Modelling the population history using population genomics : the tomato domestication as a case of study.
A bottleneck is commonly associated to the study of crop domestication, in which a population experiences a drastic reduction in size and nucleotide diversity. The population genomic era offers new opportunities to document this scenario through the study of the site frequency spectrum (SFS), a powerful method for summarizing genomic data at the genome-wide level. Using a diffusion approximation approach (Gutenkunst et al., 2009) to model SFS, we estimated the demographical history of a major crop, the cultivated tomato (Solanum lycopersicum) and its wild relative (S. pimpinellifolium). We compared the observed 2 dimensional SFS, obtained from 20 individuals and ~84,500 SNPs markers, to the modelled ones, obtained from four different scenarios. Variants were polarized to ancestral and derived alleles based on the eggplant outgroup sequences. Assuming a mutation rate of 3×10-9 and a generation time of 1 year, our results suggest that in the best fitting model, population split occurred ~3750 years ago (95%CI: 2985-4552 yrs), wild tomatoes experienced a dramatic bottleneck (effective population size: -87%; reduction of nucleotide diversity: -63%) that occurred ~420 years ago (95%CI: 337-541 yrs). After this bottleneck, migration rate, from cultivated to wild population, was estimated to less than ~1 migrant per generation. Although, 3.1% of the genes derived from neutral expectations suggesting evolutionary forces acting on. These results demonstrate the power of the approach and provide estimates of demographical parameters that fit previous studies of the tomato domestication (Blanca et al., 2015).
| Main Authors: | , , , , , , |
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| Format: | conference_item biblioteca |
| Language: | eng |
| Published: |
INRA
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| Online Access: | http://agritrop.cirad.fr/591300/ http://agritrop.cirad.fr/591300/7/ID591300.pdf |
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| Summary: | A bottleneck is commonly associated to the study of crop domestication, in which a population experiences a drastic reduction in size and nucleotide diversity. The population genomic era offers new opportunities to document this scenario through the study of the site frequency spectrum (SFS), a powerful method for summarizing genomic data at the genome-wide level. Using a diffusion approximation approach (Gutenkunst et al., 2009) to model SFS, we estimated the demographical history of a major crop, the cultivated tomato (Solanum lycopersicum) and its wild relative (S. pimpinellifolium). We compared the observed 2 dimensional SFS, obtained from 20 individuals and ~84,500 SNPs markers, to the modelled ones, obtained from four different scenarios. Variants were polarized to ancestral and derived alleles based on the eggplant outgroup sequences. Assuming a mutation rate of 3×10-9 and a generation time of 1 year, our results suggest that in the best fitting model, population split occurred ~3750 years ago (95%CI: 2985-4552 yrs), wild tomatoes experienced a dramatic bottleneck (effective population size: -87%; reduction of nucleotide diversity: -63%) that occurred ~420 years ago (95%CI: 337-541 yrs). After this bottleneck, migration rate, from cultivated to wild population, was estimated to less than ~1 migrant per generation. Although, 3.1% of the genes derived from neutral expectations suggesting evolutionary forces acting on. These results demonstrate the power of the approach and provide estimates of demographical parameters that fit previous studies of the tomato domestication (Blanca et al., 2015). |
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