The results of phylogenetic analyses of 1240 nrDNA ITS sequences of Apiaceae subfamily Apioideae, representing 292 genera and 959 species from all major clades of the subfamily except those most basally branching, were compared to a preexisting phylogenetic classification for the group based on several molecular markers and a smaller sampling of taxa. This was done to confirm previously defined tribal and generic limits and to identify additional major clades and genera whose monophyly and relationships can be tested in future studies. All species for which ITS data are available in Gen-Bank plus newly obtained sequences for 53 additional taxa were considered for inclusion in this study and their simultaneous analysis permitted misidentifications and other problematic sequences to be revealed. Analyses of these ITS data, in conjunction with results of recently published molecular studies, identified 41 major clades in Apioideae, of which 21 have already been recognized at the tribal or subtribal rank. No major changes to the preexisting phylogenetic classification of Apioideae are proposed, other than the recognition of additional major clades and the expansion of others to accommodate increased sampling. As noted in previous studies, many genera are not monophyletic; indeed, 18 genera are highly polyphyletic, with their members occurring in 2 to 7 major clades. Each of the 1240 accessions examined can be unambiguously assigned to a particular major clade. Resolution of relationships, as well as the formal recognition of several major clades, must await supporting data, such as that from the cpDNA trnQ (UUG)-5'trnK (UUU) intergenic spacer region. An ITS-based classification of the subfamily is proposed that enables direct and precise references to specific groups and facilitates sampling and hypothesis testing in future systematic studies.

Phylogenetic analyses of chloroplast gene (rbcL, matK ), intron (rpl16, rps16, rpoC1) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction sites, with supplementary data from variation in size of the chloroplast genome inverted repeat, have been used to elucidate major clades within Apiaceae (Umbelliferae) subfamily Apioideae Drude. This paper summarizes the results of previously published molecular cladistic analyses and presents a provisional classification of the subfamily based on taxonomic congruence among the data sets.Boiss., Scandiceae Spreng. and Smyrnieae Spreng.) are erected or confirmed as monophyletic, with Scandiceae comprising subtribes Daucinae Dumort., Scandicinae Tausch and Torilidinae Dumort. Seven additional clades are also recognized but have yet to be treated formally, and at least 23 genera examined to date are of dubious tribal or clade placement. The utility of these different molecular markers for phylogenetic inference in Apioideae is compared based on maximum parsimony analyses of subsets of previously published molecular data sets. Of the six loci sequenced, the ITS region is seen to be evolving most rapidly and rbcL is the most conservative. Intermediate in rate of evolution are matK and the three chloroplast introns; with rpl16 and rps16 evolving slightly faster than matK or rpoC1. The analysis of restriction sites, however, provided 2-4 times more parsimony informative characters than any single DNA locus sequenced, with estimates of divergence just slightly lower than that of the ITS region. The trees obtained from separate analyses of these reduced data sets are consistent with regard to the major clades inferred and the relationships among them. Similar phylogenies are obtained by combining data or combining trees, representing the supermatrix and supertree approaches to

The evolutionary relationships among members of Apiaceae (Umbelliferae) tribe Scandiceae and representatives of all major lineages of Apioideae (including putatively allied Caucalideae) identified in earlier molecular studies were inferred from nucleotide sequence variation in the internal transcribed spacer regions (ITS1 and ITS2) of nuclear ribosomal DNA. In all, 134 accessions representing 18 genera commonly treated in Scandiceae were analyzed. Phylogenies estimated using maximum parsimony and distance methods were generally similar and suggest that: (1) Scandiceae form a well-supported clade, consisting of the genera Anthriscus, Athamanta (in part), Balansaea, Chaerophyllum, Conopodium, Geocaryum, Kozlovia, Krasnovia, Myrrhis, Myrrhoides, Neoconopodium, Osmorhiza, Scandix, Sphallerocarpus, and Tinguarra; (2) Athamanta is polyphyletic, with A. della-cellae allied with Daucus and A. macedonica placed close to Pimpinella; and (3) Rhabdosciadium and Grammosciadium find affinity with the Aegopodium group of umbellifers, whereas the placement of the monotypic Molopospermum cannot be inferred because of its high sequence divergence. The genus Bubon has been restored with two new combinations, B. macedonicum subsp. albanicum and B. macedonicum subsp. arachnoideum. Scandiceae arise within paraphyletic Caucalideae, the latter comprising two major lineages whose relationships to Scandiceae are not clear. Therefore, a broad treatment of Scandiceae is proposed, with subtribes Scandicinae, Daucinae, and Torilidinae (the latter two representing the Daucus and Torilis subgroups, respectively, of recent molecular systematic investigations).

Scandiceae subtribe Daucinae encompasses umbellifers that have fruits with prominent secondary ridges projecting into wings (former tribe Laserpitieae) or spines (former tribe Caucalideae pro parte). It comprises several economically or medicinally important genera including Cuminum, Daucus, Laser, Laserpitium and Thapsia among others. Recent molecular studies, based mostly on nrDNA ITS sequences, revealed that neither Daucus nor Laserpitium are monophyletic. To address issues of relationships and apply respective nomenclatural changes, we obtained additional ITS sequences as well as independent data from three plastid markers—rps16 intron, rpoC1 intron and rpoB‐trnC intergenic spacer—for a comprehensive sample of the subtribe. We examined data for 260 accessions representing all genera of Daucinae and 81 of its ca. 93 species. Phylogenetic trees were estimated using maximum likelihood and Bayesian inference methods. The results indicate that former Laserpitieae constitute a paraphyletic grade at the base of the spiny‐fruited members of Daucinae while traditionally delimited Daucus and Laserpitium are polyphyletic. To maintain a monophyletic Daucus, we suggest including the following genera and species into its synonymy: Agrocharis, Melanoselinum, Monizia, Pachyctenium, Pseudorlaya, Rouya, Tornabenea, Athamanta dellacellae and Cryptotaenia elegans. The species of Laserpitium occur in seven clades and only six species of the Laserpitium s.str. clade retain the generic name. Several species are transferred to Ekimia, Laser and Thapsia; additionally, a monospecific genus Siler is restored and a new genus, Silphiodaucus, is established. The inclusion of Ammodaucus into Thapsia suggested in an earlier study is not supported. The position of Laserpitium pseudomeum requires further study.

The phylogenetic position of Koliella , a chlorophyte characterized by Klebsormidium type cell division, was inferred from analyses of partial 18S rDNA and partial 16S rDNA. Parsimony and distance analyses of separate and combined data sets indicated that the members of Koliella belonged to Trebouxiophyceae, and high decay indices and bootstrap values supported this affinity. However, the genus appeared to be polyphyletic. Koliella spiculiformis , the nomenclatural type of the genus, was allied with Nannochloris eucaryota and the "true" chlorellas ( Chlorella vulgaris , C. lobophora , C. sorokiniana , and C. kessleri ). The close relatives of Koliella longiseta ( ϵ Raphidonema longiseta ) and Koliella sempervirens appeared to be Stichococcus bacillaris and some species traditionally classified in Chlorella that were characterized by the production of secondary carotenoids under nitrogendeficient conditions. This clade was also supported by the presence of a relatively phylogenetically stable group I intron (1506) in the 18S rRNA gene. Because of the presence of Klebsormidium type cell division, some authors regarded the members of Koliella as closely related to charophytes. Molecular analyses, however, did not confirm this affinity and suggested that a Klebsormidium type cell division is homoplastic in green plants.