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The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression

https://doi.org/10.1371/journal.pgen.1007358

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization?

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A new threespine stickleback, Gasterosteus nipponicus sp. nov. (Teleostei: Gasterosteidae), from the Japan Sea region

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A part of the Japan Sea form of the threespine stickleback, Gasterosteus aculeatus, spawns in the seawater tidal pools of western Hokkaido Island, Japan

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Extensive Introgression of Mitochondrial DNA Found between two Genetically Divergent Forms of Threespine Stickleback, Gasterosteus Aculeatus, around Japan

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Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species

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A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

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Genomics of Divergence along a Continuum of Parapatric Population Differentiation

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Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

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Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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A New Method to Scan Genomes for Introgression in a Secondary Contact Model

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Genomic Admixture Analysis in European Populus spp. Reveals Unexpected Patterns of Reproductive Isolation and Mating

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Animal Species and Evolution

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inferred← citeshttps://doi.org/10.1093/biolinnean/blac135openalex-snapshot

Allopatric origin, secondary contact and subsequent isolation of sympatric rockfishes (Sebastidae: Sebastes) in the north-western Pacific

inferred← citeshttps://doi.org/10.1093/biolinnean/blad019openalex-snapshot

Species divergence despite minimal morphological differentiation and habitat overlap in the Patelloida saccharina (Patellogastropoda: Lottiidae) species complex

inferred← citeshttps://doi.org/10.1093/biolinnean/blz106openalex-snapshot

Genetic divergence outpaces phenotypic evolution among threespine stickleback populations in old freshwater habitats

inferred← citeshttps://doi.org/10.1093/evlett/qrad005openalex-snapshot

Recurrent selection and reduction in recombination shape the genomic landscape of divergence across multiple population pairs of Green-backed Tit

inferred← citeshttps://doi.org/10.1093/evolut/qpae184openalex-snapshot

Suture zones, speciation, and evolution

inferred← citeshttps://doi.org/10.1093/evolut/qpaf254openalex-snapshot

Inferring the strength of directional selection on armor plates in Lake Washington stickleback while accounting for migration and drift

inferred← citeshttps://doi.org/10.1093/gbe/evaa065openalex-snapshot

Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations

inferred← citeshttps://doi.org/10.1093/gbe/evae124openalex-snapshot

Selection Shapes the Genomic Landscape of Introgressed Ancestry in a Pair of Sympatric Sea Urchin Species

inferred← citeshttps://doi.org/10.1093/gbe/evz090openalex-snapshot

Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish

inferred← citeshttps://doi.org/10.1093/gbe/evz101openalex-snapshot

Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics

inferred← citeshttps://doi.org/10.1093/hr/uhac054openalex-snapshot

Patterns of genomic divergence in sympatric and allopatric speciation of three Mihoutao (Actinidia) species

inferred← citeshttps://doi.org/10.1093/icesjms/fsae057openalex-snapshot

Trans-Atlantic genomic differentiation and parallel environmental and allelic variation in Lumpfish (Cyclopterus lumpus)

inferred← citeshttps://doi.org/10.1093/molbev/msab179openalex-snapshot

Heterogeneous Histories of Recombination Suppression on Stickleback Sex Chromosomes

inferred← citeshttps://doi.org/10.1093/molbev/msad026openalex-snapshot

Prevalent Introgression Underlies Convergent Evolution in the Diversification ofPungitiusSticklebacks

inferred← citeshttps://doi.org/10.1093/molbev/msad192openalex-snapshot

De Novo Mutation Rates in Sticklebacks

inferred← citeshttps://doi.org/10.1093/molbev/msae006openalex-snapshot

Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species

inferred← citeshttps://doi.org/10.1093/molbev/msae201openalex-snapshot

Widespread Adaptive Introgression of Major Histocompatibility Complex Genes across Vertebrate Hybrid Zones

inferred← citeshttps://doi.org/10.1093/molbev/msy181openalex-snapshot

The Origin of a New Sex Chromosome by Introgression between Two Stickleback Fishes

inferred← citeshttps://doi.org/10.1093/molbev/msz161openalex-snapshot

Admixture between Ancient Lineages, Selection, and the Formation of Sympatric Stickleback Species-Pairs

inferred← citeshttps://doi.org/10.1093/nsr/nwac291openalex-snapshot

Sympatric or micro-allopatric speciation in a glacial lake? Genomic islands support neither

inferred← citeshttps://doi.org/10.1093/sysbio/syag029openalex-snapshot

Genomic Signatures of Speciation in Butterflies

inferred← citeshttps://doi.org/10.1098/rstb.2019.0545openalex-snapshot

The evolution of strong reproductive isolation between sympatric intertidal snails

inferred← citeshttps://doi.org/10.1098/rstb.2019.0548openalex-snapshot

Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

inferred← citeshttps://doi.org/10.1098/rstb.2020.0103openalex-snapshot

Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the ‘extended speciation continuum'

