Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

(2015) James A. Cahill et al.   MOLECULAR ECOLOGY

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

(2015) Sangeet Lamichhaney et al.   NATURE

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

HOW COMMON IS HOMOPLOID HYBRID SPECIATION?

(2014) Molly Schumer et al.   EVOLUTION

Genome-Wide Patterns of Differentiation Among House Mouse Subspecies

(2014) Megan Phifer-Rixey et al.   GENETICS

Divergence with gene flow within the recent chipmunk radiation (Tamias)

(2014) J Sullivan et al.   HEREDITY

Hybridization, Introgression, and the Nature of Species Boundaries

(2014) Richard G. Harrison et al.   JOURNAL OF HEREDITY

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

The hidden history of the snowshoe hare,Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation

(2014) José Melo-Ferreira et al.   MOLECULAR ECOLOGY

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

(2014) Zachariah Gompert et al.   MOLECULAR ECOLOGY

Theoretical models of the influence of genomic architecture on the dynamics of speciation

(2014) Samuel M. Flaxman et al.   MOLECULAR ECOLOGY

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

(2014) Emilia Huerta-Sánchez et al.   NATURE

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Single Nucleotide Polymorphisms Reveal Genetic Structuring of the Carpathian Newt and Provide Evidence of Interspecific Gene Flow in the Nuclear Genome

(2014) Piotr Zieliński 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

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

(2014) Miguel Carneiro et al.   PLoS Genetics

Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions

(2014) Leslie M Turner et al.   eLife

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

(2014) Molly Schumer et al.   eLife

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES

(2013) Rongfeng Cui et al.   EVOLUTION

GENETIC HITCHHIKING AND THE DYNAMIC BUILDUP OF GENOMIC DIVERGENCE DURING SPECIATION WITH GENE FLOW

(2013) Samuel M. Flaxman et al.   EVOLUTION

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

Does hybridization influence speciation?

(2013) N. H. Barton   JOURNAL OF EVOLUTIONARY BIOLOGY

Conditions when hybridization might predispose populations for adaptive radiation

(2013) O. Seehausen   JOURNAL OF EVOLUTIONARY BIOLOGY

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Neandertal Origin of Genetic Variation at the Cluster of OAS Immunity Genes

(2013) F. L. Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni)

(2013) P. Zieliński et al.   MOLECULAR ECOLOGY

Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

(2013) Miguel Carneiro et al.   MOLECULAR ECOLOGY

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Independent specialization of the human and mouse X chromosomes for the male germ line

(2013) Jacob L Mueller et al.   NATURE GENETICS

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea

(2012) Fernando L. Mendez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

THE LANGUAGE OF SPECIATION

(2012) Richard G. Harrison   EVOLUTION

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

The Date of Interbreeding between Neandertals and Modern Humans

(2012) Sriram Sankararaman et al.   PLoS Genetics

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

(2011) Ying Song et al.   CURRENT BIOLOGY

Testing for Ancient Admixture between Closely Related Populations

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

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2011) L. Abi-Rached et al.   SCIENCE

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Phylogeny Estimation of the Radiation of Western North American Chipmunks (Tamias) in the Face of Introgression Using Reproductive Protein Genes

(2011) Noah Reid et al.   SYSTEMATIC BIOLOGY

Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) Revealed by Species-Tree Inference and Coalescent Simulations

(2011) J. Melo-Ferreira et al.   SYSTEMATIC BIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Examination of nuclear loci across a zone of mitochondrial introgression between Tamias ruficaudus and T. amoenus

(2010) Noah Reid et al.   JOURNAL OF MAMMALOGY

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

(2009) Emily Hodges et al.   Nature Protocols

Molecular and Evolutionary History of Melanism in North American Gray Wolves

(2009) T. M. Anderson et al.   SCIENCE

What, if anything, is sympatric speciation?

(2008) B. M. FITZPATRICK et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The genetic mosaic suggests a new role for hitchhiking in ecological speciation

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

Ancient hybridization and mitochondrial capture between two species of chipmunks

(2008) JEFFREY M. GOOD et al.   MOLECULAR ECOLOGY

Mitochondrial DNA under siege in avian phylogeography

(2008) ROBERT M. ZINK et al.   MOLECULAR ECOLOGY