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Evolution of barrier loci at an intermediate stage of speciation with gene flow

https://doi.org/10.1101/703108
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Searching for Sympatric Speciation in the Genomic Era
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Interpreting differentiation landscapes in the light of long-term linked selection
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Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds
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Multicolor FISH mapping of the dioecious model plant, Silene latifolia
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Chloroplast DNA variation in the European herb Silene dioica (red campion): postglacial migration and interspecific introgression
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The Mutation Rate and the Age of the Sex Chromosomes in Silene latifolia
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Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences
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The genetic legacy of the Quaternary ice ages
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Genomic islands of divergence are not affected by geography of speciation in sunflowers
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European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation
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Making sense of genomic islands of differentiation in light of speciation
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Effective population size and patterns of molecular evolution and variation
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Genomics and the origin of species
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The origin and remolding of genomic islands of differentiation in the European sea bass
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Transitions between phases of genomic differentiation during stick-insect speciation
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Robust Locally Weighted Regression and Smoothing Scatterplots
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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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Local Adaptation by Alleles of Small Effect
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Coupling, Reinforcement, and Speciation
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The variant call format and VCFtools
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Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
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Trimmomatic: a flexible trimmer for Illumina sequence data
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Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens
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Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids
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Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice
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Fast model-based estimation of ancestry in unrelated individuals
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Genome-wide evidence for speciation with gene flow in Heliconius butterflies
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Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
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Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
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A universal mechanism generating clusters of differentiated loci during divergence-with-migration
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The demographic history of Atlantic salmon ( Salmo salar ) across its distribution range reconstructed from approximate Bayesian computations*
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Ecological divergence plays an important role in strong but complex reproductive isolation in campions (Silene)*
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Geographically congruent large-scale patterns of plastid haplotype variation in the European herbs Silene dioica and S. latifolia (Caryophyllaceae)
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Genetic structure of hybrid zones betweenSilene latifoliaandSilene dioica(Caryophyllaceae): evidence for introgressive hybridization
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hierfstat , a package for r to compute and test hierarchical F ‐statistics
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GENETIC AND ECOLOGICAL DIFFERENTIATION IN THE HYBRIDIZING CAMPIONSSILENE DIOICAANDS. LATIFOLIA
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THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER
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DYNAMICS OF DRIFT, GENE FLOW, AND SELECTION DURING SPECIATION INSILENE
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RECONCILING EXTREMELY STRONG BARRIERS WITH HIGH LEVELS OF GENE EXCHANGE IN ANNUAL SUNFLOWERS
inferredcites →https://doi.org/10.1111/jeb.12425openalex-snapshot
Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a M ytilushybrid zone
inferredcites →https://doi.org/10.1111/jeb.13047openalex-snapshot
Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow
inferredcites →https://doi.org/10.1111/jeb.13116openalex-snapshot
Evolution of recombination rates and the genomic landscape of speciation
inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot
Stacks: an analysis tool set for population genomics
inferredcites →https://doi.org/10.1111/mec.12750openalex-snapshot
Theoretical models of the influence of genomic architecture on the dynamics of speciation
inferredcites →https://doi.org/10.1111/mec.12796openalex-snapshot
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow
inferredcites →https://doi.org/10.1111/mec.13427openalex-snapshot
The large‐X effect in plants: increased species divergence and reduced gene flow on the Silene X‐chromosome
inferredcites →https://doi.org/10.1111/mec.13611openalex-snapshot
The evolution of genomic islands by increased establishment probability of linked alleles
inferredcites →https://doi.org/10.1111/mec.13765openalex-snapshot
Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow
inferredcites →https://doi.org/10.1111/mec.13774openalex-snapshot
Genomic landscape of early ecological speciation initiated by selection on nuptial colour
inferredcites →https://doi.org/10.1111/mec.13969openalex-snapshot
Sequence diversity patterns suggesting balancing selection in partially sex‐linked genes of the plant Silene latifolia are not generated by demographic history or gene flow
inferredcites →https://doi.org/10.1111/mec.14195openalex-snapshot
Genomewide patterns of variation in genetic diversity are shared among populations, species and higher‐order taxa
inferredcites →https://doi.org/10.1111/mec.14226openalex-snapshot
Gene flow and selection interact to promote adaptive divergence in regions of low recombination
inferredcites →https://doi.org/10.1111/mec.14373openalex-snapshot
Genomics of adaptive divergence with chromosome‐scale heterogeneity in crossover rate
inferredcites →https://doi.org/10.1111/mec.14562openalex-snapshot
Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation
inferredcites →https://doi.org/10.1111/mec.14792openalex-snapshot
These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists
inferredcites →https://doi.org/10.1111/nph.14202openalex-snapshot
Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi‐site transplant experiment
inferredcites →https://doi.org/10.1126/science.1253226openalex-snapshot
The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
inferredcites →https://doi.org/10.1126/science.aac9927openalex-snapshot
Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.112420openalex-snapshot
Molecular Signatures of Natural Selection
inferredcites →https://doi.org/10.1198/000313006x118430openalex-snapshot
A Lego System for Conditional Inference
inferredcites →https://doi.org/10.1371/journal.pbio.1002379openalex-snapshot
Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation
inferredcites →https://doi.org/10.1371/journal.pbio.2000234openalex-snapshot
Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence
inferredcites →https://doi.org/10.1371/journal.pgen.1000695openalex-snapshot
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1004966openalex-snapshot
Genomics of Divergence along a Continuum of Parapatric Population Differentiation
inferredcites →https://doi.org/10.1371/journal.pgen.1007358openalex-snapshot
The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression
inferredcites →https://doi.org/10.1371/journal.pone.0037135openalex-snapshot
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
inferredcites →https://doi.org/10.2307/3546096openalex-snapshot
Maintenance of the Species Boundary between Silene dioica and S. latifolia (Red and White Campion)
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7717/peerj.431openalex-snapshot
dDocent : a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
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