Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungusNeurospora discreta

The population biology of fungal invasions

(2015) P. Gladieux et al.   MOLECULAR ECOLOGY

Genetic isolation between two recently diverged populations of a symbiotic fungus

(2015) Sara Branco et al.   MOLECULAR ECOLOGY

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Clonal reproduction in fungi

(2015) John W. Taylor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in aMytilushybrid zone

(2014) C. Roux et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system

(2014) Pádraic Corcoran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

How important is intraspecific genetic admixture to the success of colonising populations?

(2014) Marc Rius et al.   TRENDS IN ECOLOGY & EVOLUTION

Discovering Functions of Unannotated Genes from a Transcriptome Survey of Wild Fungal Isolates

(2014) C. E. Ellison et al.   mBio

Secret lifestyles of Neurospora crassa

(2014) Hsiao-Che Kuo et al.   Scientific Reports

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

(2013) Camille Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Selective Sweep across Species Boundaries in Drosophila

(2013) Cara L. Brand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

History of the invasion of the anther smut pathogen onSilene latifoliain North America

(2013) Michael C. Fontaine et al.   NEW PHYTOLOGIST

Evolution, selection and isolation: a genomic view of speciation in fungal plant pathogens

(2013) Eva Holtgrewe Stukenbrock   NEW PHYTOLOGIST

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome Wide Association Identifies Novel Loci Involved in Fungal Communication

(2013) Javier Palma-Guerrero et al.   PLoS Genetics

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

Evolutionary insight from whole-genome sequencing of experimentally evolved microbes

(2012) JEREMY R. DETTMAN et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

Large-Scale Introgression Shapes the Evolution of the Mating-Type Chromosomes of the Filamentous Ascomycete Neurospora tetrasperma

(2012) Yu Sun et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Nuclear and Genome Dynamics in Multinucleate Ascomycete Fungi

(2011) Marcus Roper et al.   CURRENT BIOLOGY

Emergence of novel fungal pathogens by ecological speciation: importance of the reduced viability of immigrants

(2011) PIERRE GLADIEUX et al.   MOLECULAR ECOLOGY

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

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genes underlying the process of speciation

(2011) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

Genetic Architecture of a Reinforced, Postmating, Reproductive Isolation Barrier between Neurospora Species Indicates Evolution via Natural Selection

(2011) Elizabeth Turner et al.   PLoS Genetics

Speciation genes in plants

(2010) Loren H. Rieseberg et al.   ANNALS OF BOTANY

Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora

(2010) Rebecka Strandberg et al.   FUNGAL GENETICS AND BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research

(2010) K. McCluskey et al.   JOURNAL OF BIOSCIENCES

Reinforced postmating reproductive isolation barriers in Neurospora, an Ascomycete microfungus

(2010) E. TURNER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Linking the emergence of fungal plant diseases with ecological speciation

(2010) Tatiana Giraud et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phylogenetic and biological species diversity within theNeurospora tetraspermacomplex

(2009) A. MENKIS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Natural selection in action during speciation

(2009) S. Via   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

(2009) M. Novo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

ADZE: a rarefaction approach for counting alleles private to combinations of populations

(2008) Z. A. Szpiech et al.   BIOINFORMATICS

Divergent adaptation promotes reproductive isolation among experimental populations of the filamentous fungus Neurospora

(2008) Jeremy R Dettman et al.   BMC EVOLUTIONARY BIOLOGY

Existence of a pattern of reproductive character displacement in Homobasidiomycota but not in Ascomycota

(2008) M. LE GAC et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle

(2008) I. J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA