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Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs*

https://doi.org/10.1111/evo.14234
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What this work says

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

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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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Mitochondrial phylogeographies of five widespread Eurasian bird species
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Evolutionary stasis: the stable chromosomes of birds
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Systematics of Ficedula flycatchers (Muscicapidae): A molecular reassessment of a taxonomic enigma
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Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): Novel results from fresh source material
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The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations
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Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster
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Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial–nuclear comparison
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GLRB allelic variation associated with agoraphobic cognitions, increased startle response and fear network activation: a potential neurogenetic pathway to panic disorder
inferredcites →https://doi.org/10.1038/nature11584openalex-snapshot
The genomic landscape of species divergence in Ficedula flycatchers
inferredcites →https://doi.org/10.1038/ncomms13195openalex-snapshot
Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
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Genomic islands of divergence are not affected by geography of speciation in sunflowers
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
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Making sense of genomic islands of differentiation in light of speciation
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Genomic signatures of selection at linked sites: unifying the disparity among species
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Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation
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Modulation of defensive reactivity by GLRB allelic variation: converging evidence from an intermediate phenotype approach
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Hybridization between Pied and Collared Flycatchers—sexual selection and speciation theory
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Peripheral Nerve Demyelination Caused by a Mutant Rho GTPase Guanine Nucleotide Exchange Factor, Frabin/FGD4
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The variant call format and VCFtools
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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S weep F inder 2: increased sensitivity, robustness and flexibility
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ShinyGO: a graphical gene-set enrichment tool for animals and plants
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Hitchhiking Under Positive Darwinian Selection
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Ral GTPases: crucial mediators of exocytosis and tumourigenesis
inferredcites →https://doi.org/10.1093/molbev/msm108openalex-snapshot
Context Dependence, Ancestral Misidentification, and Spurious Signatures of Natural Selection
inferredcites →https://doi.org/10.1093/molbev/msw046openalex-snapshot
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
inferredcites →https://doi.org/10.1093/molbev/msy149openalex-snapshot
Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It
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/sysbio/syv045openalex-snapshot
Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data
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/10.1098/rspb.2016.2756openalex-snapshot
Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
inferredcites →https://doi.org/10.1098/rstb.2009.0306openalex-snapshot
Speciation in Ficedula flycatchers
inferredcites →https://doi.org/10.1098/rstb.2011.0198openalex-snapshot
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing
inferredcites →https://doi.org/10.1098/rstb.2011.0249openalex-snapshot
Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice
inferredcites →https://doi.org/10.1098/rstb.2011.0260openalex-snapshot
Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
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.204669.116openalex-snapshot
Direct estimate of the rate of germline mutation in a bird
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.4252305openalex-snapshot
Genomic scans for selective sweeps using SNP data
inferredcites →https://doi.org/10.1109/tcbb.2015.2509997openalex-snapshot
Encoding Data Using Biological Principles: The Multisample Variant Format for Phylogenomics and Population Genomics
inferredcites →https://doi.org/10.1111/1755-0998.12602openalex-snapshot
Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome
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/j.1365-294x.2008.03715.xopenalex-snapshot
Speciation with gene flow could be common
inferredcites →https://doi.org/10.1111/j.1469-7998.1999.tb00192.xopenalex-snapshot
Dynamics of a clinal hybrid zone and a comparison with island hybrid zones of flycatchers (Ficedula hypoleuca and F. albicollis)
inferredcites →https://doi.org/10.1111/j.1558-5646.1984.tb05657.xopenalex-snapshot
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
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/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.12810openalex-snapshot
A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
inferredcites →https://doi.org/10.1111/mec.13540openalex-snapshot
PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐whiteFicedulaflycatchers
inferredcites →https://doi.org/10.1111/mec.13596openalex-snapshot
Divergence in gene expression within and between two closely related flycatcher species
inferredcites →https://doi.org/10.1111/mec.13792openalex-snapshot
Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species
inferredcites →https://doi.org/10.1111/mec.14083openalex-snapshot
Correlated patterns of genetic diversity and differentiation across an avian family
inferredcites →https://doi.org/10.1111/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.14197openalex-snapshot
Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds
inferredcites →https://doi.org/10.1111/mec.14439openalex-snapshot
Abundant recent activity of retrovirus‐like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes
inferredcites →https://doi.org/10.1111/mec.14462openalex-snapshot
Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)
inferredcites →https://doi.org/10.1111/mec.14789openalex-snapshot
Sex‐biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome
inferredcites →https://doi.org/10.1111/mec.14858openalex-snapshot
A comparison of genomic islands of differentiation across three young avian species pairs
inferredcites →https://doi.org/10.1111/mec.15197openalex-snapshot
Background selection and F ST : Consequences for detecting local adaptation
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.aad0843openalex-snapshot
Stable recombination hotspots in birds
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/10.1212/01.wnl.0000345373.58618.b6openalex-snapshot
Further evidence that mutations in FGD4/frabin cause Charcot-Marie-Tooth disease type 4H
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.0050310openalex-snapshot
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
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.2006288openalex-snapshot
Recombination rate variation shapes barriers to introgression across butterfly genomes
inferredcites →https://doi.org/10.1371/journal.pbio.3000391openalex-snapshot
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
inferredcites →https://doi.org/10.1371/journal.pbio.3000597openalex-snapshot
Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation
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.pgen.1000471openalex-snapshot
Widespread Genomic Signatures of Natural Selection in Hominid Evolution
inferredcites →https://doi.org/10.1371/journal.pgen.1002752openalex-snapshot
Adaptive Introgression across Species Boundaries in Heliconius Butterflies
inferredcites →https://doi.org/10.1371/journal.pgen.1003942openalex-snapshot
Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data
inferredcites →https://doi.org/10.1371/journal.pgen.1006130openalex-snapshot
A Genomic Map of the Effects of Linked Selection in Drosophila
inferredcites →https://doi.org/10.1371/journal.pgen.1006199openalex-snapshot
Determining the Effect of Natural Selection on Linked Neutral Divergence across Species
inferredcites →https://doi.org/10.1534/genetics.104.029488openalex-snapshot
The Probability and Chromosomal Extent of trans-specific Polymorphism
inferredcites →https://doi.org/10.1534/genetics.106.061432openalex-snapshot
Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants
inferredcites →https://doi.org/10.1534/genetics.119.301991openalex-snapshot
How Linked Selection Shapes the Diversity Landscape inFicedulaFlycatchers
inferredcites →https://doi.org/10.1534/genetics.120.303469openalex-snapshot
Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps
inferredcites →https://doi.org/10.5281/zenodo.597309openalex-snapshot
cggh/scikit-allel: v0.21.2
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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