Systematic studies of the antarctic species of the phyllophoraceae (Gigartinales,Rhodophyta) based on rbcL sequence analysis

The taxonomic placement of four antarctic species of the marine red algal family Phyllophoraceae (Gigartinales) is assessed within a preliminary molecular phylogeny of the family based on direct sequence analysis of the chloroplast gene rbcL. Parsimony analysis of rbcL sequences indicates that Gymnogongrus antarcticus and Gymnogongrus turquetii cluster in a clade consisting predominantly of southern hemisphere species currently placed in Gymnogongrus and Ahnfeltiopsis, whereas Phyllophora ahnfeltioides and Phyllophora antarctica cluster in a separate clade that is widely divergent from the northern hemisphere Phyllophora clade. Results from molecular and morphological data challenge the current taxonomic concept that type of life history is a phylogenetically valid criterion for recognition of genera in the Phyllophoraceae.     

Recent developments in the systematics of the Gigartinaceae (Gigartinales, Rhodophyta) based on rbcL sequence analysis and morphological evidence

The phylogenetic systematics of the Gigartinaceae is discussed for seven genera and three undescribed generic lineages and 65 taxa representing 62 species based on an analysis of rbcL sequences and morphological evidence. An examination of rbcL trees resulting from analyses of these taxa identifies seven lineages: (i) ‘Gigartina’ alveata; (ii) Rhodoglossum/Gigartina; (iii) Chondracanthus; (iv) Ostiophyllum; (v) Sarcothalia; (vi) ‘Gigartina’ skottsbergii; and (vii) a large clade containing Iridaea/‘Sarcothalia’, Mazzaella and Chondrus. These lineages and Chondrus are strongly supported; however, two groups, Iridaea/‘Sarcothalia’ and Mazzaella, receive no bootstrap support. The morphology of the female reproductive system is investigated with the aid of computer-generated, color-coded tracings of photographs of cystocarps seen in cross section at different developmental stages. Seven basic cystocarp types were found which corresponded to species groups seen in rbcL trees. These were: (i) a ‘Gigartina’ alveata group in which the carposporangia-bearing filaments develop apomictically from gametophytic cells; (ii) a Rhodoglossum/Gigartina group in which gonimoblast filaments penetrate the surrounding envelope fusing progessively with envelope cells; (iii) a Chondracanthus group in which gonimoblast filaments penetrate the envelope but fuse with envelope cells only at late developmental stages; (iv) a Sarcothalia group in which the gonimoblast filaments displace an envelope composed mainly of secondary gametophytic filaments and link to envelope cells by terminal tubular gonimoblast cells; (v) an Iridaea group similar to the Sarcothalia group, but with an envelope composed of a mixture of medullary cells and secondary gametophytic filaments; (vi) a Mazzaella group that lacks a true envelope and in which gonimoblast filaments connect to modified gametophytic cells by means of terminal tubular cells; (vii) a Chondrus group in which gonimoblast filaments penetrate the medulla and link to modified medullary cells by means of conjunctor cells forming secondary pit connections. The further separation of these groups into genera is based largely on tetrasporangial characters.     

Molecular Systematics and Phylogenetics of Gracilariacean Species from the Mediterranean Sea

Mediterranean reports of Gracilariaceae species, in particular those assigned to the G. verrucosa complex, were re-examined with the use of molecular tools, in order to verify their systematic position and better understand their distribution. Within this complex, we recognized four distinct taxa: Gracilariopsis longissima, Gracilaria gracilis, Gracilaria longa and a possible new species. The rbcL gene sequences, together with those of other terete Mediterranean entities, were included in a broad molecular phylogeny of the family. The reproductive characters of the studied taxa do not fit completely with published hypothesis on the generic and intrageneric relationships, suggesting that the anatomy of some subgroups should be better characterized.     

