Parallel Speciation of Wild Rice Associated with Habitat Shifts

Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower

(2017) Federico Roda et al.   MOLECULAR ECOLOGY

Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae)

(2017) Emiliano Trucchi et al.   NEW PHYTOLOGIST

Recurrent origin of peripheral, coastal (sub)species in Mediterranean Senecio (Asteraceae)

(2017) Hans P. Comes et al.   Plant Ecology & Diversity

Divergent natural selection drives the evolution of reproductive isolation in an Australian wildflower

(2016) Thomas J. Richards et al.   EVOLUTION

The genetic architecture of local adaptation and reproductive isolation in sympatry within theMimulus guttatusspecies complex

(2016) Kathleen G. Ferris et al.   MOLECULAR ECOLOGY

Genomic evidence for polyphyletic origins and interlineage gene flow within complex taxa: a case study ofPicea brachytylain the Qinghai-Tibet Plateau

(2016) Dafu Ru et al.   MOLECULAR ECOLOGY

Remarkable life history polymorphism may be evolving under divergent selection in the silverleaf sunflower

(2016) Brook T. Moyers et al.   MOLECULAR ECOLOGY

Demographic modelling with whole-genome data reveals parallel origin of similarPundamiliacichlid species after hybridization

(2016) Joana I. Meier et al.   MOLECULAR ECOLOGY

The unique and multifaceted importance of the timing of flowering

(2015) Steven J. Franks   AMERICAN JOURNAL OF BOTANY

Strong premating reproductive isolation drives incipient speciation inMimulus aurantiacus

(2015) James M. Sobel et al.   EVOLUTION

Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of TwoOryzaSpecies

(2015) Jie Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genetic structure ofOryza rufipogonandOryza nivara: implications for the origin ofO. nivara

(2015) Rong Liu et al.   MOLECULAR ECOLOGY

Shared and nonshared genomic divergence in parallel ecotypes ofLittorina saxatilisat a local scale

(2015) Mark Ravinet et al.   MOLECULAR ECOLOGY

Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history ofEucalyptus grandis

(2015) Orzenil B. Silva-Junior et al.   NEW PHYTOLOGIST

The evolution of drought escape and avoidance in natural herbaceous populations

(2015) Nicholas J. Kooyers   PLANT SCIENCE

Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata

(2015) Marco Fracassetti et al.   PLoS One

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Population-Genetic Inference from Pooled-Sequencing Data

(2014) Michael Lynch et al.   Genome Biology and Evolution

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes

(2014) Kathryn R. Elmer et al.   Nature Communications

Natural variation and genetic constraints on drought tolerance

(2013) Thomas E Juenger   CURRENT OPINION IN PLANT BIOLOGY

PARALLEL EVOLUTION OF LOCAL ADAPTATION AND REPRODUCTIVE ISOLATION IN THE FACE OF GENE FLOW

(2013) Roger K. Butlin et al.   EVOLUTION

Ecogeographic Variation in the Morphology of Two Asian Wild Rice Species, Oryza nivara and Oryza rufipogon

(2013) Maria Celeste N. Banaticla-Hilario et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Genomic evidence for the parallel evolution of coastal forms in theSenecio lautuscomplex

(2013) Federico Roda et al.   MOLECULAR ECOLOGY

Advances in Ecological Speciation: an integrative approach

(2013) Rui Faria et al.   MOLECULAR ECOLOGY

QST–FST comparisons: evolutionary and ecological insights from genomic heterogeneity

(2013) Tuomas Leinonen et al.   NATURE REVIEWS GENETICS

Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

(2013) Christian Rellstab et al.   PLoS One

Nucleotide diversity of 11S seed storage protein gene and its implications for ecological adaptation ofOryza nivara

(2013) Lei HUANG et al.   Journal of Systematics and Evolution

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

GENOME SIZE IS NOT CORRELATED WITH EFFECTIVE POPULATION SIZE IN THEORYZASPECIES

(2012) Bin Ai et al.   EVOLUTION

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Magic traits in speciation: ‘magic’ but not rare?

(2011) Maria R. Servedio et al.   TRENDS IN ECOLOGY & EVOLUTION

Approximate Bayesian Computation in Evolution and Ecology

(2010) Mark A. Beaumont   Annual Review of Ecology Evolution and Systematics

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

(2010) Daniel Wegmann et al.   BMC BIOINFORMATICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara)

(2010) XIAO-MING ZHENG et al.   MOLECULAR ECOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

GENETIC ARCHITECTURE FOR THE ADAPTIVE ORIGIN OF ANNUAL WILD RICE,ORYZA NIVARA

(2009) Michael A. Grillo et al.   EVOLUTION

Testing for Spatially Divergent Selection: Comparing QST to FST

(2009) M. C. Whitlock et al.   GENETICS

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

GSTand its relatives do not measure differentiation

(2008) LOU JOST   MOLECULAR ECOLOGY

The strength and genetic basis of reproductive isolating barriers in flowering plants

(2008) D. B Lowry et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The evolving story of rice evolution

(2008) Duncan A. Vaughan et al.   PLANT SCIENCE