inferred← citeshttps://doi.org/10.1098/rstb.2021.0205openalex-snapshot

Searching for signatures of sexually antagonistic selection on stickleback sex chromosomes

inferred← citeshttps://doi.org/10.1101/2020.09.17.300236openalex-snapshot

Contrasting tempos of sex chromosome degeneration in sticklebacks

inferred← citeshttps://doi.org/10.1101/2021.08.30.458276openalex-snapshot

The information signature of diverging lineages

inferred← citeshttps://doi.org/10.1101/2022.09.25.509431openalex-snapshot

Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana )

inferred← citeshttps://doi.org/10.1101/2022.09.27.507129openalex-snapshot

The fitness of an introgressing haplotype

inferred← citeshttps://doi.org/10.1101/2024.03.10.584293openalex-snapshot

Ongoing hybridisation among clownfishes: the genomic architecture of the Kimbe Bay hybrid zone

inferred← citeshttps://doi.org/10.1101/2024.11.13.623523openalex-snapshot

Rate of de novo mutations in the three-spined stickleback

inferred← citeshttps://doi.org/10.1101/634329openalex-snapshot

Genetic homogeneity in face of morphological heterogeneity in the harbor porpoises from the Black Sea and adjacent waters

inferred← citeshttps://doi.org/10.1101/703108openalex-snapshot

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

inferred← citeshttps://doi.org/10.1101/786038openalex-snapshot

Model-based assessments of differential introgression and linked natural selection during divergence and speciation

inferred← citeshttps://doi.org/10.1101/cshperspect.a041438openalex-snapshot

Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation

inferred← citeshttps://doi.org/10.1111/dgd.12576openalex-snapshot

Parallel transcriptome evolution in stream threespine sticklebacks

inferred← citeshttps://doi.org/10.1111/eva.13767openalex-snapshot

Linked Selection and Gene Density Shape Genome‐Wide Patterns of Diversification in Peatmosses

inferred← citeshttps://doi.org/10.1111/evo.14215openalex-snapshot

Defining the speciation continuum

inferred← citeshttps://doi.org/10.1111/evo.14243openalex-snapshot

Evaluating evidence of mitonuclear incompatibilities with the sex chromosomes in an avian hybrid zone

inferred← citeshttps://doi.org/10.1111/evo.14490openalex-snapshot

Genomic changes underlying repeated niche shifts in an adaptive radiation

inferred← citeshttps://doi.org/10.1111/jeb.13664openalex-snapshot

Patterns of genomic divergence and introgression between Japanese stickleback species with overlapping breeding habitats

inferred← citeshttps://doi.org/10.1111/jeb.14034openalex-snapshot

Identification of a candidate sex determination gene in Culaea inconstans suggests convergent recruitment of an Amh duplicate in two lineages of stickleback

inferred← citeshttps://doi.org/10.1111/jeb.14190openalex-snapshot

Introgression between highly divergent fungal sister species

inferred← citeshttps://doi.org/10.1111/jfb.14686openalex-snapshot

Brown trout phylogenetics: A persistent mirage towards (too) many species

inferred← citeshttps://doi.org/10.1111/mec.14841openalex-snapshot

Functional divergence of a heterochromatin‐binding protein during stickleback speciation

inferred← citeshttps://doi.org/10.1111/mec.15011openalex-snapshot

Speciation in protists: Spatial and ecological divergence processes cause rapid species diversification in a freshwater chrysophyte

inferred← citeshttps://doi.org/10.1111/mec.15388openalex-snapshot

Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

inferred← citeshttps://doi.org/10.1111/mec.15571openalex-snapshot

Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)

inferred← citeshttps://doi.org/10.1111/mec.15908openalex-snapshot

Divergent diapause life history timing drives both allochronic speciation and reticulate hybridization in an adaptive radiation ofRhagoletisflies

inferred← citeshttps://doi.org/10.1111/mec.16021openalex-snapshot

Isolation and reconnection: Demographic history and multiple contact zones of the green odorous frog (Odorrana margaretae) around the Sichuan Basin

inferred← citeshttps://doi.org/10.1111/mec.16046openalex-snapshot

Regions of genetic divergence in depth‐separated Sebastes rockfish species pairs: Depth as a potential driver of speciation

inferred← citeshttps://doi.org/10.1111/mec.16120openalex-snapshot

Genome‐wide molecular phylogenetic analyses and mating experiments which reveal the evolutionary history and an intermediate stage of speciation of a giant water bug

inferred← citeshttps://doi.org/10.1111/mec.16189openalex-snapshot

An introgression breakthrough left by an anthropogenic contact between two ascidians

inferred← citeshttps://doi.org/10.1111/mec.16295openalex-snapshot

Cast away in the Adriatic: Low degree of parallel genetic differentiation in three‐spined sticklebacks

inferred← citeshttps://doi.org/10.1111/mec.17034openalex-snapshot

Drivers of genomic landscapes of differentiation across a Populus divergence gradient

inferred← citeshttps://doi.org/10.1111/mec.17216openalex-snapshot

Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes

inferred← citeshttps://doi.org/10.1111/mec.17365openalex-snapshot

Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci?