Phylogenetic relationships of ferns deduced from rbcL gene sequence

Part of the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) gene (rbcL) was sequenced from three fern species: Adiantum capillus-veneris, Botrypus strictus, and Osmunda cinnamomea var. fokiensis. This region included 1,333 base pairs, about 90% of the gene. Maximum likelihood analysis of the deduced amino acid sequences indicated that (1) Botrypus (Ophioglossaceae) clustered monophyletically with other ferns (Adiantum, Angiopteris, Osmunda); the closest relative to Botrypus among the three species was Osmunda, which did not support the hypothesis that the Ophioglossaceae are linked to the progymnosperm-seed plant lineage. (2) Eusporangiate ferns containing Botrypus (Ophioglossaceae) and Angiopteris (Marattiaceae) were a paraphyletic group. (3) Seed plants and the four fern species examined formed a monophyletic group, but ferns and bryophytes (liverwort) did not. Variations in rates of substitution for synonymous and nonsynonymous codons were found in fern lineages.Correspondence to: M. Hasebe     

Phylogenetic analysis ofEremosyne pectinata (Saxifragaceae s. l.) based onrbcL sequence data

Earlier analyses ofrbcL sequences clarified phylogenetic relationships of 16 of 17 subfamilies ofSaxifragaceae s. l. This study investigates the affinities of the monotypicEremosynoideae, the only subfamily ofSaxifragaceae s. l. not examined previously forrbcL sequence variation. Our analyses suggest thatEremosyne is only distantly related to core members ofSaxifragaceae s. l. (i.e.Saxifragoideae = Saxifragaceae s. str.); it is allied instead with members ofAsteridae. A particularly close relationship is indicated betweenEremosyne andEscallonia, another traditional member ofSaxifragaceae s. l. that also appears as part ofAsteridae. Inclusion ofEremosyne withinAsteridae is in agreement with embryology, as well as with 18S rDNA sequence data.     

Reinstatement of Lophocoleaceae (Jungermanniopsida) based on chloroplast gene rbcL data: exploring the importance of female involucres for the systematics of Jungermanniales

Maximum likelihood analysis of 113 rbcL sequences leads to a well resolved phylogeny of Jungermanniales. All species with perigynia or marsupia are found in one clade, whereas species with coelocaules are placed in several lineages. The broadly circumscribed Geocalycaceae (including Lophocoleaceae) of most recent authors are resolved as polyphyletic. Geocalycaceae genera which develop female involucres without involvement of stem tissue (Chiloscyphus, Heteroscyphus, Leptoscyphus, Physotheca) form a robust clade which is placed sister to Plagiochilaceae whereas the genera with involucres originating at least partly from stem tissue (Geocalycaceae s.str., Geocalyx, Harpanthus, Saccogyna) are nested within the paraphyletic Jungermanniaceae. This topology leads to the exclusion of the strictly perianth-bearing species from Geocalycaceae and the reinstatement of Lophocoleaceae. Campanocolea is nested within Chiloscyphus. Physotheca and Chiloscyphus breutelii are placed within an unsupported clade with several accessions of Leptoscyphus. Heteroscyphus forms a paraphyletic grade at the base of Chiloscyphus.     

Taxonomic Considerations of a Foliose Grateloupia Species from the Straits of Messina

Grateloupia turuturu Yamada is the currently accepted name for the invasive red alga that is present on coasts of the North Atlantic. Previously considered as G. doryphora (Montagne) M.A. Howe, populations of this invasive species were examined and their taxonomic position revised using molecular and morphological techniques. It was also thought that similar invasive populations in the Mediterranean should be identified as G. turuturu. This investigation used rbcL based molecular analyses to clarify the taxonomic position of Grateloupia “doryphora’ from the Straits of Messina. Our results indicate that this population is neither G. doryphora nor G. turuturu. It was placed separately in all analyses and grouped consistently with other Grateloupia species from the Pacific. On the basis of molecular data from this and previous investigations, it is evident that the status of the foliose Atlantic and Mediterranean entities is still unclear and a re-evaluation of the old names connected to them should be undertaken.     

