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Introgression patterns between house mouse subspecies and species reveal genomic windows of frequent exchange

https://doi.org/10.1101/168328
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What this work says

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

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Defensin‐related peptide 1 (Defr1) is allelic to Defb8 and chemoattracts immature DC and CD4+ T cells independently of CCR6
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Genetic variation in mouse salivary amylase rate of synthesis
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Neonatal Oxygen Increases Sensitivity to Influenza A Virus Infection in Adult Mice by Suppressing Epithelial Expression of Ear1
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Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations
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Nucleic Acid Recognition Orchestrates the Anti-Viral Response to Retroviruses
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Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice
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Takusan: A Large Gene Family that Regulates Synaptic Activity
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Wild mice: an ever-increasing contribution to a popular mammalian model
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Wormy mice in a hybrid zone
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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
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SERINC3 and SERINC5 restrict HIV-1 infectivity and are counteracted by Nef
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KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks
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A critical function for CD200 in lung immune homeostasis and the severity of influenza infection
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Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus
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The Transcriptional Foundations of Sp110-mediated Macrophage (RAW264.7) Resistance to Mycobacterium tuberculosis H37Ra
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Reduced expression of monocyte CD200R is associated with enhanced proinflammatory cytokine production in sarcoidosis
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The evolutionary history of bears is characterized by gene flow across species
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Interspecific introgressive origin of genomic diversity in the house mouse
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CTACK, a skin-associated chemokine that preferentially attracts skin-homing memory T cells
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The Role of Chemokines in Mesenchymal Stem Cell Homing to Wounds
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APE: Analyses of Phylogenetics and Evolution in R language
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Fast and accurate short read alignment with Burrows–Wheeler transform
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BEDTools: a flexible suite of utilities for comparing genomic features
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The variant call format and VCFtools
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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
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ART: a next-generation sequencing read simulator
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An Analysis of Signatures of Selective Sweeps in Natural Populations of the House Mouse
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/msv011openalex-snapshot
Functional Organization of the Genome May Shape the Species Boundary in the House Mouse
inferredcites →https://doi.org/10.1093/molbev/msw036openalex-snapshot
R2d2 Drives Selfish Sweeps in the House Mouse
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/sysbio/syv023openalex-snapshot
Detection and Polarization of Introgression in a Five-Taxon Phylogeny
inferredcites →https://doi.org/10.1094/phyto-08-15-0184-rvwopenalex-snapshot
The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens
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SPEER—A New Family of Testis-Specific Genes from the Mouse1
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Sex Chromosome Drive
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.187187.114openalex-snapshot
Divergence patterns of genic copy number variation in natural populations of the house mouse ( Mus musculus domesticus ) reveal three conserved genes with major population-specific expansions
inferredcites →https://doi.org/10.1101/gr.6757907openalex-snapshot
Genome-wide patterns of gene flow across a house mouse hybrid zone
inferredcites →https://doi.org/10.1111/imr.12283openalex-snapshot
The NLRP 1 inflammasomes
inferredcites →https://doi.org/10.1111/j.1095-8312.2005.00445.xopenalex-snapshot
First occurrence of the house mouse (Mus musculus domesticus Schwarz & Schwarz, 1943) in the Western Mediterranean: a zooarchaeological revision of subfossil occurrences
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05148.xopenalex-snapshot
Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05583.xopenalex-snapshot
Genome‐wide architecture of reproductive isolation in a naturally occurring hybrid zone betweenMus musculus musculusandM. m. domesticus
inferredcites →https://doi.org/10.1111/mec.12206openalex-snapshot
The role of biogeography in shaping diversity of the intestinal microbiota in house mice
inferredcites →https://doi.org/10.1111/mec.12415openalex-snapshot
Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation
inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot
A Draft Sequence of the Neandertal Genome
inferredcites →https://doi.org/10.1126/science.1209202openalex-snapshot
The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans
inferredcites →https://doi.org/10.1126/science.272.5258.67openalex-snapshot
Population Biology of Antigen Presentation by MHC Class I Molecules
inferredcites →https://doi.org/10.1186/s12862-015-0306-4openalex-snapshot
Eurasian house mouse (Mus musculus L.) differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot
inferredcites →https://doi.org/10.1186/s12862-015-0528-5openalex-snapshot
Selective sweeps versus introgression - population genetic dynamics of the murine leukemia virus receptor Xpr1 in wild populations of the house mouse (Mus musculus)
inferredcites →https://doi.org/10.1186/s13059-016-0889-0openalex-snapshot
Genome-wide introgression among distantly related Heliconius butterfly species
inferredcites →https://doi.org/10.1186/s13072-016-0099-8openalex-snapshot
Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells
inferredcites →https://doi.org/10.1371/journal.pcbi.1003649openalex-snapshot
An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
inferredcites →https://doi.org/10.1371/journal.pgen.0030144openalex-snapshot
Linkage Disequilibrium in Wild Mice
inferredcites →https://doi.org/10.1371/journal.pgen.1000930openalex-snapshot
Genetic Evidence for Hybrid Trait Speciation in Heliconius Butterflies
inferredcites →https://doi.org/10.1371/journal.pgen.1002660openalex-snapshot
The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection
inferredcites →https://doi.org/10.1371/journal.pgen.1002891openalex-snapshot
Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)
inferredcites →https://doi.org/10.1371/journal.pgen.1004438openalex-snapshot
Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex
inferredcites →https://doi.org/10.1371/journal.pone.0173746openalex-snapshot
The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units
inferredcites →https://doi.org/10.1515/mammalia-2015-0041openalex-snapshot
Subspecies differentiation of the house mouse Mus musculus Linnaeus, 1758 in the center and east of the Iranian plateau and Afghanistan
inferredcites →https://doi.org/10.1534/genetics.107.078550openalex-snapshot
Complex Signatures of Selection and Gene Conversion in the Duplicated Globin Genes of House Mice
inferredcites →https://doi.org/10.1534/genetics.108.090811openalex-snapshot
Identification of Selective Sweeps in Closely Related Populations of the House Mouse Based on Microsatellite Scans
inferredcites →https://doi.org/10.7554/elife.02504openalex-snapshot
Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions
inferredcites →https://doi.org/10.7554/elife.05959openalex-snapshot
Insights into mammalian biology from the wild house mouse Mus musculus

What points at this work

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

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A Plea for Standardized Nuclear Markers in Metazoan DNA Taxonomy
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Natural variation in the zinc-finger-encoding exon of Prdm9 affects hybrid sterility phenotypes in mice
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Ancestral variation and its impact on wild house mouse genomes
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The genomic impact of historical hybridization with massive mitochondrial DNA introgression
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Multiplex PCR for identification of two butterfly sister species: Eurema mandarina and Eurema hecabe
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Mus musculus populations in Western Australia lack VKORC1 mutations conferring resistance to first generation anticoagulant rodenticides: Implications for conservation and biosecurity
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Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in mice
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Taxonomic Revision of Tribe Aleurocanthini Takahashi 1954 stat. rev. Using Consortium Gene Analysis (Mito-Nuclear-Primary Endosymbiont) with the First Evidence for Mitochondrial Recombination in Whitefly (Hemiptera: Aleyrodidae)
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Genome admixture with massive mitochondrial DNA introgression in hares (Lepus spp.) : the relative roles of demography and natural selection.
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