Molecular systematics of Apiaceae subfamily Apioideae: phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and plastid RPO C1 intron sequences

Evolutionary relationships among representatives of Apiaceae (Umbelliferae) subfamily Apioideae have been inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer (ITS 1 and ITS 2) and plastid rpoC1 intron sequences. High levels of nucleotide sequence variation preclude the use of the ITS region for examining relationships across subfamilial boundaries in Apiaceae, whereas the rpoC1 intron is more suitably conserved for family-wide phylogenetic study but is too conserved for examining relationships among closely related taxa. In total, 126 ITS sequences from subfamily Apioideae and 100 rpoC1 intron sequences from Apiaceae (all three subfamilies) and outgroups Araliaceae and Pittosporaceae were examined. Phylogenies estimated using parsimony, neighbor-joining, and maximum likelihood methods reveal that: (1) Apiaceae subfamily Apioideae is monophyletic and is sister group to Apiaceae subfamily Saniculoideae; (2) Apiaceae subfamily Hydrocotyloideae is not monophyletic, with some members strongly allied to Araliaceae and others to Apioideae + Saniculoideae; and (3) Apiaceae subfamily Apioideae comprises several well-supported subclades, but none of these coincide with previously recognized tribal divisions based largely on morphological and anatomical characters of the fruit. Four major clades in Apioideae are provisionally recognized and provide the framework for future lower level phylogenetic analyses. A putative secondary structure model of the Daucus carota (carrot) rpoC1 group II intron is presented. Of its six major structural domains, domains II and III are the most, and domains V and VI the least, variable.     

Phylogenetic analysis of cpDNA restriction sites andrps16 intron sequences reveals relationships among Apiaceae tribes Caucalideae, Scandiceae and related taxa

Evolutionary relationships among members of Apiaceae (Umbelliferae) tribe Caucalideae Spreng. and related taxa were inferred from maximum parsimony analyses of chloroplast DNA restriction sites andrps16 intron sequences and the results compared to an existing phylogeny for the group based on nuclear ribosomal DNA internal transcribed spacer sequences. While these three data sets were not similar in size or composition, the relationships among the shared taxa, with few exceptions, were concordant. Three major lineages are recognized, coinciding with the previously delimited Scandiceae subtribes Daucinae Dumort. (Agrocharis, Ammodaucus, Cuminum, Daucus, Orlaya, Pachyctenium, Pseudorlaya), Torilidinae Dumort. (Astrodaucus, Caucalis, Glochidotheca, Lisaea, Szovitsia, Torilis, Turgenia, Yabea), and Scandicinae Tausch (Anthriscus, Kozlovia, Myrrhis, Osmorhiza, Scandix). Included in Daucinae is representation from tribe Laserpitieae (Laser, Laserpitium, Melanoselinum, Monizia, Polylophium). Daucinae and Torilidinae arise as sister taxa in the chloroplast DNA-based phylogenies, whereas in the ITS trees relationships among the three major lineages are unresolved. Unexpectedly, three species ofFerula ally with Daucinae and Torilidinae. The position ofArtedia is equivocal, occurring either sister to Daucinae in the ITS trees, within Torilidinae in the intron trees, or sister to Torilidinae upon analysis of combined ITS and intron data.Chaetosciadium trichospermum emerges withinTorilis, and is recognized asTorilis trichosperma (L.) Spreng.     

a molecular phylogeny of apiaceae subfamily Apioideae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences

