In contrast to the expected site frequency spectrum under neutral conditions, a large number of high frequency derived alleles is observed in both species (Fig 2). No high-impact substitutions were detected apart from a variant in Sh4 (a shattering gene), which encodes a premature stop codon in almost all domesticated accessions. The second call set contained fewer SNPs that adhere to a higher standard of quality. Oryza longistaminata was rejected because of its low genomic divergence from O. glaberrima (~2%). Asian and African rice have distinct phenotypic characteristics: their grains differ in colour, size, shape and taste. Since the non-shattering phenotype is a crucial trait in the domestication syndrome, the ancestral state of this substitution in a limited number of OG-II accessions presupposes that another variant—either in the same gene or in a different gene—might be causing the same phenotype. Joint variant calling and quality filtering resulted in a total of 3,923,601 SNPs. endobj One proposes that plant domestication in Africa occurred in a non-centric (geographically diffuse) manner, over a protracted period of time [9], and has been called the ‘protracted transition model’. Putative effects of segregating SNPs were predicted using SnpEff (v4.0). A large number of individuals in these populations contain substantial fractions of both ancestries, making these populations less readily distinguishable. The origin of Oryza sativa rice domestication has been a subject of much debate among those who study crop history and anthropology - whether rice originated in India or China. This limitation is overcome with the introduction of genome-wide analyses and tools. Rice accompanied African slaves across the Middle Passage throughout the New World to Brazil, the Caribbean, and the southern United States. To confirm the clustering of O. glaberrima within O. barthii, a whole genome phylogenetic tree was constructed based on 3,923,601 genome-wide SNPs. Accessions were assigned to a cluster according to their genetic background, with the colour of each sample representing the ancestral population (K = 5) that accounted for the majority (>50%) of pruned SNPs in that accession. The present distribution of O. glaberrima cultivation in West Africa is shaded in light green, based on Vaughan [18]. This low level of diversity was confirmed by subsequent genomic studies. The fact that O. glaberrima does not form a monophyletic clade, however, calls into question the assumption that it speciated through a discrete domestication event. Remaining haplotypes, consisting of a mix O. barthii and O. glaberrima accessions from a single subpopulation, are expanded with branch colours reflecting their population of origin of the O. glaberrima accessions. To account for uneven sample sizes of these populations, an equal number of individuals (n = 15) was selected for each of the five sub-populations as identified with ADMIXTURE. Jollof Rice. japonica which, as a sister taxon, is supposed to be equidistant to the outgroup as compared to O. glaberrima. Eight of the twenty genes clearly deviate from the genome-wide phylogenetic signal (S3 Table). We thus observe that, even though the total number of polymorphic sites in larger in OG-I through OG-III, the average number of pairwise differences between these individuals is lower. We evaluated genetic IBD as the correlation between pairwise relatedness, measured by the kinship coefficient (φ), and pairwise geographic distance, measured by the shortest distance between the collection sites of two accessions in kilometres. Haplotypes that consist exclusively of O. barthii are collapsed into blue nodes. To investigate to what extent population substructure in O. glaberrima and O. barthii could disqualify the hard sweep model, we re-examined the variation in both species. Indeed, it is a widely observed phenomenon that incomplete lineage causes mixed phylogenetic signals [32]. To assess whether certain domestication traits of O. glaberrima could have had multiple origins, NJ trees were constructed for several domestication genes known from recent rice genetics literature [22,25], a list of which can be found in S2 Table. Extensive LD is observed in the O. glaberrima genome, with r2 reaching half its maximum value at a distance of 175 kb and approaching baseline at 300 kb [3]. Phylogenetic results confirm the clustering of O. glaberrima within O. barthii but shed new light on the relationships between sub-populations of the wild and domesticated species. Formal analysis, Synonymous and non-coding SNPs were extracted using SnpSift (v4.0) [46]. Relative diversity estimates, selection scans and detection of population structure require fewer SNPs; for those analysis, the reduced call set was used. To test whether the observed population structure could be the result of geography, isolation by distance (IBD) was assessed among all West African accessions. Both coding and noncoding positions were used. Although the exact history of rice in Asia is still disputed, it is clear that Asian rice (Oryza sativa L.) was domesticated from a single wild species (Oryza rufipogon Griff.) The ratio of synonymous to non-synonymous substitutions and the relative proportion of protein coding variation appear to be roughly the same (between 0.80–0.85, and less than 10% of the total SNP count, respectively). %PDF-1.5 The complementation of computational studies with experimental data will be indispensable in the future—not just for understanding the broad patterns of evolution and domestication of African rice, but also to provide insights into the emergence of local adaptive traits connected with the diversification of this crop in its different geographic contexts. https://doi.org/10.1371/journal.pone.0203508.t002. The derived allele frequency spectrum was calculated for all synonymous and noncoding variants of the remaining 1,591,134 SNPs. In contrast, OG-IV is restricted to the inland areas and is located primarily south and east of OG-V. A closer inspection of the neighbouring O. barthii accessions reveals that their closest relatives all belong to the OB-B subpopulation, rather than the expected OB-C and OB-D populations (Fig 6). This may be due to the low number of geo-referenced individuals, a lack of geographic structure or both. Filtering criteria with different levels of strictness were applied (S5 Table). While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice–either by selection on different alleles, or different modes of selection. These CLR methods are superior to more common neutrality tests such as Tajima’s D, because they measure deviations of the site frequency spectrum (SFS) against the genomic ‘background’ SFS. A list of all used accessions and their metadata can be found in S1 Table. 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