DOI: 10.5061/dryad.319sr
title: Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

description: Background: The majority of the subspecies of Daucus carota have not yet
 been discriminated clearly by various molecular or morphological methods
 and hence their phylogeny and classification remains unresolved. Recent
 studies using 94 nuclear orthologs and morphological characters, and
 studies employing other molecular approaches were unable to distinguish
 clearly many of the subspecies. Fertile intercrosses among traditionally
 recognized subspecies are well documented. We here explore the utility of
 single nucleotide polymorphisms (SNPs) generated by
 genotyping-by-sequencing (GBS) to serve as an effective molecular method
 to discriminate the subspecies of the D. carota complex. Results: We used
 GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162
 accessions of Daucus and two related genera. To study Daucus phylogeny, we
 scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 %
 missing data, respectively. To investigate the subspecies of D. carota, we
 employed two data sets including 150 accessions: (i) rate of missing data
 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %,
 totaling 43,713 SNPs. Consistent with prior results, the topology of both
 data sets separated species with 2n = 18 chromosome from all other
 species. Our results place all cultivated carrots (D. carota subsp.
 sativus) in a single clade. The wild members of D. carota from central
 Asia were on a clade with eastern members of subsp. sativus. The other
 subspecies of D. carota were in four clades associated with geographic
 groups: (1) the Balkan Peninsula and the Middle East, (2) North America
 and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian
 Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but
 neither it, nor subsp. gummifer (defined in a broad sense) are
 monophyletic. Conclusions: Our study suggests that (1) the morphotypes
 identified as D. carota subspecies gummifer (as currently broadly
 circumscribed), all confined to areas near the Atlantic Ocean and the
 western Mediterranean Sea, have separate origins from sympatric members of
 other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades
 with some accessions of subsp. carota, can be distinguished from each
 other but only with poor morphological support, (3) D. carota subsp.
 capillifolius, well distinguished morphologically, is an apospecies
 relative to North African populations of D. carota subsp. carota, (4) the
 eastern cultivated carrots have origins closer to wild carrots from
 central Asia than to western cultivated carrots, and (5) large SNP data
 sets are suitable for species-level phylogenetic studies in Daucus.
description: Additional file 1 Table
 S1Additional 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.Additional file 2 Table
 S2Additional file 2: Table
 S2. Summary of processing GBS data of Daucus.Additional file 3 Figure
 S1Additional 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.Additional file 4 Figure
 S2Additional 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.Additional file 5 Figure
 S3Additional 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.Additional file 6 Figure
 S4Additional 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.Additional file 7 Figure
 S5Additional 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.Additional file 8 Figure
 S6Additional 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.Additional file 9 Figure
 S7Additional 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.Additional file 10
 Figure S8Additional 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.Additional file 11
 Figure S9Additional 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.Additional file 12
 Figure S10Additional 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.SNP data set_Daucus_0.1
 missing data_Arbizu et alData set containing 164
 accessions with 10% missing imputed genotypes.SNP data set_Daucus_0.3
 missing data_Arbizu et alData set containing 164
 accessions with 30% missing imputed genotypes.