Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

Arbizu CI, Ellison SL, Senalik D, Simon PW, Spooner DM

Date Published: October 18, 2016

DOI: http://dx.doi.org/10.5061/dryad.319sr

 

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Title Additional file 1 Table S1
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Description Additional file 1: Table S1. The 162 accessions of Daucus, and two accessions of related genera characterized in this study, improvement status, locality information and new identification.
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Title Additional file 2 Table S2
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Description Additional file 2: Table S2. Summary of processing GBS data of Daucus.
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Title Additional file 3 Figure S1
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Description Additional file 3: Figure S1. Phylogenomics of Daucus from a maximum likelihood analysis using 164 accessions and 10,814 SNPs (10% missing imputed genotypes) obtained by GBS. Numbers above branches represent bootstrap values, with only values higher than 70% shown. Names given to clades refer to the geographic origin and improvement status of the accessions of D. carota complex. Clades A and B corresponds to the two main groups of the Daucus phylogeny.
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Title Additional file 4 Figure S2
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Description Additional file 4: Figure S2. Phylogenomics of Daucus from a maximum likelihood analysis using 164 accessions and 38,920 SNPs (30% missing imputed genotypes) obtained by GBS. Numbers above branches represent bootstrap values, with only values higher than 70% shown. Names given to clades refer to the geographic origin and improvement status of the accessions of D. carota complex. Clades A and B corresponds to the two main groups of the Daucus phylogeny.
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Title Additional file 5 Figure S3
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Description Additional file 5: Figure S3. Maximum likelihood reconstruction and structure of the genetic diversity of 144 accessions of Daucus carota complex and outgroup using 43,713 SNPs (30% missing imputed genotypes) obtained by GBS. Each accession is represented by a horizontal bar, and each color corresponds to a population (nine in total). Numbers above branches represent bootstrap values, with only values higher than 70% shown. Names given to clades refer to the geographic origin and improvement status of the accessions of D. carota complex. The outgroup taxon is D. syrticus.
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Title Additional file 6 Figure S4
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Description Additional file 6: Figure S4. Bayesian phylogenetic tree of 144 accessions of Daucus carota complex and outgroup using 18,565 SNPs (10% missing imputed genotypes) obtained by GBS. Numbers above the branches represent posterior probabilities, with only values higher than 0.7 shown. Names given to clades refer to the geographic origin and improvement status of the accessions of the D. carota complex. The outgroup taxon is D. syrticus.
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Title Additional file 7 Figure S5
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Description Additional file 7: Figure S5. Relationships among 144 accessions of Daucus carota complex and outgroup from an exhaustive quartet sampling inference using 18,565 SNPs (10% missing imputed genotypes) obtained by GBS. Numbers above the branches represent bootstrap values, with only values higher than 70% shown. Names given to clades refer to the geographic origin and improvement status of the accessions of D. carota complex. ME & E refers to Middle East & Europe. Accessions designated by double stars are misplaced relative to the maximum likelihood topology of Daucus carota complex using the same number of SNPs. The outgroup taxon is D. syrticus.
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Title Additional file 8 Figure S6
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Description Additional file 8: Figure S6. Relationships among 144 accessions of Daucus carota complex and outgroup from an exhaustive quartet sampling inference using 43,713 SNPs (30% missing imputed genotypes) obtained by GBS. Numbers above branches represent bootstrap values, with only values higher than 70% shown. Names given to clades refer to the geographic origin and improvement status of the accessions of D. carota complex. ME & E refers to Middle East & Europe. Accessions designated by double stars are misplaced relative to the maximum likelihood topology of Daucus carota complex using the same number of SNPs. The outgroup taxon is D. syrticus.
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Title Additional file 9 Figure S7
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Description Additional file 9: Figure S7. Species tree of the Daucus carota complex based on a coalescent model using an exhaustive quartet sampling inference and 18,565 SNPs (10% missing imputed genotypes) obtained by GBS. Numbers above the branches represent bootstrap values. The outgroup taxon is D. syrticus.
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Title Additional file 10 Figure S8
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Description Additional file 10: Figure S8. Number of populations. A. Plot of Delta K (ΔK). B. Plot of the log likelihood; internal plot corresponds to the log likelihood (thousands) for K ranging from 1 to 9. All values were obtained from STRUCTURE HARVESTER analysis. Fourteen populations were considered in a data set of 18,565 SNPs (10% missing imputed genotypes) and 150 samples.
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Title Additional file 11 Figure S9
Downloaded 66 times
Description Additional file 11: Figure S9. Number of populations. A. Plot of Delta K (ΔK). B. Plot of the log likelihood; internal plot corresponds to the log likelihood (thousands) for K ranging from 1 to 9. All values were obtained from STRUCTURE HARVESTER analysis. Fourteen populations were considered in a data set of 43,713 SNPs (30% missing imputed genotypes) and 150 samples.
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Title Additional file 12 Figure S10
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Description Additional file 12: Figure S10. Box plot analyses of the 23 morphological characters examined for members of Daucus carota complex (subsp. sativus not included) in this study. The box plot displays individual plant values for median, 25% and 75% percentile, range, and outliers.
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Title SNP data set_Daucus_0.1 missing data_Arbizu et al
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Description Data set containing 164 accessions with 10% missing imputed genotypes.
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Title SNP data set_Daucus_0.3 missing data_Arbizu et al
Downloaded 13 times
Description Data set containing 164 accessions with 30% missing imputed genotypes.
Download SNP data set_Daucus_0.3 missing data_Arbi...al.nex (6.405 Mb)
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When using this data, please cite the original publication:

Arbizu CI, Ellison SL, Senalik D, Simon PW, Spooner DM (2016) Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae). BMC Evolutionary Biology 16: 234. http://dx.doi.org/10.1186/s12862-016-0806-x

Additionally, please cite the Dryad data package:

Arbizu CI, Ellison SL, Senalik D, Simon PW, Spooner DM (2016) Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.319sr
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