Unknown New Zealand angiosperm assigned toCunoniaceae using sequence of the chloroplastrbcL gene

We report the first example of identification of an unknown flowering plant to family level using comparison of DNA sequences. The newly-discovered New Zealand plant had not been identified by traditional methods, but has been placed in the Gondwanic familyCunoniaceae on the basis of the sequence of its chloroplastrbcL gene. It has not flowered, but its vegetative characters are typical of the family. However, it is clearly unusual in several morphological and anatomical features and appears to match no known genus. We consider that, although it probably represents an unnamed new genus, it could possibly be a mutant dwarf form ofWeinmannia racemosa, so it is not prudent to name it at this time.     

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 relationships of theJuglandaceae

A cladistic analysis of molecular data from the chloroplast generbcL was used to examine the taxonomic relationships of the walnut family (Juglandaceae). In addition, chemical and morphological data from a previous study byHufford (1992) were incorporated, expanded, and analyzed independently and in combination with the molecular data. The results of these analyses suggest that theJuglandaceae are more closely related to theFagaceae, Betulaceae, Casuarinaceae, andUrticaceae and their relatives (sensuCronquist 1981) than they are to theAnacardiaceae (sensuThorne 1983). However, sequence data fromrbcL also suggest a relationship between the higherHamamelidae and certain families in theRosidae sensuCronquist 1981 (such asRosaceae andRhamnaceae), an outcome which would add credence to the widely accepted view of the polyphyletic nature of theHamamelidae.     

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     

DNA序列在悬钩子属植物分子系统学研究中的应用进展

悬钩子属植物种类繁多,类群复杂,而且多为多倍体和杂种。该文就近年来国内外有关DNA序列在悬钩子属植物分子系统学研究中的应用现状和进展进行了综述,并对中国悬钩子属植物系统发育研究进行了展望。研究认为:叶绿体DNA序列多应用非编码区,且多与ITS序列联合分析;核基因组中ITS序列应用最为广泛,主要用于研究悬钩子属空心莓组与木莓组的进化关系、栽培品种间亲缘关系及部分杂种和多倍体的起源等;在该属植物中发现了ITS个体内多态性,但未进行ITS假基因检测,其系统学应用价值需重新评价;低拷贝核基因只有GBSSI和LEAFY有相关应用。同时认为,悬钩子属植物系统学研究中应用的DNA序列及研究类群均较少,缺乏对整个悬钩子属全面而系统的研究。指出应进一步选择具有代表性的样本、筛选合适的DNA片段,并结合形态学、孢粉学和细胞学等手段对中国悬钩子属植物系统关系进行深入研究。     

Polyphyly and Convergent Morphological Evolution in Commelinales and Commelinidae: Evidence from rbcL Sequence Data

Phylogenetic relationships of the five families of the order Commelinales remain an area of deep uncertainty in higher-level monocot systematics, despite intensive morphological and anatomical study. To test the monophyly of the Commelinales and the subclass Commelinidae, evaluate their relationships, and analyze evolutionary trends in their morphology, ecology, and biogeography, we conducted parsimony analyses on 95 rbcL sequences representing 17 taxa of Commelinales, 16 taxa of other Commelinidae, and 63 taxa from Arecidae, Liliidae, and Zingiberidae. Commelinales is polyphyletic and Commelinidae paraphyletic, with Eriocaulaceae and Xyridaceae sister to Poaceae and its relatives, Rapateaceae sister to Bromeliaceae and Mayacaceae, and Commelinaceae sister to Philydrales and allies. Thurnia is sister to Prionium at the base of Cyperaceae-Juncaceae; only 1 of Cronquist's multifamily commelinoid orders is diagnosed as monophyletic. We propose a revised Commelinidae, incorporating 4 revised superorders (Bromelianae, Commelinanae, Dasypogonanae, Arecanae) and 10 orders ((Poales, Eriocaulales, Cyperales, Typhales, Bromeliales), (Commelinales, Philydrales, Zingiberales), (Dasypogonales), (Arecales)). Morphological and anatomical characters used to define the original Commelinales and Commelinidae appear to be plesiomorphic or to reflect convergence or recurrent mutation; several characters supporting our revised classification are anatomical traits that seem relatively insulated from environmental selection pressures. The Commelinidae distal to the Arecales arose in South America, with amphiatlantic Bromeliaceae-Mayacaceae-Rapateaceae originating in the Guayana Shield. Ecological diversification involved the repeated invasion of shady, infertile, or arid microsites. The numbers of species in families of the revised Commelinidae are related partly to the extent of adaptive radiation in those families, but seem more strongly related to nonadaptive features promoting speciation, such as restricted seed dispersal (especially in forest interior groups with fleshy fruits), polyploidy, aneuploidy, and apomixis. Species diversity is unrelated to the rate/amount of rbcL sequence evolution.     