A simple and rapid technique to PCR amplify plastid genes from spores of <Emphasis Type="Italic">Porphyra</Emphasis> C. Agardh (Bangiales,Rhodophyta)

A user-friendly and fast protocol using PCR was developed to amplify the plastid rbcL gene of Porphyra, the most economically valuable genus of Rhodophyta. The technique involved the use of monospores, providing the advantage of a small and genetically homogeneous set of cells and thus reducing the risk of biological or chemical contamination. An additional factor in the choice of the rbcL gene was the huge amount of sequence data deposited in molecular biology databases and their utility as molecular markers in taxonomic studies.     

Amino acids and low-molecular-weight carbohydrates of some marine red algae

Amino acids and low-MW carbohydrates of 18 red algae have been analyzed. Several non-protein amino acids have been identified, including pyrrolidine-2,5-dicarboxylic acid (3c) and N-methylmethionine sulfoxide (5), new natural products, and 13 known compounds, citrulline, β-alanine, γ-aminobutyric acid, baikiain (1), pipecolic acid (2), domoic acid (3a), kainic acid (3b), azetidine-2-carboxylic acid (4), methionine sulfoxide taurine, N-methyltaurine, N,N-dimethyltaurine and N,N,N-trimethyltaurine. Sugars present were mainly floridoside, isofloridoside and mannoglyceric acid. Details of the structural elucidation of new compounds are also given.     

Comparative morphology and systematics of Chondrymenia lobata from the Mediterranean Sea and a phylogeny of the Chondrymeniaceae fam. nov. (Rhodophyta) based on rbcL sequence analyses

The Chondrymeniaceae Rodríguez-Prieto, G. Sartoni, S.-M. Lin & Hommersand, fam. nov., is proposed for Chondrymenia lobata. Analyses of rbcL sequences place the new family in a large gigartinalean assemblage that comprises the Cystocloniaceae–Solieriaceae complex. Plants are decumbent and growth takes place by division of multiple apical cells at the margin of the blade. Thalli consist of an outer cortex of subspherical to elongate cortical cells arranged in anticlinal rows, a subcortex of cells cross-linked by lateral arms, and a large central medulla composed of primary medullary filaments intermixed with numerous rhizoidal filaments. Male stages are reported in monoecious individuals. Inactive carpogonial branches consist of a two-celled filament that is directed inwards from the supporting cell. Functional carpogonial branches are oriented outwardly, with the carpogonia and trichogynes pointed towards the thallus surface. After presumed fertilization, the carpogonium fuses with the hypogynous cell and transfers the zygote nucleus. The hypogynous cell, in turn, fuses with the supporting cell which contains many haploid nuclei. The resulting fusion cell functions as an auxiliary cell that cuts off a single gonimoblast initial, which produces the gonimoblast filaments. Gametophytic cells close to the auxiliary cell unite with it to form a placental fusion network of variable size and outline, and a placental fusion cell. Proximal gonimoblast cells fuse with the placental fusion cell, while the distal cells differentiate into branched chains of subspherical carposporangia. The superficial similarity of the outwardly developed osteolate cystocarp is responsible for Kylin's (1956) placement of Chondrymenia in his family Sarcodiaceae; however, the manner in which the placenta is formed is more like that seen in the Cystocloniaceae–Solieriaceae complex.     

