Richard G. Olmstead

Phylogenetic relationships of Dipsacales based on rbcL sequences

Nucleotide sequences of the chloroplast gene rbcL were obtained from Lonicera, Sambucus, Adoxa, and Cornus. Phylogenetic analyses of these sequences, along with previously sequenced Dipsacales and placeholders for other Asteridae and Rosidae, lead to the following conclusions: (1) the genera of Caprifoliaceae (in any traditional sense) do not form a monophyletic group; (2) Symphoricarpos and Lonicera (representing Caprifoliaceae sens. str.) are related and are united with Valerianaceae and Dipsacaceae; and (3) Adoxa and Sambucus are directly linked and are possibly related to Viburnum

Disintegration of the scrophulariaceae.

A molecular systematic study of Scrophulariaceae sensu lato using DNA sequences of three plastid genes (rbcL, ndhF, and rps2) revealed at least five distinct monophyletic groups. Thirty-nine genera representing 24 tribes of the Scrophulariaceae s.l. (sensu lato) were analyzed along with representatives of 15 other families of Lamiales. The Scrophulariaceae s.s. (sensu stricto) include part or all of tribes Aptosimeae, Hemimerideae, Leucophylleae, Manuleae, Selagineae, and Verbasceae (= Scrophularieae) and the conventional families Buddlejaceae and Myoporaceae. Veronicaceae includes all or part of tribes Angelonieae, Antirrhineae, Cheloneae, Digitaleae, and Gratioleae and the conventional families Callitrichaceae, Globulariaceae, Hippuridaceae, and Plantaginaceae. The Orobanchaceae include tribes Buchnereae, Rhinantheae, and the conventional Orobanchaceae. All sampled members of Orobanchaceae are parasitic, except Lindenbergia, which is sister to the rest of the family. Family Calceolariaceae Olmstead is newly erected herein to recognize the phylogenetic distinctiveness of tribe Calceolarieae. The Calceolariaceae are close to the base of the Lamiales. The Stilbaceae are expanded by the inclusion of Halleria. Mimulus does not belong in any of these five groups.

Monophyly of the Asteridae and Identification of Their Major Lineages Inferred From DNA Sequences of rbcL

A parsimony analysis of 57 angiosperm rbcL sequences was conducted to test the monophyly of the Asteridae and to identify major lineages within the Asteridae. Three major clades, the Caryophyllidae, the Rosidae plus Dilleniidae, and the Asteridae sensu lato, emerge from an unresolved radiation in the «higher» dicots. The Asteridae sens. lat. include the Ericales, Cornales, and Apiales in addition to the Asteridae sens. str. Two major lineages within the Asteridae sens. lat. are identified: the Dipsacales, Apiales, Asterales, and Campanulales in one, and the Gentianales, Scrophulariales, Lamiales, Boraginales, and Solanales in the other (...)

Angiosperm phylogeny: 17 genes, 640 taxa

PREMISE OF THE STUDY Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

Utility of 17 Chloroplast Genes for Inferring the Phylogeny of the Basal Angiosperms

Sequences from 14 slowly evolving chloroplast genes (including three highly conserved introns) were obtained for representative basal angiosperm and seed-plant taxa, using novel primers described here. These data were combined with published sequences from atpB, rbcL, and newly obtained sequences from ndhF. Combined data from these 17 genes permit sturdy, well-resolved inference of major aspects of basal angiosperm relationships, demonstrating that the new primers are valuable tools for sorting out the deepest events in flowering plant phylogeny. Sequences from the inverted repeat (IR) proved to be particularly reliable (low homoplasy, high retention index). Representatives of Cabomba and Illicium were the first two successive branches of the angiosperms in an initial sampling of 19 exemplar taxa. This result was strongly supported by bootstrap analysis and by two small insertion/deletion events in the slowly evolving introns. Several paleoherb groups (representatives of Piperales) formed a strongly supported clade with taxa representing core woody magnoliids (Laurales, Magnoliales, and Winteraceae). The monophyly of the sampled eudicots and monocots was also well supported. Analyses of three major partitions of the data showed many of the same clades and supported the rooting seen with all the data combined. While Amborella trichopoda was supported as the sister group of the remaining angiosperms when we added Amborella and Nymphaea odorata to the analysis, a strongly conflicting rooting was observed when Amborella alone was added.

Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels

Asterids comprise 1/4-1/3 of all flowering plants and are classified in 10 orders and >100 families. The phylogeny of asterids is here explored with jackknife parsimony analysis of chloroplast DNA from 132 genera representing 103 families and all higher groups of asterids. Six different markers were used, three of the markers represent protein coding genes, rbcL, ndhF, and matK, and three other represent non-coding DNA; a region including trnL exons and the intron and intergenic spacers between trnT (UGU) to trnF (GAA); another region including trnV exons and intron, trnM and intergenic spacers between trnV (UAC) and atpE, and the rps16 intron. The three non-coding markers proved almost equally useful as the three coding genes in phylogenetic reconstruction at the high level of orders and families in asterids, and in relation to the number of aligned positions the non-coding markers were even more effective. Basal interrelationships among Cornales, Ericales, lamiids (new name replacing euasterids I), and campanulids (new name replacing euasterids II) are resolved with strong support. Family interrelationships are fully or almost fully resolved with medium to strong support in Cornales, Garryales, Gentianales, Solanales, Aquifoliales, Apiales, and Dipsacales. Within the three large orders Ericales, Lamiales, and Asterales, family interrelationships remain partly unclear. The analysis has contributed to reclassification of several families, e.g., Tetrameristaceae, Ebenaceae, Styracaceae, Montiniaceae, Orobanchaceae, and Scrophulariaceae (by inclusion of Pellicieraceae, Lissocarpaceae, Halesiaceae, Kaliphoraceae, Cyclocheilaceae, and Myoporaceae+Buddlejaceae, respectively), and to the placement of families that were unplaced in the APG-system, e.g., Sladeniaceae, Pentaphylacaceae, Plocospermataceae, Cardiopteridaceae, and Adoxaceae (in Ericales, Ericales, Lamiales, Aquifoliales, and Dipsacales, respectively), and Paracryphiaceae among campanulids. Several families of euasterids remain unclassified to order.

A parsimony analysis of the Asteridae sensu lato based on rbcL sequences

A parsimony analysis of 156 representative sequences of the Asteridae sensu lato and 28 outgroup sequences was conducted using a two-tiered approach. First, an analysis of the entire group, including 105 sequences, examined relationships among major lineages within the Asteridae s.l.; subsequently, several clades within the larger group were examined individually in greater detail by including more sequences for the group in question. The search strategy was designed to discover multiple islands of equal parsimony using the heuristic search routine in PAUP. In the broad search and in each more detailed search of subclades, multiple islands were found that imply substantially different relationships

Many Parallel Losses of infA from Chloroplast DNA during Angiosperm Evolution with Multiple Independent Transfers to the Nucleus

We used DNA sequencing and gel blot surveys to assess the integrity of the chloroplast gene infA, which codes for translation initiation factor 1, in >300 diverse angiosperms. Whereas most angiosperms appear to contain an intact chloroplast infA gene, the gene has repeatedly become defunct in ∼24 separate lineages of angiosperms, including almost all rosid species. In four species in which chloroplast infA is defunct, transferred and expressed copies of the gene were found in the nucleus, complete with putative chloroplast transit peptide sequences. The transit peptide sequences of the nuclear infA genes from soybean and Arabidopsis were shown to be functional by their ability to target green fluorescent protein to chloroplasts in vivo. Phylogenetic analysis of infA sequences and assessment of transit peptide homology indicate that the four nuclear infA genes are probably derived from four independent gene transfers from chloroplast to nuclear DNA during angiosperm evolution. Considering this and the many separate losses of infA from chloroplast DNA, the gene has probably been transferred many more times, making infA by far the most mobile chloroplast gene known in plants.

MICROSTRUCTURAL CHANGES IN NONCODING CHLOROPLAST DNA: INTERPRETATION, EVOLUTION, AND UTILITY OF INDELS AND INVERSIONS IN BASAL ANGIOSPERM PHYLOGENETIC INFERENCE

Microstructural changes in several very slowly evolving chloroplast introns and intergenic spacers were characterized across a broad range of angiosperms, including most of the major basal lineages. Insertion/deletion events (indels) in the surveyed noncoding regions of the large inverted repeat (IR) region were shown to be rarer than nucleotide substitutions and thus constitute one of the slowest and least homoplastic types of data available to plant systematists. In our study we scored 180 indels in noncoding regions, of which 36 were parsimony informative within the angiosperms. Because they are relatively few in number, their general utility is currently limited. However, they provide support for specific major taxa, including the angiosperms as a whole, the water lilies, and Illiciaceae and relatives. Support for the basalmost angiosperm split is largely inconclusive, but a single indel supported a basal placement of the water lilies, not Amborella. We estimate that roughly double or triple the current amount (ca. 2.2 kb) of noncoding IR DNA would be required to obtain indel support for most of the deepest branches at the base of the angiosperms. A variety of molecular processes appear to be responsible for the observed indels. Indels are more frequently associated with tandem repeat sequences than not. Insertions are significantly more frequently associated with tandem repeats than are deletions. The latter finding may be, in part, a function of an ascertainment bias for insertions versus deletions. Single‐base indels were the most common size class, but there was an unexplained deficit of some other small indel size classes. Coding indels can be problematical, particularly when they overlap among taxa in an alignment. We favor one simple scheme for coding overlapping indels but argue that no existing scheme for coding overlapping indels for phylogenetic analysis, or dealing with them in alignment, is ideal. Several small inversions were observed. These included the most homoplastic microstructural character in the current study. Each inversion was associated with short flanking inverted repeats.

A Chloroplast DNA Phylogeny of the Solanaceae: Subfamilial Relationships and Character Evolution

Phylogenetic relationships among 42 species of Solanaceae representing 12 of the 14 currently recognized tribes were assessed by chloroplast DNA restriction site mapping. Over 1,000 cleavage sites were identified for 10 restriction enzymes and of these, 447 provided information concerning relationships among the included taxa and the outgroup, Ipomoea (Convolvulaceae). The results establish that subfamily Cestroideae is ancestral in the family and is paraphyletic, and that the subfamily Solanoideae is derived from within the Cestroideae and is monophyletic, if it is circumscribed to include Nolana (...)