Integrated Molecular and Morphological Studies of Daucus

Ninety-four nuclear orthologs were used to analyze phylogenetic structure in 92 accessions of 13 species and two subspecies of Daucus, and 15 accessions of related genera. A near parallel set of accessions was used for morphological analyses of germplasm. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage; trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; and the use of all 94 markers vs. a reduced subset of markers. Morphological analyses included character state distributions, stepwise discriminant analyses, canonical variants analyses, and hierarchical cluster analyses. Our maximum parsimony and maximum likelihood DNA trees are highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. The single allele analysis gave slightly better topological resolution in some clades. Trimming homopolymers provided potentially more reliable data. The pure exonic data had 570% more parsimony-informative characters. Similar phylogenetic results demonstrating the same dominant topology can be obtained with many fewer markers. Concordant with molecular analyses, most species form phenetic groups, but problems are shown in the recognition of the subspecies of D. carota; D. sahariensis and D. syrticus; and D. broteri and D. guttatus. The status of D. broteri and D. guttatus is unresolved, with the present data supporting three taxa. Our research highlights some difficult species groups in Daucus, and discovered misidentifications in germplasm collections. It highlights a useful subset of nuclear orthologs and methodological approaches for future studies of dominant topologies in Daucus.