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Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/evl3.14openalex-snapshot
Interpreting differentiation landscapes in the light of long-term linked selection
inferredcites →https://doi.org/10.1002/evl3.46openalex-snapshot
Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds
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Hybridization Reveals the Evolving Genomic Architecture of Speciation
inferredcites →https://doi.org/10.1016/j.tig.2012.03.009openalex-snapshot
The genomics of speciation-with-gene-flow
inferredcites →https://doi.org/10.1016/j.tig.2015.07.002openalex-snapshot
The genomics of organismal diversification illuminated by adaptive radiations
inferredcites →https://doi.org/10.1016/j.tree.2019.02.008openalex-snapshot
A Combinatorial View on Speciation and Adaptive Radiation
inferredcites →https://doi.org/10.1017/s0016672300014634openalex-snapshot
The hitch-hiking effect of a favourable gene
inferredcites →https://doi.org/10.1017/s0016672300029827openalex-snapshot
Inbreeding coefficients and coalescence times
inferredcites →https://doi.org/10.1038/217624a0openalex-snapshot
Evolutionary Rate at the Molecular Level
inferredcites →https://doi.org/10.1038/246096a0openalex-snapshot
Slightly Deleterious Mutant Substitutions in Evolution
inferredcites →https://doi.org/10.1038/nature11584openalex-snapshot
The genomic landscape of species divergence in Ficedula flycatchers
inferredcites →https://doi.org/10.1038/nature14181openalex-snapshot
Evolution of Darwin’s finches and their beaks revealed by genome sequencing
inferredcites →https://doi.org/10.1038/ncomms2833openalex-snapshot
Genomic islands of divergence are not affected by geography of speciation in sunflowers
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nrg.2016.133openalex-snapshot
Making sense of genomic islands of differentiation in light of speciation
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The genic view of the process of speciation
inferredcites →https://doi.org/10.1073/pnas.1017351108openalex-snapshot
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
inferredcites →https://doi.org/10.1073/pnas.76.10.5269openalex-snapshot
Mathematical model for studying genetic variation in terms of restriction endonucleases.
inferredcites →https://doi.org/10.1073/pnas.90.16.7729openalex-snapshot
Origin of floral isolation between ornithophilous and sphingophilous plant species.
inferredcites →https://doi.org/10.1073/pnas.90.3.990openalex-snapshot
Effects of hybridization and selection on floral isolation.
inferredcites →https://doi.org/10.1086/284325openalex-snapshot
Phylogenies and the Comparative Method
inferredcites →https://doi.org/10.1086/521987openalex-snapshot
Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btg1029openalex-snapshot
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btm071openalex-snapshot
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
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DensiTree: making sense of sets of phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/biolinnean/bly063openalex-snapshot
What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species
inferredcites →https://doi.org/10.1093/gbe/evv250openalex-snapshot
Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2Recombinant Crosses as an Example
inferredcites →https://doi.org/10.1093/genetics/134.4.1289openalex-snapshot
The effect of deleterious mutations on neutral molecular variation.
inferredcites →https://doi.org/10.1093/genetics/141.4.1605openalex-snapshot
Deleterious background selection with recombination.
inferredcites →https://doi.org/10.1093/genetics/155.2.909openalex-snapshot
Genetic Drift in an Infinite Population: The Pseudohitchhiking Model
inferredcites →https://doi.org/10.1093/molbev/msr048openalex-snapshot
Testing for Ancient Admixture between Closely Related Populations
inferredcites →https://doi.org/10.1093/molbev/msu269openalex-snapshot
Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
inferredcites →https://doi.org/10.1093/molbev/msy228openalex-snapshot
SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model
inferredcites →https://doi.org/10.1093/nar/gki442openalex-snapshot
InterProScan: protein domains identifier
inferredcites →https://doi.org/10.1093/nar/gkr944openalex-snapshot
Phytozome: a comparative platform for green plant genomics
inferredcites →https://doi.org/10.1093/nar/gkt1069openalex-snapshot
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
inferredcites →https://doi.org/10.1093/nar/gkv1209openalex-snapshot
Ensembl Genomes 2016: more genomes, more complexity
inferredcites →https://doi.org/10.1093/oso/9780198505235.001.0001openalex-snapshot
The Ecology of Adaptive Radiation
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025953openalex-snapshot
Measures of divergence between populations and the effect of forces that reduce variability
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040703openalex-snapshot
A statistical test for detecting geographic subdivision.