Phylogenetic relationships among 40 New World and Old World members of Apiaceae subfamily Apioideae, representing seven of the eight tribes and eight of the ten subtribes commonly recognized in the subfamily, were inferred from nucleotide sequence variation in the internal transcribed spacer (ITS) regions of 18-26S nuclear ribosomal DNA. Although the sequences are alignable, with only 11% of sites excluded from the analyses because of alignment ambiguity, divergence values in pairwise comparisons of unambiguous positions among all taxa were high and ranged from 0.5 to 33.2% of nucleotides in ITS 1 and from 0 to 33.2% of nucleotides in ITS 2. Average sequence divergence across both spacer regions was 18.4% of nucleotides. Phylogenies derived from ITS sequences estimated using neighbor-joining analysis of substitution rates, and maximum likelihood and parsimony methods give trees of essentially similar topology and indicate that: (1) there is little support for any existing system of classification of the subfamily that is based largely on morphological and anatomical features of the mericarp; (2) there is a major phylogenetic division within the subfamily, with one clade comprising the genus Smyrnium and those taxa belonging to Drude's tribes Dauceae, Scandiceae, and Laserpitieae and the other clade comprising all other examined taxa; and (3) the genera Arracacia, Coaxana, Coulterophytum, Enantiophylla, Myrrhidendron, Prionosciadium, and Rhodosciadium, all endemic to Mexico and Central America, comprise a clade but their relationships to other New World taxa are equivocal. A phylogeny derived from parsimony analysis of chloroplast DNA rpoC1 intron sequences is consistent with, but considerably less resolved than, relationships derived from these ITS regions. This study affirms that ITS sequences are useful for phylogenetic inference among closely related members of Apioideae but, owing to high rates of nucleotide substitution, are less useful in resolving relationships among the more ancestral nodes of the phylogeny.     

Major lineages within Apiaceae subfamily Apioideae: a comparison of chloroplast restriction site and DNA sequence data

Traditional sources of taxonomic characters in the large and taxonomically complex subfamily Apioideae (Apiaceae) have been confounding and no classification system of the subfamily has been widely accepted. A restriction site analysis of the chloroplast genome from 78 representatives of Apioideae and related groups provided a data matrix of 990 variable characters (750 of which were potentially parsimony-informative). A comparison of these data to that of three recent DNA sequencing studies of Apioideae (based on ITS, rpoCl intron, and matK sequences) shows that the restriction site analysis provides 2.6–3.6 times more variable characters for a comparable group of taxa. Moreover, levels of divergence appear to be well suited to studies at the subfamilial and tribal levels of Apiaceae. Cladistic and phenetic analyses of the restriction site data yielded trees that are visually congruent to those derived from the other recent molecular studies. On the basis of these comparisons, six lineages and one paraphyletic grade are provisionally recognized as informal groups. These groups can serve as the starting point for future, more intensive studies of the subfamily.     

Polyphyletic origin in <Emphasis Type="Italic">Pimpinella</Emphasis> (Apiaceae): evidence in Western Europe

The genus Pimpinella L. comprises about 150 species, being one of the largest genera within the family Apiaceae (subfamily Apioideae). Previous molecular phylogenetic studies have shown that Pimpinella is a taxonomically complex group. In this study, evolutionary relationships among representatives from Western Europe have been inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer (ITS 1 and ITS 2) and plastid sequences (trnL intron and the trnL-F spacer), with a representative sampling included (168 accessions in the ITS analysis, representing 158 species; and 42 accessions in the cpDNA analysis representing 35 taxa of Pimpinella and closely related species). All analyses resolved that Pimpinella is a non-monophyletic group, and Pimpinella’s taxa that grow in Western Europe are part of phylogenetically independent groups that correspond to three different tribes of the subfamily Apioideae: Pimpinelleae (core group), Pyramidoptereae and Smyrnieae.     

Discordance of chloroplast and nuclear ribosomal DNA data in Osmorhiza (Apiaceae)

Phylogenetic studies were conducted to evaluate interspecific relationships in Osmorhiza (Apiaceae: Apioideae) using sequences of the ITS regions of nuclear ribosomal DNA, the chloroplast ndhF gene, and two noncoding regions (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer). All data sets suggest the monophyly of the New World taxa and showed that Osmorhiza aristata from Asia is relatively divergent from other members of the genus, even though it is morphologically similar to the eastern North American O. claytonii and O. longistylis. The ITS and chloroplast DNA trees differ in the relationships among the New World taxa, especially the phylogenetic position of O. occidentalis, O. glabrata, and O. depauperata. The lack of congruence between the two data sets may be a result of hybridization or introgression. Although there is high discordance between nrITS and two chloroplast DNA data sets, the latter two show similar topologies.     

