. Synstylae (Rosaceae) based on genomic evidence from conserved orthologs.

  2024cites this paper
• Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model

  2024cites this paper
• A Review of Pangasiid Catfish Genomics for Conservation and Aquaculture: Current Status and Way Forward

  2024cites this paper
• That's Not a Hybrid: How to Distinguish Patterns of Admixture and Isolation By Distance

  2024cites this paper
• Understanding species limits through the formation of phylogeographic lineages

  2024cites this paper
• Multi-Approach Unveils Potential Gene Introgression of Oil Camellias

  2024cites this paper
• Suture zones, speciation, and evolution.

  2024cites this paper
• Evidence of a small, island-associated population of common bottlenose dolphins in the Mariana Islands

  2024cites this paper
• Microsatellite and mtDNA-based exploration of inter-generic hybridization and patterns of genetic diversity in major carps of Punjab, Pakistan

  2024influential citation
• Speciation, Hybridization, and Phylogeography of the Silk Moth Genus Hyalophora Duncan, 1841 (Insecta: Lepidoptera: Saturniidae)

  2024cites this paper
• Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex

  2024cites this paper
• A Minimal Hybrid Sterility Genome Assembled by Chromosome Swapping Between Mouse Subspecies (Mus musculus)

  2024cites this paper
• Beyond Haldane’s rule: Sex-biased hybrid dysfunction for all modes of sex determination

  2024cites this paper
• Recent secondary contact, genome-wide admixture, and asymmetric introgression of neo-sex chromosomes between two Pacific island bird species

  2024cites this paper
• Phylotranscriptomic analyses reveal the evolutionary complexity of Paris L. (Melanthiaceae), a morphologically distinctive genus with significant pharmaceutical importance.

  2024cites this paper
• Genomic insights into hybrid zone formation: the role of climate, landscape, and demography in the emergence of a novel hybrid lineage between Populus trichocarpa and P. balsamifera

  2024cites this paper
• Clinal variation in autosomal satellite DNA clusters across a contact zone in Barker Frogs.

  2024cites this paper
• Selection leads to false inferences of introgression using popular methods

  2024cites this paper
• Genomic regions of current low hybridisation mark long-term barriers to gene flow in scarce swallowtail butterflies

  2024cites this paper
• Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone

  2024cites this paper
• Global and Local Ancestry and its Importance: A Review

  2024cites this paper
• Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae).

  2024cites this paper
• Climate Change Responses of High-Elevation Polylepis Forests

  2024cites this paper
• Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

  2024cites this paper
• High sexual display trait diversity without measured genetic divergence in a montane hybrid zone involving young species (Habronattus americanus subgroup, Araneae: Salticidae)

  2024cites this paper
• Historical and contemporary processes driving the origin and structure of an admixed population within a contact zone between subspecies of a north temperate diadromous fish

  2024cites this paper
• Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species

  2024cites this paper
• Phytop: a tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL

  2024cites this paper
• Termite females prefer hybrid mating to parthenogenesis when conspecific males are absent

  2024cites this paper
• Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus).

  2024cites this paper
• SiPhyNetwork: An R package for Simulating Phylogenetic Networks

  2023cites this paper
• A community genomics approach to natural hybridization

  2023cites this paper
• Temporal Variation in Introgressed Segments’ Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses

  2023cites this paper
• Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds

  2023cites this paper
• Phylogenomics of the narrowly endemic Eurycheilichthys (Siluriformes: Loricariidae): sympatric species with non-sister relationships suggest mainly allopatric speciation.

  2023cites this paper
• Diversity across organisational scale emerges through dispersal ability and speciation dynamics in tropical fish

  2023cites this paper
• Pericentromeric recombination suppression and the ‘large X effect’ in plants

  2023cites this paper
• Localizing Post-Admixture Adaptive Variants with Object Detection on Ancestry-Painted Chromosomes

  2023cites this paper
• Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae).

  2023cites this paper
• Disentangling the causes of high polymorphism sharing in sympatric Petunia species from subtropical highland grasslands: insights from nuclear diversity

  2023cites this paper
• Genome Shock in a Synthetic Allotetraploid Wheat Invokes Subgenome-Partitioned Gene Regulation, Meiotic Instability and Karyotype Variation.

  2023cites this paper
• Combining genomic and field analyses to reveal migratory status in a burrowing owl population

  2023cites this paper
• Recent secondary contact, genome-wide admixture, and limited introgression of neo-sex chromosomes between two Pacific island bird species

  2023cites this paper
• The puzzle of plant hybridisation: a high propensity to hybridise but few hybrid zones reported

  2023cites this paper
• The genomes of Darwin's primroses reveal chromosome-scale adaptive introgression and differential permeability of species boundaries.

  2023cites this paper
• A yeast love triangle: multiple hybridizations shape genome evolution in the Pichia cactophila species complex

  2023cites this paper
• Genomic signatures of ecological divergence between savanna and forest populations of a neotropical tree.

  2023cites this paper
• Genetic and reproductive evidence of incomplete isolations barriers between Pterodon emarginatus and P. pubescens (Leguminosae, Papilionoideae)

  2023cites this paper