The complex geography of domestication of the African rice Oryza glaberrima

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes

(2018) Philippe Cubry et al.   CURRENT BIOLOGY

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Targeted resequencing reveals genomic signatures of barley domestication

(2018) Artem Pankin et al.   NEW PHYTOLOGIST

The domestication of plant architecture in African rice

(2018) Min Hu et al.   PLANT JOURNAL

Multiple Origin but Single Domestication Led to Oryza sativa

(2018) Jae Young Choi et al.   G3-Genes Genomes Genetics

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots

(2018) Daniel J. Lawson et al.   Nature Communications

Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice

(2018) Yongzhen Wu et al.   Nature Communications

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

(2017) Hongru Wang et al.   GENOME RESEARCH

The K = 2 conundrum

(2017) Jasmine K. Janes et al.   MOLECULAR ECOLOGY

Signatures of adaptation in the weedy rice genome

(2017) Lin-Feng Li et al.   NATURE GENETICS

A novel mutation conferring the nonbrittle phenotype of cultivated barley

(2017) Peter Civáň et al.   NEW PHYTOLOGIST

Geographic mosaics and changing rates of cereal domestication

(2017) Robin G. Allaby et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

(2017) Kelly Swarts et al.   SCIENCE

Evidence for mid-Holocene rice domestication in the Americas

(2017) Lautaro Hilbert et al.   Nature Ecology & Evolution

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Estimating the Number of Subpopulations ( K ) in Structured Populations

(2016) Robert Verity et al.   GENETICS

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Domestication history and geographical adaptation inferred from a SNP map of African rice

(2016) Rachel S Meyer et al.   NATURE GENETICS

A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication

(2016) Khin Thanda Win et al.   NEW PHYTOLOGIST

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Estimating the Number of Subpopulations ( K ) in Structured Populations

(2016) Robert Verity et al.   GENETICS

Improving the estimation of genetic distances from Next-Generation Sequencing data

(2015) Filipe G. Vieira et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Evolution of the Grain Dispersal System in Barley

(2015) Mohammad Pourkheirandish et al.   CELL

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice

(2015) Lei Hua et al.   PLANT CELL

Archaeogenetic study of prehistoric rice remains from Thailand and India: evidence of early japonica in South and Southeast Asia

(2015) Cristina Cobo Castillo et al.   Archaeological and Anthropological Sciences

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Archaeological and genetic insights into the origins of domesticated rice

(2014) B. L. Gross et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

(2014) D. Q. Fuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

(2013) Kenneth M. Olsen et al.   Annual Review of Plant Biology

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

OsLG1 regulates a closed panicle trait in domesticated rice

(2013) Takashige Ishii et al.   NATURE GENETICS

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

An-1 Encodes a Basic Helix-Loop-Helix Protein That Regulates Awn Development, Grain Size, and Grain Number in Rice

(2013) J. Luo et al.   PLANT CELL

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia

(2013) W. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergence of Agriculture in the Foothills of the Zagros Mountains of Iran

(2013) S. Riehl et al.   SCIENCE

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

(2012) Xuehui Huang et al.   NATURE

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

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

Independent Domestication of Asian Rice Followed by Gene Flow from japonica to indica

(2011) C.-c. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication

(2011) B.-F. Zhu et al.   PLANT PHYSIOLOGY

Sunflower domestication alleles support single domestication center in eastern North America

(2011) B. K. Blackman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular evidence for a single evolutionary origin of domesticated rice

(2011) J. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences

(2011) Zhi-Ming Li et al.   THEORETICAL AND APPLIED GENETICS

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

(2011) Ziwen He et al.   PLoS Genetics

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice

(2010) K. Sugimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic perspectives on crop domestication

(2010) Briana L. Gross et al.   TRENDS IN PLANT SCIENCE

Consilience of genetics and archaeobotany in the entangled history of rice

(2010) Dorian Q. Fuller et al.   Archaeological and Anthropological Sciences

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

Nonindependent Domestication of the Two Rice Subspecies, Oryza sativa ssp. indica and ssp. japonica , Demonstrated by Multilocus Microsatellites

(2008) Li-zhi Gao et al.   GENETICS

Control of a key transition from prostrate to erect growth in rice domestication

(2008) Lubin Tan et al.   NATURE GENETICS

Genetic control of rice plant architecture under domestication

(2008) Jian Jin et al.   NATURE GENETICS

The evolving story of rice evolution

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

The complex origins of domesticated crops in the Fertile Crescent

(2008) Terence A. Brown et al.   TRENDS IN ECOLOGY & EVOLUTION

Gene Nomenclature System for Rice

(2008) Susan R. McCouch et al.   Rice