inferred← citeshttps://doi.org/10.1111/mec.17414openalex-snapshot

Drivers of genomic differentiation landscapes in populations of disparate ecological and geographical settings within mainland Apis cerana

inferred← citeshttps://doi.org/10.1111/mec.17814openalex-snapshot

3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback

inferred← citeshttps://doi.org/10.1111/mec.70249openalex-snapshot

Shared and Unique Patterns of Genomic Differentiation and Introgression Between Japanese Stickleback Species Across Three Sympatric Sites

inferred← citeshttps://doi.org/10.1111/nph.19361openalex-snapshot

The genomes of Darwin's primroses reveal chromosome‐scale adaptive introgression and differential permeability of species boundaries

inferred← citeshttps://doi.org/10.1126/science.aau5656openalex-snapshot

A key metabolic gene for recurrent freshwater colonization and radiation in fishes

inferred← citeshttps://doi.org/10.1134/s1995425524701026openalex-snapshot

Mechanisms of Diversification during Changes in Habitat in the Three-Spine Stickleback (Gasterosteus aculeatus) Are Fundamentally Different from the Mechanisms of Speciation within the Genus Gasterosteus

inferred← citeshttps://doi.org/10.1186/s12862-020-01713-5openalex-snapshot

Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

inferred← citeshttps://doi.org/10.1186/s12862-025-02440-5openalex-snapshot

Functional mutations in the thyroid-stimulating hormone receptor in natural stickleback populations at sites identical to human disease-causing mutations

inferred← citeshttps://doi.org/10.1242/jeb.208975openalex-snapshot

Diversity in reproductive seasonality in the three-spined stickleback, Gasterosteus aculeatus

inferred← citeshttps://doi.org/10.1371/journal.pbio.3002185openalex-snapshot

The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location

inferred← citeshttps://doi.org/10.1371/journal.pgen.1010027openalex-snapshot

Predictors of genomic differentiation within a hybrid taxon

inferred← citeshttps://doi.org/10.1371/journal.pgen.1011585openalex-snapshot

The recombination landscape of introgression in yeast

inferred← citeshttps://doi.org/10.1534/g3.118.200166openalex-snapshot

Sex Differences in Recombination in Sticklebacks

inferred← citeshttps://doi.org/10.24072/pcjournal.172openalex-snapshot

Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?

inferred← citeshttps://doi.org/10.3099/0027-4100-163.2.47openalex-snapshot

THE SQUAMATE TREE OF LIFE

inferred← citeshttps://doi.org/10.3389/fevo.2020.611672openalex-snapshot

Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion

inferred← citeshttps://doi.org/10.3389/fgene.2022.925786openalex-snapshot

Extreme intraspecific divergence in mitochondrial haplotypes makes the threespine stickleback fish an emerging evolutionary mutant model for mito-nuclear interactions

inferred← citeshttps://doi.org/10.3389/fpls.2022.911467openalex-snapshot

Genomic Differentiation and Demographic Histories of Two Closely Related Salicaceae Species

inferred← citeshttps://doi.org/10.3389/fpls.2023.1223148openalex-snapshot

The role of recombination landscape in species hybridisation and speciation

inferred← citeshttps://doi.org/10.3390/app12073219openalex-snapshot

Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy

inferred← citeshttps://doi.org/10.3390/genes14040821openalex-snapshot

A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of Populus davidiana

inferred← citeshttps://doi.org/10.3410/f.734136775.793555749openalex-snapshot

Faculty Opinions recommendation of The Origin of a New Sex Chromosome by Introgression between Two Stickleback Fishes.

inferred← citeshttps://doi.org/10.37247/paasc.1.22.18openalex-snapshot

Brown trout (Salmo trutta) Phylogentics

inferred← citeshttps://doi.org/10.6084/m9.figshare.13185852openalex-snapshot

Additional file 1 of Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

inferred← citeshttps://doi.org/10.6084/m9.figshare.13185855openalex-snapshot

Additional file 2 of Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

inferred← citeshttps://doi.org/10.6084/m9.figshare.13185858openalex-snapshot

Additional file 3 of Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

inferred← citeshttps://doi.org/10.6084/m9.figshare.13185867openalex-snapshot

Additional file 6 of Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

inferred← citeshttps://doi.org/10.6084/m9.figshare.13185870openalex-snapshot

Additional file 7 of Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

inferred← citeshttps://doi.org/10.7717/peerj.21378openalex-snapshot

Peculiar pigment pattern and population profile of a poisonous pufferfish

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