Using RAD seq for reconstructing phylogenies of highly diverged taxa: A test using the tribe Scandiceae (Apiaceae)

The angiosperm Apiaceae tribe Scandiceae includes four major clades—subtribes Daucinae, Ferulinae, Torilidinae, and Scandicinae—that originated ca. 20 Mya. Although all four subtribes are highly supported in molecular analyses, and morphological data indicate a sister relationship between Daucinae and Torilidinae, their branching order has not been resolved using standard Sanger multilocus data. Therefore, in this study, we test the utility of genomic RAD seq data in resolving deep phylogenetic relationships (up to 20 Mya) in Apiaceae subfamily Apioideae, with special emphasis on tribe Scandiceae using 12 representative species. We used two bioinformatic pipelines, pyRAD and RADIS (based on STACKS), to assemble RAD seq data and we tested the influence of various combinations of parameters on the robustness of the inferred tree topologies. Although different data processing approaches produced alignments with various amounts of missing data, they converged to two well‐supported topologies, irrespective of the phylogenetic method applied. Highly supported trees showed Scandicinae as sister to all other clades and indicated that Daucinae and Torilidinae are sister groups, thus confirming the relationship inferred from morphology. We conclude that the RAD seq method can be successfully used to resolve deep relationships formed 20 Mya within Apiaceae. We provide recommendations for parameter settings in RADIS and pyRAD for the analysis of taxa that have accumulated considerable genomic divergence.     

A phylogeny of Apiaceae tribe Scandiceae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences

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).     

A molecular phylogenetic study of southern African Apiaceae

It has been suggested that southern Africa is the origin of the predominantly herbaceous Apiaceae subfamily Apioideae and that the woody habit is plesiomorphic. We expand previous molecular phylogenetic analyses of the family by considering all but three of the approximately 38 genera native to southern Africa, including all genera whose members, save one, have a woody habit. Representatives of five other genera are included because they may be closely related to these southern African taxa. Chloroplast DNA rps16 intron and/or nuclear rDNA ITS sequences for 154 accessions are analyzed using maximum parsimony, Bayesian, and maximum likelihood methods. Within Apioideae, two major clades hitherto unrecognized in the subfamily are inferred. The monogeneric Lichtensteinia clade is sister group to all other members of the subfamily, whereas the Annesorhiza clade (Annesorhiza, Chamarea, and Itasina) plus Molopospermum (and Astydamia in the ITS trees) are the successive sister group to all Apioideae except Lichtensteinia. Tribe Heteromorpheae is expanded to include Pseudocarum, "Oreofraga" ined., and five genera endemic to Madagascar. The southern African origin of subfamily Apioideae is corroborated (with subsequent migration northward into Eurasia along two dispersal routes), and the positions of the herbaceous Lichtensteinia and Annesorhiza clades within the subfamily suggest, surprisingly, that its ancestor was herbaceous, not woody.     

Phylogenetic placement of DethawiaMeum,and Rivasmartinezia (Apioideae,Apiaceae): Evidence from nuclear and plastid DNA sequences

The flora of Western Europe is rich in endemic species of Apiaceae, many of which have been poorly investigated and whose phylogenetic relationships are poorly known. To investigate relationships among three endemic European genera (Dethawia, Meum, and Rivasmartinezia gen. nov.) and to ascertain their higher-level phylogenetic placements within the subfamily Apioideae, we examined nuclear ribosomal DNA ITS sequences and the plastid trnL-trnF region. Phylogenies estimated using parsimony and Bayesian inference reveal that (1) the historically known “Conioselinum chinense” Clade (Conioselinum chinense; C. scopulorum; Ligusticum canadense; L. porteri; Meum athamanticum; Mutellina purpurea; and Trochiscanthes nodiflora) comprise a strongly supported monophyletic group (100% BS); (2) the genera Dethawia and Meum comprise a strongly supported monophyletic group also included in the “Conioselinum chinense” Clade; and finally (3) a new genus (Rivasmartinezia) with one species (R. vazquezii) from the Northwestern of the Iberian Peninsula, and placed in the basal position in the “Conioselinum chinense” Clade, is described for the family Apiaceae subfamily Apioideae.     

