A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences: towards a suprageneric classification of subfamily Apioideae.

The higher level relationships within Apiaceae (Umbelliferae) subfamily Apioideae are controversial, with no widely acceptable modern classification available. Comparative sequencing of the intron in chloroplast ribosomal protein gene rpl16 was carried out in order to examine evolutionary relationships among 119 species (99 genera) of subfamily Apioideae and 28 species from Apiaceae subfamilies Saniculoideae and Hydrocotyloideae, and putatively allied families Araliaceae and Pittosporaceae. Phylogenetic analyses of these intron sequences alone, or in conjunction with plastid rpoC1 intron sequences for a subset of the taxa, using maximum parsimony and neighbor-joining methods, reveal a pattern of relationships within Apioideae consistent with previously published chloroplast DNA and nuclear ribosomal DNA ITS based phylogenies. Based on consensus of relationship, seven major lineages within the subfamily are recognized at the tribal level. These are referred to as tribes Heteromorpheae M. F. Watson & S. R. Downie Trib. Nov., Bupleureae Spreng. (1820), Oenantheae Dumort. (1827), Pleurospermeae M. F. Watson & S. R. Downie Trib. Nov., Smyrnieae Spreng. (1820), Aciphylleae M. F. Watson & S. R. Downie Trib. Nov., and Scandiceae Spreng. (1820). Scandiceae comprises subtribes Daucinae Dumort. (1827), Scandicinae Tausch (1834), and Torilidinae Dumort. (1827). Rpl16 intron sequences provide valuable characters for inferring high-level relationships within Apiaceae but, like the rpoC1 intron, are insufficient to resolve relationships among closely related taxa.

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).

Phylogenetic analysis of apiaceae subfamily apioideae using nucleotide sequences from the chloroplast rpoC1 intron.

Phylogenetic relationships among 25 members of Apiaceae (Umbelliferae) subfamily Apioideae, representing 7 of the 8 tribes and 8 of the 10 subtribes traditionally recognized in the subfamily, and 5 outgroups from Apiaceae subfamilies Hydrocotyloideae and Saniculoideae and allied families Araliaceae and Pittosporaceae have been inferred from nucleotide sequence variation in the intron of the chloroplast gene RNA polymerase C1 (rpoC1). Sequence divergence values in pairwise comparisons of unambiguous positions among all taxa ranged from 0 to 11.3% of nucleotides and averaged 3.8%. Trees derived from rpoC1 intron sequences estimated using maximum parsimony or maximum likelihood methods are of essentially similar topology, and indicate that (1) subfamily Apioideae, with Heteromorpha as its most basal element, is monophyletic and is a sister-group to Eryngium, the only representative examined of Apiaceae subfamily Saniculoideae, (2) Aralia (Araliaceae) arises from within a paraphyletic Apiaceae subfamily Hydrocotyloideae (represented by Centella and Hydrocotyle) and this clade is a sister-group to Apioideae+Saniculoideae, (3) there is a major phylogenetic division within Apioideae (excluding the basal Heteromorpha), with one clade comprising the genus Smyrnium and those taxa traditionally grouped in tribes Dauceae, Scandiceae, and Laserpitieae, and the other clade comprising all other examined taxa, and (4) relationships within each of these 2 major clades of Apioideae are largely equivocal owing to the low levels of nucleotide sequence divergence observed. Although rpoC1 intron sequences can provide valuable characters for addressing phylogenetic relationships among the outgroups and distantly related members of Apioideae, they have little power for resolving relationships among closely related taxa.

Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution.

We have determined the nucleotide sequence of the Pelargonium x hortorum ORF2280 homolog, the largest gene in the plastid genome of most land plants, and compared it to published homologs from Nicotiana tabacum, Epifagus virginiana, Spinacia oleracea, and Marchantia polymorpha. Multiple alignment of protein sequences requires an extraordinary number of gaps, indicating a very high frequency of insertion/deletion events during the evolution of the protein; however, the overall predicted size of the protein varies relatively little among the five species. At 2,109 codons, the Pelargonium gene is smaller than other land plant ORF2280 homologs and exhibits a rate of nucleotide substitution several times higher relative to Nicotiana, Epifagus, and Spinacia. Southern-blot and restriction-mapping studies were carried out to uncover length variation in ORF2280 homologs from 279 species (representing 111 families) of angiosperms. In many independent angiosperm lineages, this gene has sustained deletions ranging in size from 200 bp to almost 6 kb. Based on the severity of deletions, we postulate that the chloroplast homolog of ORF2280 has become nonfunctional in at least four independent lineages of angiosperms.

Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes.

The nucleotide sequence of a 7.4 kb region containing the entire plastid ribosomal RNA operon of the nongreen parasitic plant Epifagus virginiana has been determined. Analysis of the sequence indicates that all four rRNA genes are intact and almost certainly functional. In contrast, the split genes for tRNA(Ile) and tRNA(Ala) present in the 16S-23S rRNA spacer region have become pseudogenes, and deletion upstream of the 16S rRNA gene has removed a tRNA(Val) gene and most of the promoter region for the rRNA operon. The rate of nucleotide substitution in 16S and 23S rRNAs is several times higher in Epifagus than in tobacco, a related photosynthetic plant. Possible reasons for this, including relaxed translational constraints, are discussed.