Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species

ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process

(2016) Pier Francesco Palamara   BIOINFORMATICS

Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

(2016) Hugo F. Gante et al.   MOLECULAR ECOLOGY

Sympatric speciation of spiny mice,Acomys, unfolded transcriptomically at Evolution Canyon, Israel

(2016) Kexin Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat

(2016) Huajing Teng et al.   G3-Genes Genomes Genetics

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era

(2016) Feng Gao et al.   G3-Genes Genomes Genetics

Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

(2016) David A. Marques et al.   PLoS Genetics

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

(2016) Alvaro Martinez Barrio et al.   eLife

Genomic landscape of rat strain and substrain variation

(2015) Roel Hermsen et al.   BMC GENOMICS

Hybridization and the species problem in conservation

(2015) Benjamin M. Fitzpatrick et al.   Current Zoology

Molecular phylogenetic characterization of common murine rodents from Manipur, Northeast India

(2015) Dhananjoy S. Chingangbam et al.   GENES & GENETIC SYSTEMS

Recent Evolution inRattus norvegicusIs Shaped by Declining Effective Population Size

(2015) Eva E. Deinum et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional Organization of the Genome May Shape the Species Boundary in the House Mouse

(2015) Václav Janoušek et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detection of selective sweeps in structured populations: a comparison of recent methods

(2015) Alexandra I. Vatsiou et al.   MOLECULAR ECOLOGY

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Changes in the expression of neurotransmitter receptors in Parkin and DJ-1 knockout mice – A quantitative multireceptor study

(2015) J.N. Cremer et al.   NEUROSCIENCE

Sympatric speciation revealed by genome-wide divergence in the blind mole ratSpalax

(2015) Kexin Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets

(2015) Laura C. Norris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

(2015) M. Malinsky et al.   SCIENCE

Hybridization and the species problem in conservation

(2015) Benjamin M. Fitzpatrick et al.   Current Zoology

The Evolutionary Genomics of Cichlid Fishes: Explosive Speciation and Adaptation in the Postgenomic Era

(2014) Frederico Henning et al.   Annual Review of Genomics and Human Genetics

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

Mitochondrial DNA Phylogeography of the Norway Rat

(2014) Ying Song et al.   PLoS One

Interspecific introgressive origin of genomic diversity in the house mouse

(2014) Kevin J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation

(2014) Chris S. Clarkson et al.   Nature Communications

How Does Climate Influence Speciation?

(2013) Xia Hua et al.   AMERICAN NATURALIST

Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat

(2013) Santosh S. Atanur et al.   CELL

A Fast Estimate for the Population Recombination Rate Based on Regression

(2013) K. Lin et al.   GENETICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

(2012) S. Kumar et al.   BIOINFORMATICS

Absence of TI-VAMP/Vamp7 Leads to Increased Anxiety in Mice

(2012) L. Danglot et al.   JOURNAL OF NEUROSCIENCE

Population genetic structure and geographic differentiation in the hot spring snake Thermophis baileyi (Serpentes, Colubridae): Indications for glacial refuges in southern-central Tibet

(2012) Sylvia Hofmann   MOLECULAR PHYLOGENETICS AND EVOLUTION

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

(2012) Shancen Zhao et al.   NATURE GENETICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Evolution Out of Africa: The Role of Refugia and Climate Change

(2012) J. R. Stewart et al.   SCIENCE

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Nuclear Gene Variation in Wild Brown Rats

(2012) Rob W. Ness et al.   G3-Genes Genomes Genetics

Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

(2012) Fabian Staubach et al.   PLoS Genetics

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Persistence in Peripheral Refugia Promotes Phenotypic Divergence and Speciation in a Rainforest Frog

(2011) Conrad J. Hoskin et al.   AMERICAN NATURALIST

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice

(2011) Ying Song et al.   CURRENT BIOLOGY

The Microevolution of V1r Vomeronasal Receptor Genes in Mice

(2011) Seong Hwan Park et al.   Genome Biology and Evolution

Expression Patterns and Function of Chromatin Protein HMGB2 during Mesenchymal Stem Cell Differentiation

(2011) Noboru Taniguchi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Migration of Norway Rats Resulted in the Worldwide Distribution of Seoul Hantavirus Today

(2011) X.-D. Lin et al.   JOURNAL OF VIROLOGY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii)

(2011) JIN-XIAN LIU et al.   MOLECULAR ECOLOGY

Molecular evidence for Pleistocene refugia at the eastern edge of the Tibetan Plateau

(2011) XIANGJIANG ZHAN et al.   MOLECULAR ECOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

(2011) L. Abi-Rached et al.   SCIENCE

Recent and Rapid Speciation with Limited Morphological Disparity in the Genus Rattus

(2011) Kevin C. Rowe et al.   SYSTEMATIC BIOLOGY

Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

(2010) Marie Pagès et al.   BMC EVOLUTIONARY BIOLOGY

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Speciation genetics: current status and evolving approaches

(2010) J. B. W. Wolf et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Genetic Analysis of Baker's Yeast Msh4-Msh5 Reveals a Threshold Crossover Level for Meiotic Viability

(2010) K. T. Nishant et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Liver-specific Loss of Long Chain Acyl-CoA Synthetase-1 Decreases Triacylglycerol Synthesis and β-Oxidation and Alters Phospholipid Fatty Acid Composition

(2009) Lei O. Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau

(2009) Y. QU et al.   MOLECULAR ECOLOGY

Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe's First Farmers

(2009) B. Bramanti et al.   SCIENCE

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

Progress and prospects in rat genetics: a community view

(2008) Timothy J Aitman et al.   NATURE GENETICS