inferredcites →https://doi.org/10.1098/rspb.2015.1666openalex-snapshot
Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers
inferredcites →https://doi.org/10.1101/167981openalex-snapshot
Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations
inferredcites →https://doi.org/10.1101/326256openalex-snapshot
Background selection and the statistics of population differentiation: consequences for detecting local adaptation
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.159426.113openalex-snapshot
Genome-wide evidence for speciation with gene flow in Heliconius butterflies
inferredcites →https://doi.org/10.1101/gr.196485.115openalex-snapshot
Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
inferredcites →https://doi.org/10.1101/gr.212522.116openalex-snapshot
Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
inferredcites →https://doi.org/10.1101/gr.6743907openalex-snapshot
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
inferredcites →https://doi.org/10.1111/1755-0998.12424openalex-snapshot
Exploring linkage disequilibrium
inferredcites →https://doi.org/10.1111/1755-0998.12968openalex-snapshot
Tree‐sequence recording in SLiM opens new horizons for forward‐time simulation of whole genomes
inferredcites →https://doi.org/10.1111/evo.12118openalex-snapshot
MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING
inferredcites →https://doi.org/10.1111/evo.12589openalex-snapshot
Strong premating reproductive isolation drives incipient speciation inMimulus aurantiacus
inferredcites →https://doi.org/10.1111/evo.12807openalex-snapshot
The geography of divergence with gene flow facilitates multitrait adaptation and the evolution of pollinator isolation inMimulus aurantiacus
inferredcites →https://doi.org/10.1111/j.0014-3820.2005.tb00968.xopenalex-snapshot
CONTRASTING PATTERNS OF FLORAL AND MOLECULAR VARIATION ACROSS A CLINE IN MIMULUS AURANTIACUS
inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03946.xopenalex-snapshot
Divergent selection and heterogeneous genomic divergence
inferredcites →https://doi.org/10.1111/j.1420-9101.2006.01216.xopenalex-snapshot
Environment and pollinator‐mediated selection on parapatric floral races of Mimulus aurantiacus
inferredcites →https://doi.org/10.1111/j.1420-9101.2012.02599.xopenalex-snapshot
Hybridization and speciation
inferredcites →https://doi.org/10.1111/j.1558-5646.2007.00308.xopenalex-snapshot
TOWARD A SELECTION THEORY OF MOLECULAR EVOLUTION
inferredcites →https://doi.org/10.1111/j.1558-5646.2011.01486.xopenalex-snapshot
THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER
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.13108openalex-snapshot
Dissecting differentiation landscapes: a linked selection's perspective
inferredcites →https://doi.org/10.1111/jeb.13110openalex-snapshot
Glittering gold and the quest for Isla de Muerta
inferredcites →https://doi.org/10.1111/jeb.13442openalex-snapshot
Variation in ecophysiological traits might contribute to ecogeographic isolation and divergence between parapatric ecotypes ofMimulus aurantiacus
inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot
Stacks: an analysis tool set for population genomics
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.13645openalex-snapshot
Geographic cline analysis as a tool for studying genome‐wide variation: a case study of pollinator‐mediated divergence in a monkeyflower
inferredcites →https://doi.org/10.1111/mec.14083openalex-snapshot
Correlated patterns of genetic diversity and differentiation across an avian family
inferredcites →https://doi.org/10.1126/science.1159978openalex-snapshot
Natural Selection on a Major Armor Gene in Threespine Stickleback
inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot
A Draft Sequence of the Neandertal Genome
inferredcites →https://doi.org/10.1126/science.1252136openalex-snapshot
Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation
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/10.1126/science.aar3684openalex-snapshot
Natural selection interacts with recombination to shape the evolution of hybrid genomes
inferredcites →https://doi.org/10.1146/annurev.es.16.110185.000553openalex-snapshot
Analysis of Hybrid Zones
inferredcites →https://doi.org/10.1159/000084979openalex-snapshot
Repbase Update, a database of eukaryotic repetitive elements
inferredcites →https://doi.org/10.1186/1471-2105-12-491openalex-snapshot
