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Evolutionary history of the brown rat: out of southern East Asia and selection

https://doi.org/10.1101/096800
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Rapid Neighbour-Joining
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GCTA: A Tool for Genome-wide Complex Trait Analysis
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Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians
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Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat
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Negative regulation of T-cell activation and autoimmunity by Mgat5 N-glycosylation
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Out of southern East Asia: the natural history of domestic dogs across the world
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Molecular evolution of FOXP2, a gene involved in speech and language
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Genome sequence of the Brown Norway rat yields insights into mammalian evolution
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Genome-wide detection and characterization of positive selection in human populations
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A genomic history of Aboriginal Australia
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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
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Improved whole-chromosome phasing for disease and population genetic studies
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
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Origins and dispersals of Pacific peoples: Evidence from mtDNA phylogenies of the Pacific rat
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Evidence for higher rates of nucleotide substitution in rodents than in man.
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Mice Deficient in Nervous System-specific Carbohydrate Epitope HNK-1 Exhibit Impaired Synaptic Plasticity and Spatial Learning
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Animal domestication and behavior
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Rodent-borne diseases and their risks for public health
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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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Aboriginal and Invasive Rats of Genus Rattus as Hosts of Infectious Agents
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The Behavior of the Laboratory Rat
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TimeTree: a public knowledge-base of divergence times among organisms
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TopHat: discovering splice junctions with RNA-Seq
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TimeTree2: species divergence times on the iPhone
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Artificial Selection on Brain-Expressed Genes during the Domestication of Dog
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Tree of Life Reveals Clock-Like Speciation and Diversification
inferredcites →https://doi.org/10.1093/molbev/msv126openalex-snapshot
Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size
inferredcites →https://doi.org/10.1093/molbev/msw054openalex-snapshot
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
inferredcites →https://doi.org/10.1093/nar/gkr378openalex-snapshot
g:Profiler—a web server for functional interpretation of gene lists (2011 update)
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Of mice and (Viking?) men: phylogeography of British and Irish house mice
inferredcites →https://doi.org/10.1098/rspb.2016.1762openalex-snapshot
Global population divergence and admixture of the brown rat ( Rattus norvegicus )
inferredcites →https://doi.org/10.1101/gr.088336.108openalex-snapshot
Darwinian and demographic forces affecting human protein coding genes
inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot
Fast model-based estimation of ancestry in unrelated individuals
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.4252305openalex-snapshot
Genomic scans for selective sweeps using SNP data
inferredcites →https://doi.org/10.1101/gr.631202openalex-snapshot
Interrogating a High-Density SNP Map for Signatures of Natural Selection
inferredcites →https://doi.org/10.1111/j.1365-2699.2009.02228.xopenalex-snapshot
Phylogeography of the introduced species Rattus rattus in the western Indian Ocean, with special emphasis on the colonization history of Madagascar
inferredcites →https://doi.org/10.1126/science.1124309openalex-snapshot
Positive Natural Selection in the Human Lineage
inferredcites →https://doi.org/10.1126/science.1253714openalex-snapshot
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
inferredcites →https://doi.org/10.1126/science.8171325openalex-snapshot
Mutagenesis and Mapping of a Mouse Gene, Clock , Essential for Circadian Behavior
inferredcites →https://doi.org/10.1126/science.aaf3161openalex-snapshot
Genomic and archaeological evidence suggest a dual origin of domestic dogs
inferredcites →https://doi.org/10.1128/jvi.00725-11openalex-snapshot
Migration of Norway Rats Resulted in the Worldwide Distribution of Seoul Hantavirus Today
inferredcites →https://doi.org/10.1186/gb-2003-4-5-p3openalex-snapshot
DAVID: Database for Annotation, Visualization, and Integrated Discovery
inferredcites →https://doi.org/10.1186/gb-2008-9-8-r124openalex-snapshot
Metabolic changes in schizophrenia and human brain evolution
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Inferring the Demographic History and Rate of Adaptive Substitution in Drosophila
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Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
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Elevated Oxidative Membrane Damage Associated with Genetic Modifiers of Lyst-Mutant Phenotypes
inferredcites →https://doi.org/10.1371/journal.pgen.1002967openalex-snapshot
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1003905openalex-snapshot
Robust Demographic Inference from Genomic and SNP Data
inferredcites →https://doi.org/10.1371/journal.pgen.1003995openalex-snapshot
Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1371/journal.pone.0040642openalex-snapshot
Species Specific Behavioural Patterns (Digging and Swimming) and Reaction to Novel Objects in Wild Type, Wistar, Sprague-Dawley and Brown Norway Rats
inferredcites →https://doi.org/10.1371/journal.pone.0043059openalex-snapshot
Origins of Albino and Hooded Rats: Implications from Molecular Genetic Analysis across Modern Laboratory Rat Strains
inferredcites →https://doi.org/10.1371/journal.pone.0088425openalex-snapshot
Mitochondrial DNA Phylogeography of the Norway Rat
inferredcites →https://doi.org/10.1534/g3.112.004713openalex-snapshot
Nuclear Gene Variation in Wild Brown Rats
inferredcites →https://doi.org/10.1534/genetics.112.145037openalex-snapshot
Ancient Admixture in Human History
inferredcites →https://doi.org/10.2307/1223169openalex-snapshot
Mammal Species of the World: A Taxonomic and Geographic Reference
inferredcites →https://doi.org/10.2307/2970openalex-snapshot
Recent Mammals of the World: A Synopsis of Families
inferredcites →https://doi.org/10.2307/j.ctv1nthqkopenalex-snapshot
Singapore and the Silk Road of the Sea, 1300–1800
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The maritime boundaries of the Indian Ocean region
inferredcites →https://doi.org/10.5860/choice.37-4853openalex-snapshot
The Atlas of European Mammals
inferredcites →https://doi.org/10.5962/bhl.title.64280openalex-snapshot
The house rat /

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inferred← citeshttps://doi.org/10.1007/978-1-4939-9581-3_1openalex-snapshot
The Rat: A Model Used in Biomedical Research
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