Kenneth G. Karol

Molecules, Morphology, and Dahlgren's Expanded Order Capparales

Nucleotide sequences for the chloroplast gene rbcL have been obtained for three species of Salvadoraceae and for the unispecific Pentadiplandraceae, thus completing a survey of all known mustard-oil families. Phylogenetic analyses of the sequences based on maximum parsimony reveal two separate lineages of plants that produce mustard oil glucosides. A major mustard-oil clade comprises the core capparalean families of Brassicaceae, Capparaceae, Gyrostemonaceae, Resedaceae, and Tovariaceae and includes Akania- ceae, Bataceae, Bretschneideraceae, Caricaceae, Koeberliniaceae, Limnanthaceae, Moringaceae, Pentadipland- raceae, Salvadoraceae, and Tropaeolaceae. A second unrelated lineage consists of the genus Drypetes, traditionally placed in Euphorbiaceae. The major mustard-oil clade recovered from the rbcL analysis is congruent in many topological aspects with that found in a recent cladistic study of morphological characters, and in turn the molecular and morphological results confirm Dahlgrens radically expanded Capparales. An approach combining molecular and morphological evidence yields robust support for several lineages within this major mustard-oil clade.

Nucleotide Sequences of the rbcL Gene Indicate Monophyly of Mustard Oil Plants

Nucleotide sequences for the chloroplast rbcL gene were obtained from representatives of 11 of the 15 plant families known to produce glucosinolates (mustard oil glucosides). Parsimony analyses indicate that these constitute two widely separated groups and thus imply two independent origins of the mustard oil/myrosin cell syndrome. A strongly supported, major group comprises the mustard family Brassicaceae and its near relatives Capparaceae, Resedaceae, and Tovariaceae along with such morphologically diverse taxa as Bataceae, Bretschneideraceae, Caricaceae, Limnanthaceae, Moringaceae, and Tropaeolaceae. The second mustard oil group is restricted to the euphorbiaceous genus Drypetes

Circumscription of the Malvales and relationships to other Rosidae: evidence from RBCL sequence data

The order Malvales remains poorly circumscribed, despite its seemingly indisputable core constituents: Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae. We conducted a two-step parsimony analysis on 125 rbcL sequences to clarify the composition of Malvales, to determine the relationships of some controversial families, and to identify the placement of the Malvales within Rosidae. We sampled taxa that have been previously suggested to be within, or close to, Malvales (83 sequences), plus additional rosids (26 sequences) and nonrosid eudicots (16 sequences) to provide a broader framework for the analysis. The resulting trees strongly support the monophyly of the core malvalean families, listed above. In addition, these data serve to identify a broader group of taxa that are closely associated with the core families. This expanded malvalean clade is composed of four major subclades: (1) the core families (Bombacaceae, Malvaceae, Sterculiaceae, Tiliaceae); (2) Bixaceae, Cochlospermaceae, and Sphaerosepalaceae (Rhopalocarpaceae); (3) Thymelaeaceae sensu lato (s.l.); and (4) Cistaceae, Dipterocarpaceae s.l., Sarcolaenaceae (Chlaenaceae), and Muntingia. In addition, Neurada (Neuradaceae or Rosaceae) falls in the expanded malvalean clade but not clearly within any of the four major subclades. This expanded malvalean clade is sister to either the expanded capparalean clade of Rodman et al. or the sapindalean clade of Gadek et al. Members of Elaeocarpaceae, hypothesized by most authors as a sister group to the four core malvalean families, are shown to not fall close to these taxa. Also excluded as members of, or sister groups to, the expanded malvalean clade were the families Aextoxicaceae, Barbeyaceae, Cannabinaceae, Cecropiaceae, Dichapetalaceae, Elaeagnaceae, Euphorbiaceae s.l., Huaceae, Lecythidaceae, Moraceae s.l., Pandaceae, Plagiopteraceae, Rhamnaceae, Scytopetalaceae, Ulmaceae, and Urticaceae.

Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication.

The domestication history of eggplant (Solanum melongena L.) has long been debated, with studies unable to narrow down where domestication occurred within a broad region of tropical Asia. The most commonly hypothesized region is India, however China has an equally old written record of eggplant use dating ca. 2000 years before present. Both regions have a high diversity of landraces and populations of putatively wild eggplant: Solanum incanum L. in India and Solanum undatum Lam. in SE Asia. An additional complication is that there is taxonomic confusion regarding the two candidate progenitors. Here, we synthesize historic, morphologic, and molecular data (nrITS sequence and AFLP) to interpret the phylogeographic relationships among candidate progenitors and Asian eggplant landraces in order to test theories of domestication. A minimum of two domestication events is supported: one in India and one in southern China/SE Asia. Results also support separate domestication of S. melongena subsp. ovigerum, a group of morphologically distinct eggplants found in SE Asia, and suggest Asian S. incanum and S. undatum may not be genetically distinct. Routes of the spread of eggplant cultivation throughout Asia are proposed, and evolutionary relationships among allied species are discussed.

PHYLOGENY OF THE CONJUGATING GREEN ALGAE BASED ON CHLOROPLAST AND MITOCHONDRIAL NUCLEOTIDE SEQUENCE DATA

The conjugating green algae represent a lineage of charophyte green algae known for their structural diversity and unusual mode of sexual reproduction, conjugation. These algae are ubiquitous in freshwater environments, where they are often important primary producers, but few studies have investigated evolutionary relationships in a molecular systematic context. A 109‐taxon data set consisting of three gene fragments (two from the chloroplast and one from the mitochondrial genome) was used to estimate the phylogeny of the genera of the conjugating green algae. Maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) were used to estimate relationships from the 4,047 alignable nucleotides. This study confirmed the polyphyly of the Zygnemataceae and Mesotaeniaceae with respect to one another. The Peniaceae were determined to be paraphyletic, and two genera traditionally classified among the Zygnematales appear to belong to the lineage that gave rise to the Desmidiales. Six genera, Euastrum, Cosmarium, Cylindrocystis, Mesotaenium, Spondylosium, and Staurodesmus, were polyphyletic in this analysis. These findings have important implications for the evolution of structural characteristics in the group and will require some taxonomic changes. More work will be required to delineate lineages of Zygnematales in particular and to identify structural synapomorphies for some of the newly identified clades.