New and old problems in the taxonomy of the Gelidiales (Rhodophyta)

The order Gelidiales includes over 140 agar-producing taxa. Many species are taxonomically confused; the boundaries of one family and all but four genera recently have been contested, and the controversy over ordinal status has lasted for over 25 years. This study reviews recent developments in the taxonomy of the group and suggests future areas for studies. The order cannot be defined by a few exclusive characters, as intended in the past, but it shows a unique combination of characters. Additional studies on Gelidiella and Acanthopeltis seem advisable to clarify family limits. The segregation of Onikusa and Pterocladiastrum is doubtful. Only three of six characters discriminate Gelidium from Pterocladia. None allows complete generic segregation and all need variability studies. Analysis of nomenclatural types in the light of morphological variation would permit an understanding of species limits in Gelidium and Pterocladia. Similar studies are needed in Gelidiella and Ptilophora.     

Chemical soil conditions in pristineNothofagus forests of New Zealand as compared to German forests

In many German forest soils low base saturation of CEC in deeper soil layers was reported and acidic deposition is seen as the major cause of these findings. To test this hypothesis we sampled 5 New Zealand forest soils from pristine beech (Nothofagus fusca, N. menziesii, N. solandri) sites under climatic and geological conditions comparable to higher elevations in Germany. The soils developed from granite and greywacke. Soil samples were analyzed for pH and the exchangeable cations were extracted with 1M NH₄Cl. The base saturation of all soil profiles was very low, even in deeper layers and was thus similar to the patterns found in many German forest soils. The pH was generally higher in the New Zealand soils as compared to Germany. The reason for the depletion of base cations in deeper soil layers of New Zealand forest soils is most likely the leaching of base cations with HCO₃ ^- resulting from the dissociation of carbonic acid in connection with high amounts of seepage. Thus, under high rainfall conditions, the low base saturation found in deeper layers of forest soils cannot exclusively be attributed to the effects of acidic depositions and land use. ei]Section editor: R F Huettl     

Pervasive RNA Editing Among Hornwort rbcL Transcripts Except Leiosporoceros

RNA editing affecting chloroplast and mitochondrial genomes has been identified in all major clades of land plants. The frequency of edited sites varies greatly between lineages but hornworts represent an extreme in propensity for editing in both their chloroplast and mitochondrial genomes. cDNA sequences from seven taxonomically diverse hornwort rbcL sequences combined with a survey of 13 additional DNA sequences for potential edited sites demonstrate the presence of 62 edited sites and predict a minimum of 10 additional sites. These 72 total edited sites represent 43 C-to-U and 28 U-to-C nucleotide conversions, with 1 site exhibiting editing in both directions. With one exception, all taxa are heavily edited, with each having from 20 to 34 edited sites. However, a single sample, Leiosporoceros, is shown to lack edited sites. Phylogenetic reconstruction of hornworts results in ambiguous resolution of Leiosporoceros depending on whether edited sites are maintained or eliminated from the analyses. Depending on the inferred relationship of Leiosporoceros to the hornworts, at least two explanations for the origin and maintenance of pervasive editing in hornworts are possible. The absence of edited sites in Leiosporoceros could represent either the absence or a low level of editing ability in the common ancestor of hornworts, as represented by Leiosporoceros, or the loss of editing sites in this lineage after the primary diversification events in the group.     

The harvesting of macroalgae in New Zealand

Several species of algae have been commercially harvested in New Zealand, mainly for extraction of agar and alginates. In the past, the harvest was comprised mostly of shore-cast plants. There has been more recent interest, however, in harvesting attached plants of Pterocladia spp., Porphyra spp., Gracilaria sordida, Durvillaea spp., Macrocystis pyrifera, and Ecklonia radiata. The ecological effects of harvesting attached algae depend largely on the sizes of plants, the season of removal, the patch size of clearances, and the proximity and identity of mature plants. These have not been well-studied for seaweeds in New Zealand, but population and life history studies indicate that harvesting methods affect the continuity of algal resources, at least on a local scale, and are crucial factors in their management.     

Resource biology of Pterocladia capillacea (Gelidiales,Rhodophyta) populations in Brazil

Pterocladia capillacea has been already exploited in Brazil and Uruguay, but exploitation was discontinued due to source depletion. Our attempts to cultivate this species in the sea, or in tanks, gave poor results. In this communication we present some ecological data as a contribution to evaluate the possibility of a production increase in natural beds on the southeast coast of Brazil.Our results show that: (i) the populations are perennial varying from 323 (i.c._0.05 = 51) to 600 (i.c._0.05 = 78) g dry weight throughout the year; (ii) horizontal distribution is affected by irradiance, with higher biomass in shaded areas and by water movement, with higher biomass in intermediate sites; (iii) vertical distribution is limited above by desiccation and below by herbivores — sea urchins removal increases cover by 20–50%; (iv) Sargassum vulgare is the main competitor for space, and its removal on areas of contact between both populations increases coverage of P. capillacea by ca 80%.     

