Molecular Phylogeny of Daucus (Apiaceae)

We studied the phylogeny of 22 accessions of Daucus and seven accessions in related genera, with DNA sequences from eight nuclear orthologs and one plastid (psbA/trnH) region. Maximum parsimony and maximum likelihood analyses of the concatenated data matrix of 7,212 aligned nucleotides provided excellent bootstrap support for many clades. Concordant with prior molecular results Pseudorlaya pumila was firmly imbedded within Daucus, as was Margottia gummifera, a new finding. All accessions of D. capillifolius, D. carota, and D. sahariensis formed a 2n = 18 clade with all other species within the Daucus clade with chromosome numbers of = 20, 22, and 44 (D. glochidiatus). Sister to the D. carota clade was a clade containing Margottia gummifera and Pseudorlaya pumila, sister to these species was D. crinitus, sister to all the above was D. muricatus, and sister to all of the above was a clade containing the remaining Daucus species. Bayesian analyses of individual regions analyzed separately and averaged over multiple trees with *BEAST software (a coalescent approach), however, provided a phylogeny at variance with the concatenated approach, most notably in firmly imbedding Turgenia latifolia within Daucus. Keywords—Carrot, taxonomy, Umbelliferae. The Umbelliferae Juss. comprise some 300–455 genera and 3,000–3,750 species (Constance 1971; Pimenov and Leonov 1993). The family is cosmopolitan and most diverse in the northern hemisphere. Carrot is by far its economically most important member, but the family also contains the vegetables, flavorings, or garnishes angelica, anise, caraway, celeriac, celery, chervil, coriander (cilantro), cumin, dill, fennel, lovage, parsley, and parsnip. Most members of Umbelliferae are easily identifiable to family by the distinctive characters such as herbs with hollow or pith-filled stems, pinnately divided leaves with sheathing bases, small unspecialized flowers in compound umbels, and specialized fruits (Heywood 1971, 1986a). The ease of identifying members of the Umbelliferae, however, is strongly contrasted with vague circumscription of genera within the family. Traditional classifications within the Umbelliferae are presented byDrude (1897–1898), Heywood (1971, 1993), and Pimenov and Leonov (1993). Recent molecular investigations using DNA sequences from nuclear ribosomal ITS, plastid rpoC1 intron and rpl16 intron sequences, plastid matK coding sequences and plastid DNA restriction site data (Downie and Katz-Downie 1996; Plunkett et al. 1996; Lee and Downie 1999, 2000; Downie et al. 2000; 2001; KuoFang et al. 2005; Spalik and Downie 2007) do not support many genera within the Umbelliferae as monophyletic. Indeed, fully 11 of 16 genera with more than one species examined per genus in these molecular studies have not been supported as monophyletic (Aciphylla, Arracacia, Conioselinum, Daucus, Ferula, Heracleum, Ligusticum, Pastinaca, Peucedanum, Pleurospermum, and Seseli). Similarly, studies investigating Daucus have clearly documented the paraphyly of the genus as currently circumscribed as it contains the following species in other genera (followed by their distribution): Agrocharis, three species (northeastern, tropical, southern Africa) Athamanta dellacellae (Libya),Cryptotainia elegans (Canary Islands),Melanoselenium decipiens (Madeira), Monizia edulis (Madeira), Pachyctenium mirabile (Libya), Pseudorlaya minuscula (Portugal, Spain), Pseudorlaya pumila (Morocco, Israel, France, Spain, Greece, Albania, Bulgaria, Crete, Sicily), Tornabenea annua (Cape Verde Islands), Tornabenea tenuissima (Cape Verde Islands). Daucus is most common in the Mediterranean region, with some species in other continents and in the southern hemisphere. The latest comprehensive taxonomic monograph of Daucus was by Sáenz Laı́n (1981), but this is largely an intuitive classification lacking a modern phylogeny, specimen citations, distribution maps, detailed descriptions, and use of living specimens for analysis; and it was produced from an examination of a limited number of herbarium specimens. Sáenz Laı́n (1981) recognized 20 species divided into five sections:Anisactis, Chrysodaucus, Daucus,Meoides, and Platyspermum. The sole cultivated species, Daucus carota L., exists in both cultivated and wild forms. More than 60 species have been proposed for variants within the “D. carota complex” alone, for which there are no or only poorly developed barriers to interbreeding among either the wild forms or their domesticates (Small 1978). Sáenz Laı́n (1981) recognized four subspecies within D. carota, Heywood (1986b) 11 subspecies, and Pujadas Salvà (2002) ten subspecies for the Iberian Peninsula alone. The subspecies are diverse phenotypically (Small 1978). Currently, germplasm curators and taxonomists are forced to rely on local floras for identifying Daucus germplasm and herbarium specimens. Current molecular phylogenetic studies of Daucus are conducted with few gene regions. As additional gene regions are being discovered for phylogenetic estimation, we are beginning to appreciate that different genes often provide different reconstructions of phylogeny, and that different unlinked loci can have conflicting genealogical histories as a result of the stochastic process of coalescence of alleles due to random genetic drift and incomplete lineage sorting (Wendel and Doyle 1998). Different methods have been used to sort out this problem; one to analyze data from many genes together (a concatenated approach), or to reconstruct a phylogeny from individual gene trees analyzed separately and generating a single tree by averaging over multiple trees (a coalescent approach).