In a previous study using 94 nuclear orthologs, we reported the species status of the Daucus guttatus complex to be unresolved, partitioned into three clades. In the present study, a subset of ten of these 94 orthologs was used to infer the phylogeny of the D. guttatus complex and related species. A near parallel set of accessions, planted in a common garden, was used for morphological analyses. The molecular trees are highly resolved for most of the clades, grouping accessions of the D. guttatus complex into four clades. Bayesian concordance analysis and a coalescent approach gave slightly different topologies. Morphological data likewise support four taxa in the complex. Moreover, herbarium research from a companion study informs nomenclature for taxa of the complex. We identify these four clades as D. bicolor, D. conchitae, D. guttatus, and D. setulosus; internested in or among these segregates are the phenetically distinctive species D. glochidiatus, D. involucratus, D. littoralis, and D. pusillus. Our research redefines species variation in the D. guttatus complex, clarifies species names, interspecific relationships, confirms a useful subset of nuclear orthologs for studies of dominant topologies of Daucus, and discovers morphological characters allowing proper identification of the four species of the D. guttatus complex and related species.
DNA sequences of species of the Daucus guttatus complex , and others
DNA sequences and trees obtained using Maximum Parsimony
Arbizu-Berrocal.nex
Supplementary Figure 1
SUPPL. FIG. 1. Maximum parsimony phylogenetic reconstruction of the Daucus guttatus complex including species that belong to Clades A and B using 10 nuclear orthologs. Numbers above branches represent bootstrap values. Clades 1, 2, and 3 were identified in Arbizu et al. (2014a). Clade 4 is a new finding in the present study.
Suppl Fig 1.pdf
Supplementary Figure 2
SUPPL. FIG. 2. Box plot (histogram) analyses of the 41 morphological characters examined for all taxa in this study. The box plot displays individual plant values for median, 25% and 75% percentile, range, and outliers.
Suppl Fig 2.pdf
Supplementary Figure 3
SUPPL. FIG. 3. Hierarchical cluster analysis of the Daucus guttatus complex, D. involucratus, and D. littoralis.
Suppl Fig 3.pdf
Supplementary Figure 4
SUPPL. FIG. 4. Mericarp measurements. A. Commissural face (Daucus setulosus Ames 25608) showing mericarp length (1), mericarp width (2), length of spines (3), crest width (4) and spine width (5). B. Cross section of mericarp (D. conchitae Ames 25878) showing elliptical vittae. C. Cross section of mericarp (D. setulosus PI 652329) showing triangular vitae length (1) and width (2) (photos: F. Martínez-Flores).
Suppl Fig 4.pdf
Supplementary Data 1
Supplementary data 1. The 83 accessions of Daucus, and one accession of related genus examined in this study, the new identification and the locality information. (a) These names correspond to those in the Germplasm Resources Information Network (GRIN) database. The 14 accessions designated with an asterisk sign were not analyzed using morphological characters, but DNA sequences only. The 38 accessions designated with a plus sign were only analyzed using 11 morphological mericarp characters (results not shown in this study). DNA sequences of the 31 accessions designated with a pound sign were obtained from Arbizu et al. (2014a). The 25 accessions designated with a square sign were used in Bayesian concordance analysis. The 2n chromosome numbers are those known for the species, not the individual accessions, according to Grzebelus et al. (2011) and IPCN Chromosome Reports (http://www.tropicos.org/Project/IPCN). (b) Plant Introduction (PI) numbers are permanent numbers designated to germplasm accessions maintained at the National Plant Germplasm System (NPGS) in Ames, Iowa, USA. Ames numbers are assigned for carrots and other Apiaceae in the NPGS temporarily to newly acquired germplasm until passport data of an accession and taxonomy is verified. Also, accessions with Ames numbers have to be determined they are not duplicate accession, and that they can be successfully maintained. These accessions may or may not be assigned a PI number after the assessment period. (c) Location refers to where the germplasm was collected in the wild, while source refers to germplasm obtained through another entity such as a market vendor or genebank.
Suppl data 1.pdf
Supplementary Data 2
Supplementary data 2. GenBank accession numbers for new sequence data, and model of evolution of the ten nuclear orthologs used for ML, BCA, and coalescent approach for the study of the phylogeny of Daucus. (a) Models of evolution were obtained in jModelTest. The second model, in parentheses, was the next lower AIC value accepted in MrBayes and BEAST analysis. Models for the concatenated data are just for reference. They were not used for any analyses.
Suppl data 2.pdf