Evidence for a composite phylogenetic origin of the plastid genome of the brown alga Pylaiella littoralis (L.) Kjellm

The nucleotide sequence and the 5 flanking region of the rbcL gene coding for the large subunit of ribulose bisphosphate-1,5-carboxylase/oxygenase of Pylaiella littoralis, a brown alga, has been determined and the deduced amino-acid sequence has been compared to those of various photosynthetic and chemoautotrophic Eubacteria, of a red alga and of green plastids (Euglena gracilis, green algae and higher plants). Unlike the rbcL genes of green plastids which are more closely related to those of cyanobacteria the P. littoralis rbcL gene is more closely related to that of a -purple bacterium, as was found for the rbcS gene of another chromophytic alga [Boczar et al., Proc Natl Acad Sci USA 86: 4996–4999, 1989]. Matrix data of homology between the rbcL gene of P. littoralis and the same gene of other organisms are presented. Based on our previous report, the gene coding for the 16S rRNA from P. littoralis is closely related to that of E. gracilis (Markowicz et al., Curr Genet 14: 599–608, 1988). We suggest that the large plastid DNA molecule of P. littoralis is a phylogenetically composite genome which probably resulted from mixed endosymbiosis events, or from a horizontal transfer of DNA.     

Protoplast isolation and regeneration in the marine red alga Porphyra nereocystis

We have developed a method for isolating viable protoplasts from the blade phase of the epiphytic marine red alga Porphyra nereocystis Anderson, using a two-step enzymatic digestion with commercially available enzymes. The first step uses papain, the second step uses abalone acetone powder. The method is rapid and gives a high yield of viable protoplasts. In liquid culture in enriched seawater medium, the protoplasts can undergo regeneration along three pathways: they directly form filaments resembling the conchocelis phase of Porphyra; they form calli with relatively thick-walled, pigmented cells; and they indirectly form blades from the edges of these calli. Porphyra nereocystis protoplasts also may serve as an alternative propagation method in aquaculture and be useful for studies of cell-wall formation, cell division, and thallus differentiation. They may also be used in somatic selection, somatic hybridization and gene-transfection experiments.Abbreviations AAP abalone acetone powder - PAP papain - FDA fluorescein diacetate This paper is dedicated to the memory of the late Dr. Munenao Kurogi (1921–1988), Professor Emeritus of Hokkaido UniversityThis research was supported by the Washington Sea Grant Program (National Oceanic and Atmospheric Administration). We thank Professor Y. Fujita (Nagasaki University, Japan), Professor S.-J. Wang (Shanghai University of Fisheries, P.R. China) and Dr. H. Kito (Seikai Regional Fisheries Research Laboratory, Nagasaki, Japan) for sharing their experience with Porphyra protoplast production with us. We thank J.S. Charleston for expert technical assistance in preparation of the electron-microscopy specimens. We also thank Dr. S.K. Herbert and John Carrier (Friday Harbor Laboratories) and Dr. John Merrill and D. Gillingham (American Sea Vegetable Co. and Applied Algal Research, Seattle) for collections of P. nereocystis.     

Evolutionary Patterns of Codon Usage in the Chloroplast Gene rbcL

In this study we reconstruct the evolution of codon usage bias in the chloroplast gene rbcL using a phylogeny of 92 green-plant taxa. We employ a measure of codon usage bias that accounts for chloroplast genomic nucleotide content, as an attempt to limit plausible explanations for patterns of codon bias evolution to selection- or drift-based processes. This measure uses maximum likelihood-ratio tests to compare the performance of two models, one in which a single codon is overrepresented and one in which two codons are overrepresented. The measure allowed us to analyze both the extent of bias in each lineage and the evolution of codon choice across the phylogeny. Despite predictions based primarily on the low G+C content of the chloroplast and the high functional importance of rbcL, we found large differences in the extent of bias, suggesting differential molecular selection that is clade specific. The seed plants and simple leafy liverworts each independently derived a low level of bias in rbcL, perhaps indicating relaxed selectional constraint on molecular changes in the gene. Overrepresentation of a single codon was typically plesiomorphic, and transitions to overrepresentation of two codons occurred commonly across the phylogeny, possibly indicating biochemical selection. The total codon bias in each taxon, when regressed against the total bias of each amino acid, suggested that twofold amino acids play a strong role in inflating the level of codon usage bias in rbcL, despite the fact that twofolds compose a minority of residues in this gene. Those amino acids that contributed most to the total codon usage bias of each taxon are known through amino acid knockout and replacement to be of high functional importance. This suggests that codon usage bias may be constrained by particular amino acids and, thus, may serve as a good predictor of what residues are most important for protein fitness. Present address (Joshua T. Herbeck): JBP Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA     