Morphology and biogeography of Apiaceae subfamily Saniculoideae as inferred by phylogenetic analysis of molecular data

The phylogenetic placements of several African endemic genera at the base of Apiaceae subfamilies Saniculoideae and Apioideae have revolutionized ideas of relationships that affect hypotheses of character evolution and biogeography. Using an explicit phylogeny of subfamily Saniculoideae, we reconstructed the evolutionary history of phenotypic characters traditionally important in classification, identified those characters most useful in supporting relationships, and inferred historical biogeography. The 23 characters examined include those of life history, vegetative morphology, inflorescences, and fruit morphology and anatomy. These characters were optimized over trees derived from maximum parsimony analysis of chloroplast DNA trnQ-trnK sequences from 94 accessions of Apiaceae. The results revealed that many of these characters have undergone considerable modification and that traditional assumptions regarding character-state polarity are often incorrect. Infrasubfamilial relationships inferred by molecular data are supported by one to five morphological characters. However, none of these morphological characters support the monophyly of subfamilies Saniculoideae or Apioideae, the clade of Petagnaea, Eryngium and Sanicula, or the sister-group relationship between Eryngium and Sanicula . Southern African origins of Saniculoideae and of its tribes Steganotaenieae and Saniculeae are supported based on dispersal-vicariance analysis.     

Rice chloroplast RNA polymerase genes: The absence of an intron in rpoC1 and the presence of an extra sequence in rpoC2

Summary The chloroplast genome contains sequences homologous to the Escherichia coli rpoA, rpoB and rpoC genes. The Choroplast rpoC gene is divided into rpoC1 and rpoC2, of which rpoC1 contains an intron. Comparison of the rice rpo genes with those from tobacco, spinach and liverwort revealed unique features of the rice genes; the lack of an intron in rpoC1 and the presence of an extra sequence of 381 by in rpoC2. The intron in rpoC1 is thus optional, and possible intron boundary sites in split rpoC1 genes can be estimated by comparison with rice rpoC1. The extra sequence is located in the middle of rpoC2 and has repeated structures. The amino acid sequence deduced from this sequence is extremely hydrophilic and anionic. The origin and function of this sequence are discussed.     

Clarification of the relationship beteen Apiaceae and Araliaceae based on matK and rbcL sequence data

Apiaceae and Araliaceae (Apiales) represent a particularly troublesome example of the difficulty in understanding evolutionary relationships between tropical-temperate family pairs. Previous studies based on rbcL sequence data provided insights at higher levels, but were unable to resolve fully the family-pair relationship. In this study, sequence data from a more rapidly evolving gene, matK, was employed to provide greater resolution. In Apiales, matK sequences evolve an average of about two times faster than rbcL sequences. Results of phylogenetic analysis of matK sequences were first compared to those obtained previously from rbcL data; the two data sets were then combined and analyzed together. Molecular analyses confirm the polyphyly of apiaceous subfamily Hydrocotyloideae and suggest that some members of this subfamily are more closely related to Araliaceae than to other Apiaceae. The remainder of Apiaceae forms a monophyletic group with well-defined subclades corresponding to subfamilies Apioideae and Saniculoideae. Both the matK and the combined rbcL-matK analyses suggest that most Araliaceae form a monophyletic group, including all araliads sampled except Delarbrea and Mackinlaya. The unusual combination of morphological characters found in these two genera and the distribution of matK and rbcL indels suggest that these taxa may be the remnants of an ancient group of pro-araliads that gave rise to both Apiaceae and Araliaceae. Molecular data indicate that the evolutionary history of the two families is more complex than simple derivation of Apiaceae from within Araliaceae. Rather, the present study suggests that there are two well-defined "families," both of which may have been derived from a lineage (or lineages) or pro-araliads that may still have extant taxa.     