Molecular Systematics of the Green Algae

Ranging from unicells to complex “plantlike” organisms that are adapted to habitats from subaerial or terrestrial to freshwater or marine, the green algae represent a diversity of life forms that offer a daunting challenge in the search for shared morphological characters. The ultrastuctural techniques that fueled the 1970s and early 1980s revolution in algal systematics revealed a suite of new morphological characters, but many were not global (i.e., present in all of the taxa). Controversy over the interpretation of the importance of ultrastructural features (e.g., of cell division versus flagellar apparatus) led to conflicting hypotheses. Also, different researchers studied different details of different taxa, and thus a data matrix reporting a complete set of morphological and ultrastructural characters over a wide range of algal taxa was not available. Thus, it is no wonder that many researchers interested in unraveling the mystery of green algal phylogeny embraced molecular systematics, hoping that its early promise of relatively simple access to ample global characters would lead, finally, to a “true” phylogeny. The extent to which this promise has been fulfilled, or is likely to be fulfilled, is the subject of this chapter.

Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes

BackgroundTortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-tolerant plant.ResultsThe Tortula chloroplast genome is ~123,500 bp, and differs in a number of ways from that of Physcomitrella patens, the first published moss chloroplast genome. For example, Tortula lacks the ~71 kb inversion found in the large single copy region of the Physcomitrella genome and other members of the Funariales. Also, the Tortula chloroplast genome lacks petN, a gene found in all known land plant plastid genomes. In addition, an unusual case of nucleotide polymorphism was discovered.ConclusionsAlthough the chloroplast genome of Tortula ruralis differs from that of the only other sequenced moss, Physcomitrella patens, we have yet to determine the biological significance of the differences. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for mosses) of the generation of DNA markers for fine-level phylogenetic studies, or to investigate individual variation within populations.

The Complete Plastid Genome Sequence of Angiopteris evecta (G. Forst.) Hoffm. (Marattiaceae)

ABSTRACT We have sequenced the complete plastid genome of the fern Angiopteris evecta. This taxon belongs to a major lineage (marattioid ferns) that, in most recent phylogenetic analyses, emerges near the base of the monilophytes. We used fluorescence activated cell sorting (FACS) to isolate organelles, rolling circle amplification (RCA) to amplify the plastid genome, followed by shotgun sequencing to 8X depth coverage, and then we assembled these reads to obtain the plastid genome sequence. The circular genome map has 153,901 bp, containing inverted repeats of 21,053 bp each, a large single-copy region of 89,709 bp, and a small single-copy region of 22,086 bp. Gene order is similar to that of Psilotum. Several unique characters are observed in the Angiopteris plastid genome, such as repeat structure in a pseudogene. We make structural comparisons to Psilotum and Adiantum plastid genomes. However, the overall structural similarity to Psilotum indicates either wholesale conservation of genome organization, or (less likely) repeated convergence to a stable structure. The results are discussed in relation to a growing comparative database of genomic and morphological characters across the green plants.

Phylogeny of North American Tolypella (Charophyceae, Charophyta) based on plastid DNA sequences with a description of Tolypella ramosissima sp. nov.

Characeae (Charophyceae, Charophyta) contains two tribes with six genera: tribe Chareae with four genera and tribe Nitelleae, which includes Tolypella and Nitella. This paper uses molecular and morphological data to elucidate the phylogeny of Tolypella species in North America. In the most comprehensive taxonomic treatment of Characeae, 16 Tolypella species worldwide were subsumed into two species, T. intricata and T. nidifica, in two sections, Rothia and Tolypella respectively. It was further suggested that Tolypella might be a derived group within Nitella. In this investigation into species diversity and relationships in North American Tolypella, sequence data from the plastid genes atpB, psbC, and rbcL were assembled for a broad range of charophycean and land plant taxa. Molecular data were used in conjunction with morphology to test monophyly of the genus and species within it. Phylogenetic analyses of the sequence data showed that Characeae is monophyletic but that Nitelleae is paraphyletic with Tolypella sister to a monophyletic Nitella + Chareae. The results also supported the monophyly of Tolypella and the sections Rothia and Tolypella. Morphologically defined species were supported as clades with little or no DNA sequence differences. In addition, molecular data revealed several lineages and a new species (T. ramosissima sp. nov.), which suggests greater species diversity in Tolypella than previously recognized.

Chloroplast DNA Sequences Confirm the Placement of the Enigmatic Oceanopapaver within Corchorus (Grewioideae: Malvaceae s.l., Formerly Tiliaceae)

The monotypic genus Oceanopapaver is an endemic shrub found growing on serpentine soils in New Caledonia. Since the description of Oceanopapaver neocaledonicum by A. Guillaumin in 1932, five families have been suggested for it: Capparaceae, Cistaceae, Oceanopapaveraceae, Papaveraceae, and Tiliaceae. Phylogenetic analyses using DNA sequences of the chloroplast genes rbcL and ndhF strongly support the inclusion of Oceanopapaver in a clade of former Tiliaceae, Grewioideae (Malvaceae s.l.). Within Grewioideae, Oceanopapaver is nested within the pantropical genus Corchorus.