The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression
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Title
The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression
Authors
Keywords
Introgression, Japan, Pacific Ocean, Sticklebacks, Gene flow, Speciation, Phylogenetic analysis, Atlantic Ocean
Journal
PLoS Genetics
Volume 14, Issue 5, Pages e1007358
Publisher
Public Library of Science (PLoS)
Online
2018-05-24
DOI
10.1371/journal.pgen.1007358
References
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Note: Only part of the references are listed.- Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes
- (2017) Asano Ishikawa et al. EVOLUTION
- Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow
- (2017) M. Ravinet et al. JOURNAL OF EVOLUTIONARY BIOLOGY
- Frequency dependence limits divergent evolution by favouring rare immigrants over residents
- (2017) Daniel I. Bolnick et al. NATURE
- Ancient hybridization fuels rapid cichlid fish adaptive radiations
- (2017) Joana I. Meier et al. Nature Communications
- The genomic mosaicism of hybrid speciation
- (2017) Tore O. Elgvin et al. Science Advances
- Transitions between phases of genomic differentiation during stick-insect speciation
- (2017) Rüdiger Riesch et al. Nature Ecology & Evolution
- Tipping points in the dynamics of speciation
- (2017) Patrik Nosil et al. Nature Ecology & Evolution
- Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species
- (2016) Christina A. Muirhead et al. AMERICAN NATURALIST
- Powerful methods for detecting introgressed regions from population genomic data
- (2016) Benjamin K. Rosenzweig et al. MOLECULAR ECOLOGY
- Demographic modelling with whole-genome data reveals parallel origin of similarPundamiliacichlid species after hybridization
- (2016) Joana I. Meier et al. MOLECULAR ECOLOGY
- Reproductive isolation and introgression between sympatricMimulusspecies
- (2016) Amanda M. Kenney et al. MOLECULAR ECOLOGY
- Making sense of genomic islands of differentiation in light of speciation
- (2016) Jochen B. W. Wolf et al. NATURE REVIEWS GENETICS
- Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth
- (2016) Christopher H. Martin et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback
- (2016) David A. Marques et al. PLoS Genetics
- The geography of introgression in a patchy environment and the thorn in the side of ecological speciation
- (2016) Nicolas Bierne et al. Current Zoology
- 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
- Evidence for archaic adaptive introgression in humans
- (2015) Fernando Racimo et al. NATURE REVIEWS GENETICS
- Evolution of stickleback in 50 years on earthquake-uplifted islands
- (2015) Emily A. Lescak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Detection and Polarization of Introgression in a Five-Taxon Phylogeny
- (2015) James B. Pease et al. SYSTEMATIC BIOLOGY
- Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data
- (2015) Alexander Nater et al. SYSTEMATIC BIOLOGY
- The genomics of ecological vicariance in threespine stickleback fish
- (2015) Marius Roesti et al. Nature Communications
- Genomics of Divergence along a Continuum of Parapatric Population Differentiation
- (2015) Philine G. D. Feulner et al. PLoS Genetics
- A New Method to Scan Genomes for Introgression in a Secondary Contact Model
- (2015) Anthony J. Geneva et al. PLoS One
- Genome-Wide Patterns of Differentiation Among House Mouse Subspecies
- (2014) Megan Phifer-Rixey 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
- ABC inference of multi-population divergence with admixture from unphased population genomic data
- (2014) John D. Robinson 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
- Inferring human population size and separation history from multiple genome sequences
- (2014) Stephan Schiffels et al. NATURE GENETICS
- Genomics and the origin of species
- (2014) Ole Seehausen et al. NATURE REVIEWS GENETICS
- Comparative Analysis of Japanese Three-Spined Stickleback Clades Reveals the Pacific Ocean Lineage Has Adapted to Freshwater Environments while the Japan Sea Has Not
- (2014) Mark Ravinet et al. PLoS One
- Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation
- (2014) V. Soria-Carrasco et al. SCIENCE
- Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species
- (2014) Kohta Yoshida et al. PLoS Genetics
- Genomic divergence between nine- and three-spined sticklebacks
- (2013) Baocheng Guo et al. BMC GENOMICS
- Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies
- (2013) Simon H. Martin et al. GENOME RESEARCH
- The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing
- (2013) Julian Catchen et al. MOLECULAR ECOLOGY
- Stacks: an analysis tool set for population genomics
- (2013) Julian Catchen et al. MOLECULAR ECOLOGY
- Recombination in the threespine stickleback genome-patterns and consequences
- (2013) Marius Roesti et al. MOLECULAR ECOLOGY
- Understanding the origin of species with genome-scale data: modelling gene flow
