Patterns of Genome-Wide Diversity and Population Structure in the Drosophila athabasca Species Complex

The search for causal traits of speciation: Divergent female mate preferences target male courtship song, not pheromones, inDrosophila athabascaspecies complex

(2016) Roman Yukilevich et al.   EVOLUTION

Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts

(2016) Owen G. Osborne et al.   Genome Biology and Evolution

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

(2015) Helen Attrill et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

CHROMOSOMAL REARRANGEMENTS AND THE GENETICS OF REPRODUCTIVE BARRIERS INMIMULUS(MONKEY FLOWERS)

(2013) Lila Fishman et al.   EVOLUTION

Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population

(2013) Rajiv C. McCoy et al.   MOLECULAR ECOLOGY

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila

(2012) Q. Zhou et al.   SCIENCE

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

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

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Studies of the species barrier between Drosophila subobscura and D. madeirensis V: the importance of sex-linked inversion in preserving species identity

(2011) M. KHADEM et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Testing for Ancient Admixture between Closely Related Populations

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

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

THE CONTRIBUTION OF GENE MOVEMENT TO THE “TWO RULES OF SPECIATION”

(2010) Leonie C. Moyle et al.   EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The molecular evolutionary basis of species formation

(2010) Daven C. Presgraves   NATURE REVIEWS GENETICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

(2010) David B. Lowry et al.   PLOS BIOLOGY

How and Why Chromosome Inversions Evolve

(2010) Mark Kirkpatrick   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

THE BIOLOGY OF SPECIATION

(2009) James M. Sobel et al.   EVOLUTION

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

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

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Sex chromosomes and speciation in Drosophila

(2008) Daven C. Presgraves   TRENDS IN GENETICS