Phylogenetic Diversity of New Zealand Gelidiales as Revealed by rbcL Sequence Data

Diversity and phylogenetic relationships of New Zealand representatives of the red algal order Gelidiales have been examined using rbcL sequence data. Extensive field collections have been made from throughout the New Zealand region. Six genera have been reported previously from New Zealand (Capreolia, Gelidium, Pterocladia, Pterocladiella, Pterocladiastrum, Ptilophora). This research has revealed species with very restricted local distributions, as well as the discovery of several undescribed, cryptic taxa. The common and widespread Gelidium caulacantheum is confirmed to be more closely related to Capreolia than to other species of Gelidium. The generic concept of Capreolia, based on life history characters, will need to be modified to accommodate additional species possessing “Gelidium” life histories. A species endemic to New Zealand, Gelidium ceramoides, has been found to differ significantly from all other members of the Gelidiales and requires reclassification in another genus and order. Examination of field collections and herbarium specimens in addition to molecular sequence data have led us to conclude that specimens previously placed in the genera Ptilophora and Pterocladiastrum belong within Pterocladia lucida.     

Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

The complete sequence of the 18 S ribosomal RNA gene(18S rRNA) from Lymantria dispar was cloned and analysed here. 18 S rRNA and mitochondrial cytochrome c oxidasel(cox1) gene sequences of Lymantria dispar were compared with homologous sequences of other nine insects from different orders. Analytic results showed that 18 S rRNA of these insects had two conserved domains and the second domain was an even more conserved region. The phylogenetic trees based on the full-length sequence and the second domain fragment of 18 S rRNA as well as sequence of cox1 from different orders indicated that Lepidoptera and Trichoptera, which belongs to Amphiesmenoptera, had a closer phylogenetic relationship and fewer differences were observed comparing with traditional taxonomic results.     

The diagnostic value of reproductive organs in some genera of articulated Coralline red algae

Clearcut differences exist between the reproductive organs of Corallina and Jania. Fully formed spermatangial conceptacles in Corallina have low ceillings and pronounced beaks whereas in Jania they have high ceilings and lack beaks. Fusion cells in carposporophytic conceptacles are thin and broad in the former genus and thick and narrow in the latter. Tetrasporangial conceptacles have less capacity in Jania than in Corallina and the fertile areas in young conceptacles cover a smaller area.

Haliptylon is changed from group to generic status and Corallina subulata is transferred to this genus. Haliptylon is characterised by conceptacles similar in all known respects to those of Jania, but the branching is pinnate, as in Corallina.

From the available evidence it appears possible that organisms having Corallina-type conceptacles diverged phylogenetically long ago from those having Jania-type conceptacles.     

Molecular systematics and biogeography of theCardamine pratensis complex (Brassicaceae)

Representatives of theC. pratensis complex were analysed for allozymes, ITS, non-coding cpDNA, and RAPDs to elucidate phylogenetic relationships and the historical biogeography of this species group. Our concepts differ in some important aspects from current ideas. Two diploid species from southeastern Europe form the Basal Group of the complex. A diploid from the Iberian Peninsula represents another old lineage. The phylogenetically younger Derived Group comprises diploid taxa and all known polyploid taxa. The two old lineages represent pleistocene relicts which were not involved in the formation of the Derived Group. All polyploids evolved in postglacial time from diploids of the Derived Group which may have survived the glaciations in refugia centered around and within the Alps. The arctic-circumpolarC. nymanii is of young age and migrated to Scandinavia in postglacial times from south to north.