- (2013) Vitor Sousa et al. NATURE REVIEWS GENETICS
- Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)
- (2013) Deren A. R. Eaton et al. SYSTEMATIC BIOLOGY
- Critiquing blind dating: the dangers of over-confident date estimates in comparative genomics
- (2013) Christopher W. Wheat et al. TRENDS IN ECOLOGY & EVOLUTION
- Genomic islands of divergence are not affected by geography of speciation in sunflowers
- (2013) S. Renaut et al. Nature Communications
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- (2013) Krystyna Nadachowska-Brzyska et al. PLoS Genetics
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- (2012) Carole M. Smadja et al. EVOLUTION
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- Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty
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- Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs
- (2012) MARIUS ROESTI et al. MOLECULAR ECOLOGY
- The biogeography of mitochondrial and nuclear discordance in animals
- (2012) DAVID P. L. TOEWS et al. MOLECULAR ECOLOGY
- The genomic basis of adaptive evolution in threespine sticklebacks
- (2012) Felicity C. Jones et al. NATURE
- The genomics of speciation-with-gene-flow
- (2012) Jeffrey L. Feder et al. TRENDS IN GENETICS
- abc: an R package for approximate Bayesian computation (ABC)
- (2012) Katalin Csilléry et al. Methods in Ecology and Evolution
- 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
- The variant call format and VCFtools
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- A signature of balancing selection in the region upstream to the human UGT2B4 gene and implications for breast cancer risk
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- (2011) Heng Li et al. NATURE
- Genomic divergence during speciation: causes and consequences
- (2011) P. Nosil et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Genomic impacts of chromosomal inversions in parapatric Drosophila species
- (2011) S. E. McGaugh et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation
- (2011) Joseph Heled 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
- phytools: an R package for phylogenetic comparative biology (and other things)
- (2011) Liam J. Revell Methods in Ecology and Evolution
- Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection
- (2011) Vincent Castric et al. PLoS Genetics
- phangorn: phylogenetic analysis in R
- (2010) Klaus Peter Schliep BIOINFORMATICS
- Fast and SNP-tolerant detection of complex variants and splicing in short reads
- (2010) T. D. Wu et al. BIOINFORMATICS
- Genomic Admixture Analysis in European Populus spp. Reveals Unexpected Patterns of Reproductive Isolation and Mating
- (2010) C. Lexer et al. GENETICS
- Ecological divergence and habitat isolation between two migratory forms of Japanese threespine stickleback (Gasterosteus aculeatus)
- (2010) M. KUME et al. JOURNAL OF EVOLUTIONARY BIOLOGY
- ABC as a flexible framework to estimate demography over space and time: some cons, many pros
- (2010) G. BERTORELLE et al. MOLECULAR ECOLOGY
- Genome scan of hybridizing sunflowers from Texas (Helianthus annuusandH. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation
- (2010) M. SCASCITELLI et al. MOLECULAR ECOLOGY
- msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis
- (2010) P. PAVLIDIS et al. Molecular Ecology Resources
- Approximate Bayesian Computation (ABC) in practice
- (2010) Katalin Csilléry et al. TRENDS IN ECOLOGY & EVOLUTION
- Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
- (2010) Paul A. Hohenlohe et al. PLoS Genetics
- Population Genomics of Secondary Contact
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- Statistical Phylogeography
- (2009) L. Lacey Knowles Annual Review of Ecology Evolution and Systematics
- ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
- (2009) Gabriela Bindea et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- The World's Oldest Fossil Threespine Stickleback Fish
- (2009) Michael A. Bell et al. COPEIA
- THE EVOLUTION OF STRONG REPRODUCTIVE ISOLATION
- (2009) Nicholas H. Barton et al. EVOLUTION
- 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
- Along the speciation continuum in sticklebacks
- (2009) A. P. Hendry et al. JOURNAL OF FISH BIOLOGY
- introgress: a software package for mapping components of isolation in hybrids
- (2009) ZACHARIAH GOMPERT et al. Molecular Ecology Resources
- A role for a neo-sex chromosome in stickleback speciation
- (2009) Jun Kitano et al. NATURE
- Non-linear regression models for Approximate Bayesian Computation
- (2009) Michael G. B. Blum et al. STATISTICS AND COMPUTING
- Ecological explanations for (incomplete) speciation
- (2009) Patrik Nosil et al. TRENDS IN ECOLOGY & EVOLUTION
- A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE
- (2008) Michael P. Cummings et al. EVOLUTION
- Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
- (2008) Nathan A. Baird et al. PLoS One
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