DOI: 10.5061/dryad.t7g7cj4
title: Data from: The complex geography of domestication of the African rice Oryza glaberrima

description: While the domestication history of Asian rice has been extensively
 studied, details of the evolution of African rice remain elusive. The
 inner Niger delta has been suggested as the center of origin but molecular
 data to support this hypothesis is lacking. Here, we present a
 comprehensive analysis of the evolutionary and domestication history of
 African rice. By analyzing whole genome re-sequencing data from 282
 individuals of domesticated African rice Oryza glaberrima and its
 progenitor O. barthii, we hypothesize a non-centric (i.e. multiregional)
 domestication origin for African rice. Our analyses showed genetic
 structure within O. glaberrima that has a geographical association.
 Furthermore, we have evidence that the previously hypothesized O. barthii
 progenitor populations in West Africa have evolutionary signatures similar
 to domesticated rice and carried causal domestication mutations,
 suggesting those progenitors were either mislabeled or may actually
 represent feral wild-domesticated hybrids. Phylogeographic analysis of
 genes involved in the core domestication process suggests that the origins
 of causal domestication mutations could be traced to wild progenitors in
 multiple different locations in West and Central Africa. In addition,
 measurements of panicle threshability, a key early domestication trait for
 seed shattering, were consistent with the gene phylogeographic results. We
 suggest seed non-shattering was selected from multiple genotypes, possibly
 arising from different geographical regions. Based on our evidence, O.
 glaberrima was not domesticated from a single centric location but was a
 result of diffuse process where multiple regions contributed key alleles
 for different domestication traits.
description: ngsAdmix ancestry
 proportionngsAdmix results
 estimating ancestry proportions from K=2 to K=9 for all 282
 samples.ngsAdmix.zipO. rufipogon genome aligned to O. barthii or O. glaberrimaO. rufipogon reference genome sequence was aligned to O. barthii or O. glaberrima reference genome. For every O. barthii or O. glaberrima coordinate was converted into O. rufipogon sequence resulting in a O. barthii-ized or O. glaberrima-ized O. rufipogon genome sequence. Not alignable regions were indicated as 'N'.Oruf_outgroup_genome.zipHaplotype NetworkPhased vcf file for the genes sh1, sh4, and PROG1 region. Data used to estimate the haplotype network.HaploNetwork.zipngsCovar PCA resultGenotype likelihood based PCA analysis of O. glaberrima population.ngsCovar.zipPhylogenomic and phylogenetic tree plotted with iTolNewick format trees for genome-wide and the 3 domestication genes. Tree can be visualized on iTol (http://itol.embl.de) and colored using the supplied itol file.ngsDist.zipPairwise Fst valuesAll pairwise genome-wide Fst values calculated using ANGSD.ANGSD_FST.zipTheta and related population genetics statisticsGenome-wide theta and related population genetics statistics calculated using ANGSD.ANGSD_THETA.zipLD statisticsLD values calculated using PLINK for each genetic group.r2mean_1000bin.txtGenotypes surrounding domestication geneFile used to visualize the SNPs (genotypes) surroinding domestication gene of interest.HAPLOTYPE_VIEW.zipBinary plink file for silhouette score filtered individualsBinary plink files used for treemix study. Contains individuals and their SNPs after implementing the silhouette score based filtering.SilhouetteScoreFilteredGroup.zipFiltered VCF file used in study (chr1) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr1.final.recode.vcf.gzFiltered VCF file used in study (chr2) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr2.final.recode.vcf.gzFiltered VCF file used in study (chr3) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr3.final.recode.vcf.gzFiltered VCF file used in study (chr4) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr4.final.recode.vcf.gzFiltered VCF file used in study (chr5) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr5.final.recode.vcf.gzFiltered VCF file used in study (chr6) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr6.final.recode.vcf.gzFiltered VCF file used in study (chr7) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr7.final.recode.vcf.gzFiltered VCF file used in study (chr8) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr8.final.recode.vcf.gzFiltered VCF file used in study (chr9) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr9.final.recode.vcf.gzFiltered VCF file used in study (chr10) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr10.final.recode.vcf.gzFiltered VCF file used in study (chr11) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr11.final.recode.vcf.gzFiltered VCF file used in study (chr12) - glaberrima as reference genomeO. glaberrima reference genome based SNP calls. Filtering process described in paper.chr12.final.recode.vcf.gzFiltered VCF file used in study (chr1) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr1.final.recode.vcf.gzFiltered VCF file used in study (chr2) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr2.final.recode.vcf.gzFiltered VCF file used in study (chr3) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr3.final.recode.vcf.gzFiltered VCF file used in study (chr4) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr4.final.recode.vcf.gzFiltered VCF file used in study (chr5) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr5.final.recode.vcf.gzFiltered VCF file used in study (chr6) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr6.final.recode.vcf.gzFiltered VCF file used in study (chr7) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr7.final.recode.vcf.gzFiltered VCF file used in study (chr8) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr8.final.recode.vcf.gzFiltered VCF file used in study (chr9) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr9.final.recode.vcf.gzFiltered VCF file used in study (chr10) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr10.final.recode.vcf.gzFiltered VCF file used in study (chr11) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr11.final.recode.vcf.gzFiltered VCF file used in study (chr12) - barthii as reference genomeO. barthii reference genome based SNP calls. Filtering process described in paper.chr12.final.recode.vcf.gz