Phylogenetic signal common to three data sets: Combining data which initially appear heterogeneous

This study makes use of three sources of data, morphology and two chloroplast DNA sequences,ndhF andrbcL, to resolve relationships in Gesneriaceae. Cladograms from each of the three data sets separately are not topologically congruent. Statistical indices suggest that each data set is congruent with thendhF data althoughrbcL and morphology are themselves incongruent. Consensus methods provide no resolution of taxonomic relationships when trees from the different data sets are combined. Combining data sets generally results in cladograms that are more fully resolved than each of the data sets analyzed separately and support for the clades increases based on higher decay index and bootstrap values. These results indicate that there is a phylogenetic signal common to each of the data sets, however, the noise (errors due to homoplasy, mis-scoring, etc.) unique to each data source masks this signal. In combining the data, the evidence for the common evolutionary history in each data set overcomes the noise and is apparent in the resulting trees.     

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.     

Phylogenetic relationships of the enigmatic fern families Hymenophyllopsidaceae and Lophosoriaceae: Evidence fromrbcL nucleotide sequences

Nucleotide sequences fromrbcL were used to infer relationships of Lophosoriaceae and Hymenophyllopsidaceae. The phylogenetic positions of these two monotypic fern families have been debated, and neither group had been included in recent molecular systematic studies of ferns. Maximum parsimony analysis of our data supported a sister relationship betweenLophosoria andDicksonia, and also betweenHymenophyllopsis andCyathea. Thus, both newly-examined families appear to be part of a previously characterized and well-supported clade of tree ferns. The inferred relationships ofLophosoria are consistent with most (but not all) recent treatments. However,Hymenophyllopsis includes only small delicate plants superficially similar to filmy ferns (Hymenophyllaceae), very different from the large arborescent taxa. Nevertheless, some synapomorphic characteristics are shared with the tree fern clade. Further studies on gametophytes ofHymenophyllopsis are needed to test these hypotheses of relationship.     

The presence of gigartinine in a New Zealand Gracilaria species

Gigartinine, 5-(3-amidinoureido)-2-aminovaleric acid, serves as achemotaxonomic marker to distinguish two species of Gracilaria withvery similar morphologies. Gigartinine was identified by ¹³C-NMRspectroscopy and amino acid analysis of a cold-water extract from Gracilaria sp. nov., collected from a sheltered harbour localityat Blockhouse Bay, Auckland, New Zealand. Levels of this amino acid,naturally ca. 5% by dry weight of seaweed, were able to be depleted andthen restored during a nitrogen pulsing experiment. In contrast, native andpulsed samples of Gracilaria chilensis from Point Arthur, Wellingtonshowed no extractable gigartinine. Although these two species are unableto be distinguished in the field by morphological characteristics, they canbe separated by the presence or absence of gigartinine.     

The biogeography of three Boeckella species (Copepoda: Calanoida) in New Zealand

The New Zealand distributions of three species of Boeckella (Copepoda, Calanoida), B. triarticulata, B. dilatata and B. hamata are mapped. B. triarticulata is primarily a pond dweller but is also found in reservoirs and shallow lakes. B. dilatata is mainly found in the deeper glacial lakes and ponds in the central region of the South Island and B. hamata has a more widespread distribution in lakes and ponds in the South Island and lower half of the North Island. Differences in temperature optima, food requirements and dispersal ability among the three Boeckella species are related to vicariant events to explain their distribution in New Zealand.     

Trichothecene production by Fusarium species isolated from grain and pasture throughout New Zealand

Liquid cultures of 200 Fusarium isolates selected to represent the most common species found in autumn pasture (70 isolates) and in grain (130 isolates) grown in New Zealand were analysed for trichothecenes and related compounds. Production of butenolide, cyclonerodiol derivatives and culmorins was also measured. The principal trichothecenes produced were derivatives of either nivalenol (NIV), deoxynivalenol (DON) or scirpentriol (Sctol), in order of frequency. The principal trichothecene producing species were F. crookwellense, F. culmorum and F. graminearum. Isolates of the first two species were predominantly NIV-chemotypes with one or two isolates respectively as Sctol-chemotypes. F. graminearum showed equal quantities of NIV- and DON-chemotypes, with the DON-chemotypes producing primarily 15-acetyldeoxynivalenol (15-ADON).