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Multiple origin but single domestication led to Oryza sativa

https://doi.org/10.1101/127688
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s10722-017-0518-0openalex-snapshot
Origin of rice (Oryza sativa L.) domestication genes
inferredcites →https://doi.org/10.1007/s12520-010-0035-yopenalex-snapshot
Consilience of genetics and archaeobotany in the entangled history of rice
inferredcites →https://doi.org/10.1007/s12520-015-0236-5openalex-snapshot
Archaeogenetic study of prehistoric rice remains from Thailand and India: evidence of early japonica in South and Southeast Asia
inferredcites →https://doi.org/10.1016/j.tree.2013.08.003openalex-snapshot
Population genomics of rapid adaptation by soft selective sweeps
inferredcites →https://doi.org/10.1023/a:1005825519998openalex-snapshot
Alien introgression in rice
inferredcites →https://doi.org/10.1038/nature10842openalex-snapshot
Insights into hominid evolution from the gorilla genome sequence
inferredcites →https://doi.org/10.1038/nature11128openalex-snapshot
The bonobo genome compared with the chimpanzee and human genomes
inferredcites →https://doi.org/10.1038/nature11532openalex-snapshot
A map of rice genome variation reveals the origin of cultivated rice
inferredcites →https://doi.org/10.1038/nbt.2050openalex-snapshot
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
inferredcites →https://doi.org/10.1038/ng.197openalex-snapshot
Control of a key transition from prostrate to erect growth in rice domestication
inferredcites →https://doi.org/10.1038/ng.247openalex-snapshot
Genetic control of rice plant architecture under domestication
inferredcites →https://doi.org/10.1038/ng.3825openalex-snapshot
Signatures of adaptation in the weedy rice genome
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nplants.2015.164openalex-snapshot
Three geographically separate domestications of Asian rice
inferredcites →https://doi.org/10.1038/nrg2986openalex-snapshot
Genotype and SNP calling from next-generation sequencing data
inferredcites →https://doi.org/10.1038/nrg3605openalex-snapshot
Evolution of crop species: genetics of domestication and diversification
inferredcites →https://doi.org/10.1073/pnas.1308942110openalex-snapshot
Archaeological and genetic insights into the origins of domesticated rice
inferredcites →https://doi.org/10.1093/bioinformatics/btu041openalex-snapshot
ngsTools: methods for population genetics analyses from next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/molbev/mss136openalex-snapshot
A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans
inferredcites →https://doi.org/10.1093/molbev/msv150openalex-snapshot
FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.
inferredcites →https://doi.org/10.1093/molbev/msw296openalex-snapshot
Deleterious variants in Asian rice and the potential cost of domestication
inferredcites →https://doi.org/10.1093/molbev/msx049openalex-snapshot
The rice paradox: Multiple origins but single domestication in Asian rice
inferredcites →https://doi.org/10.1093/nar/gkw290openalex-snapshot
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040517openalex-snapshot
Relationships between gene trees and species trees.
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.114751.110openalex-snapshot
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
inferredcites →https://doi.org/10.1101/gr.204800.116openalex-snapshot
Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice
inferredcites →https://doi.org/10.1105/tpc.15.00260openalex-snapshot
LABA1 , a Domestication Gene Associated with Long, Barbed Awns in Wild Rice
inferredcites →https://doi.org/10.1111/bij.12511openalex-snapshot
Improving the estimation of genetic distances from Next-Generation Sequencing data
inferredcites →https://doi.org/10.1111/evo.12118openalex-snapshot
MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04708.xopenalex-snapshot
Molecular evolution of shattering loci in U.S. weedy rice
inferredcites →https://doi.org/10.1111/j.1469-8137.2009.02984.xopenalex-snapshot
Selection on grain shattering genes and rates of rice domestication
inferredcites →https://doi.org/10.1111/j.1744-7909.2007.00510.xopenalex-snapshot
The Puzzle of Rice Domestication
inferredcites →https://doi.org/10.1126/science.1123604openalex-snapshot
Rice Domestication by Reducing Shattering
inferredcites →https://doi.org/10.1146/annurev-genet-111212-133526openalex-snapshot
Detecting Natural Selection in Genomic Data
inferredcites →https://doi.org/10.1186/1471-2105-14-289openalex-snapshot
Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data
inferredcites →https://doi.org/10.1186/2047-217x-3-7openalex-snapshot
The 3,000 rice genomes project
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pgen.0030163openalex-snapshot
Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice
inferredcites →https://doi.org/10.1371/journal.pgen.1002100openalex-snapshot
Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes
inferredcites →https://doi.org/10.1534/genetics.104.035642openalex-snapshot
Genetic Structure and Diversity in Oryza sativa L.
inferredcites →https://doi.org/10.1534/genetics.106.068072openalex-snapshot
Nonindependent Domestication of the Two Rice Subspecies,Oryza sativassp.indicaand ssp.japonica, Demonstrated by Multilocus Microsatellites
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

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inferred← citeshttps://doi.org/10.1007/978-3-319-71997-9_20openalex-snapshot
Oryza nivara Sharma et Shastry
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