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
inferredcites →https://doi.org/10.1186/s13059-016-0951-yopenalex-snapshot
OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot
Second-generation PLINK: rising to the challenge of larger and richer datasets
inferredcites →https://doi.org/10.1371/journal.pbio.0030285openalex-snapshot
Genomic Islands of Speciation in Anopheles gambiae
inferredcites →https://doi.org/10.1371/journal.pbio.1002112openalex-snapshot
Natural Selection Constrains Neutral Diversity across A Wide Range of Species
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.2006288openalex-snapshot
Recombination rate variation shapes barriers to introgression across butterfly genomes
inferredcites →https://doi.org/10.1371/journal.pcbi.1004842openalex-snapshot
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
inferredcites →https://doi.org/10.1371/journal.pcbi.1006581openalex-snapshot
Efficient pedigree recording for fast population genetics simulation
inferredcites →https://doi.org/10.1371/journal.pgen.1000862openalex-snapshot
Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
inferredcites →https://doi.org/10.1371/journal.pgen.1003385openalex-snapshot
Divergent Selection Drives Genetic Differentiation in an R2R3-MYB Transcription Factor That Contributes to Incipient Speciation in Mimulus aurantiacus
inferredcites →https://doi.org/10.1371/journal.pgen.1004410openalex-snapshot
Speciation and Introgression between Mimulus nasutus and Mimulus guttatus
inferredcites →https://doi.org/10.1371/journal.pone.0047768openalex-snapshot
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
inferredcites →https://doi.org/10.1534/g3.111.000240openalex-snapshot
Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
inferredcites →https://doi.org/10.1534/genetics.112.141861openalex-snapshot
Patterns of Neutral Diversity Under General Models of Selective Sweeps
inferredcites →https://doi.org/10.1534/genetics.112.142018openalex-snapshot
Genomic Variation in Natural Populations ofDrosophila melanogaster
inferredcites →https://doi.org/10.1534/genetics.114.164293openalex-snapshot
A RAD-Tag Genetic Map for the Platyfish ( Xiphophorus maculatus ) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish
inferredcites →https://doi.org/10.1534/genetics.117.300610openalex-snapshot
Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback
inferredcites →https://doi.org/10.1534/genetics.119.301991openalex-snapshot
How Linked Selection Shapes the Diversity Landscape inFicedulaFlycatchers
inferredcites →https://doi.org/10.2307/2657117openalex-snapshot
Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences
inferredcites →https://doi.org/10.3732/ajb.1700234openalex-snapshot
Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulus sect. Diplacus)
inferredcites →https://doi.org/10.5281/zenodo.16202676openalex-snapshot
STUDIES IN THE GENUS DIPLACUS, SCROPHULARIACEAE
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1101/2021.12.01.470789openalex-snapshot
Genomic architecture drives population structuring in Amazonian birds
inferred← citeshttps://doi.org/10.1101/537423openalex-snapshot
An olfactory receptor gene underlies reproductive isolation in perfume-collecting orchid bees
inferred← citeshttps://doi.org/10.1101/592105openalex-snapshot
Contingent Convergence: The ability to detect convergent genomic evolution is dependent on population size and migration
inferred← citeshttps://doi.org/10.1111/mec.15499openalex-snapshot
Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish
inferred← citeshttps://doi.org/10.1111/nyas.14177openalex-snapshot
What can be learned by scanning the genome for molecular convergence in wild populations?
inferred← citeshttps://doi.org/10.1534/genetics.118.301747openalex-snapshot
Local PCA Shows How the Effect of Population Structure Differs Along the Genome
inferred← citeshttps://doi.org/10.1534/genetics.119.302261openalex-snapshot
Selection, Linkage, and Population Structure Interact To Shape Genetic Variation Among Threespine Stickleback Genomes
inferred← citeshttps://doi.org/10.1534/genetics.119.302892openalex-snapshot
The Temporal Dynamics of Background Selection in Nonequilibrium Populations
inferred← citeshttps://doi.org/10.3390/genes10121027openalex-snapshot
The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes
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