Analysis of the genus Petagnaea Caruel (Apiaceae), using new molecular and literature data

In Southern Italy, an endemic monotypic genus belonging to family Apiaceae occurs: Petagnaea (P. gussonei), relict of Tertiary flora, belonging to subfamily Saniculoideae. At present, P. gussonei is an endangered species and is included in various lists of species deserving special protection. The genus belongs to scapose hemicryptophytes and shares a sciaphilous habitat (hygrophilous woodland). This study is aimed at doing a complete contribution about the evolutionary history of Petagnaea, using molecular markers as plastidial DNA (cpDNA), nuclear ribosomal DNA (rDNA) and data present in literature. We used nucleotide sequences from four regions of the chloroplast genome (rps16 intron, trnL^(UAA) intron, atpB-rbcL intergenic spacer, and partial matK gene) to investigate possible haplotypes in Petagnaea populations. To have an idea of the molecular relationships of all populations of P. gussonei, the internal transcribed spacer (ITS) sequences, already employed in recent studies, were obtained for 18 populations. These sequences in combination with other Saniculoideae ITS sequences available from GenBank have been used for a further phylogenetic analysis. The results agree with the current classification of Saniculoideae in placing P. gussonei in tribe Saniculeae, since P. gussonei is in basal position to Sanicula. According to intraspecific chloroplast DNA diversity, no different haplotypes were detected. In addition to molecular data, morphology, cytology, phytochemistry and conservation status have been considered in the discussion.     

Occurrence of 1,5-dimethylcyclodeca-1,5,7-triene (Pregeijerene) in Pimpinella species and chemosystematic implications

The essential oils from fresh roots of 66 species, representing 39 general of the Apiaceae (Umbelliferae), subfamily Apioideae, were surveyed for pregeijerene. Of all plants examined, only the 11 species of the genus Pimpinella were shown to contain pregeijerene. According to its extremely restricted occurrence in the Apiaceae, its possible taxonomic value with regard to the definition of the genus Pimpinella is discussed.     

为《Flora of China》提供的伞形科新资料

在为编写《Flora of China》伞形科而进行的修订工作中,提出了11个新组合,即矮小丝瓣芹Acronema minus (M. F. Watson) M. F. Watson & Z. H. Pan, 短柄丝瓣芹A. brevipedicellatum Z. H. Pan & M. F. Watson, 川西当归Angelica sinensis var. wilsonii (H. Wolff) Z. H. Pan & M. F. Watson, 云南细裂芹Harrysmithia franchetii (M. Hiroe) M. L. Sheh, 钝叶独活Heracleum candicans var. obtusifolium (Wall. ex DC.) F. T. Pu & M. F. Watson, 中华天胡荽Hydrocotyle hookeri ssp. chinensis (Dunn ex R. H. Shan & S. L. Liou) M. F. Watson & M. L. Sheh, 普渡天胡荽H. hookeri ssp. handelii (H. Wolff) M. F. Watson & M. L. Sheh, 锐棱岩风Libanotis grubovii (V. M. Vinogradova) M. L. Sheh & M. F. Watson, 美脉藁本Ligusticum likiangense (H. Wolff) F. T. Pu & M. F. Watson和线叶藁本L. nematophyllum (Pimenov & Kljuykov) F. T. Pu & M. F. Watson, 无管藁本L. nullivittatum (K. T. Fu) F. T. Pu & M. F. Watson和二色棱子芹Pleurospermum bicolor (Franch.) C. Norman ex Z. H. Pan & M. F. Watson.; 发现了1个新种,即短柄丝瓣芹。此外,还为Pleurospermum govanianum var. bicolor Franch.指定了后选模式。