基于ITS和trnL-trnF序列的草木樨种群遗传多样性研究

以白花草木樨(Melilotus alba)和黄花草木樨(Melilotus officinalis)18个地理种群植物为材料,用ITS序列和trnL-trnF序列研究了2种草木樨不同种群间的遗传多样性。结果表明:(1)trnL-trnF序列对位后长度为459bp,其中包括6个变异位点,6个简约信息位点,G+C含量为33.1%;ITS序列对位后长度为714bp,其中包括5个变异位点,3个简约信息位点,G+C含量为48.9%。(2)在基于trnL-trnF序列构建的系统发育树中,2种草木樨能够形成单系分支,说明trnL-trnF序列在草木樨中的鉴别能力较强。(3)单倍型多样性以及核苷酸多样性分析表明,黄花草木樨的遗传多样性高于白花草木樨。     

Phylogenetic relationships in Rosaceae inferred from chloroplast matK and trnL-trnF nucleotide sequence data

 Phylogenetic relationships in Rosaceae were studied using parsimony analysis of nucleotide sequence data from two regions of the chloroplast genome, the matK gene and the trnL-trnF region. As in a previously published phylogeny of Rosaceae based upon rbcL sequences, monophyletic groups were resolved that correspond, with some modifications, to subfamilies Maloideae and Rosoideae, but Spiraeoideae were polyphyletic. Three main lineages appear to have diverged early in the evolution of the family: 1) Rosoideae sensu stricto, including taxa with a base chromosome number of 7 (occasionally 8); 2) actinorhizal Rosaceae, a group of taxa that engage in symbiotic nitrogen fixation; and 3) the rest of the family. The spiraeoid genus Gillenia, not included in the rbcL study, was strongly supported as the sister taxon to Maloideae sensu lato. A New World origin of Maloideae is suggested. The position of the economically important genus Prunus and the status of subfamily Amygdaloideae remain unresolved. Received February 27, 2001 Accepted October 11, 2001     

Molecular phylogeny of the endemic fern genera Cyrtomidictyum and Cyrtogonellum (Dryopteridaceae) from East Asia

Cyrtomidictyum Ching and Cyrtogonellum Ching are two eastern Asian endemic genera whose taxonomic affinities and phylogenetic relationships have long been controversial. The main uncertainty surrounds the separation of the two genera from the species-rich genus Polystichum. Here we present a phylogenetic study focusing on the phylogenetic relationships of these polystichoid ferns. We reconstructed the relationships based on DNA sequence variation in four chloroplast genome regions, rbcL, atpB, and the intergenic spacers (IGS) rps4-trnS and trnL-trnF. Maximum likelihood and Bayesian inference analyses confirm earlier results that were based on less comprehensive taxon sampling and either only a single gene (rbcL) or two IGS (rps4-trnS and trnL-trnF). Cyrtomidictyum is the sister of the clade of polystichoid ferns that includes Cyrtogonellum, Cyrtomium subser. Balansana and three sections of Polystichum. Cyrtogonellum groups with several species of Polystichum, and constitutes the sister taxon to Polystichum sect. Sphaenopolystichum. We support the recognition of Cyrtomidictyum as circumscribed initially, rather than expansion of the genus to include either several Polystichum species or Cyrtogonellum, some Polystichum and Cyrtomium species. The monophyly of Cyrtomidictyum is supported by morphological characters such as once-pinnate leaves, free venation, prolongated leaf apices, and exindusiate sori. Two synapomorphic indels in the chloroplast genome, one 15-bp deletion in rps4-trnS, and one 3-bp insertion in trnL-trnF further differentiate Cyrtomidictyum from other polystichoid ferns. The close affinity of Cyrtogonellum to section Sphaenopolystichum of Polystichum s.s. is highly supported by molecular data. However, no shared morphological characters or molecular indels have been detected, although the distinctness of Cyrtogonellum is shown by a 13-bp insertion in the rps4-trnS alignment.     

Phylogeny inLabiatae s. l., inferred from cpDNA sequences

Sequences ofrbcL andndhF were analysed independently and in combination to resolve phylogenetic relationships inLabiatae s. l. Monophyly ofLabiatae s. l was supported by all three analyses.Congea tomentosa (Symphoremataceae) is nested withinLabiatae s. l. in therbcL analysis, but emerges as the sister group ofLabiatae s. l. in thendhF and combined analyses. Four noteworthy clades ofLabiate s. l. also are supported by all analyses corresponding to subfamiliesNepetoideae, Lamioideae, Pogostemonoideae andScutellarioideae. Monophyly of subfamiliesChloanthoideae andViticoideae is not supported. A clade comprisingTeucrioideae plusAjuga is supported byndhF and the combined analysis.     

rbcL sequences support exclusion ofRetzia,Desfontainia, andNicodemia from theGentianales

The taxonomic positions ofRetzia, Desfontainia, andNicodemia have been much discussed, and all three genera have been included inLoganiaceae (Gentianales). We have made a cladistic analysis ofrbcL gene sequences to determine the relationships of these taxa toGentianales. Four newrbcL sequences are presented; i.e., ofRetzia, Desfontainia, Diervilla (Caprifoliaceae), andEuthystachys (Stilbaceae). Our results show thatRetzia, Desfontainia, andNicodemia are not closely related toLoganiaceae or theGentianales. Retzia is most closely related toEuthystachys and is better included inStilbaceae. The positions ofDesfontainia andNicodemia are not settled, butDesfontainia shows affinity for theDipsacales s.l. andNicodemia for theLamiales s.l.     

Comparative analysis of chloroplast DNA variability in wild and cultivated<Emphasis Type="Italic"> Citrullus</Emphasis> species

PCR amplification and restriction site analysis of chloroplast (cp) DNA regions was used to detect inter- and intraspecific differences in the genus Citrullus. More than 55 C. lanatus and 15 C. colocynthis accessions collected from diverse geographical areas, C. ecirrhosus and C. rehmii were used. Most of the cpDNA variation within Citrullus was the result of large indels and transitions and transversions. Indels at the ndhA, trnS-trnfM and trnC-trnD regions and several substitutions at restriction enzyme sites can be used to separate C. colocynthis from the other Citrullus species. A nucleotide substitution at a restriction enzyme site at the 3 flanking region of ndhF provided a diagnostic haplotype for C. lanatus var. lanatus, the cultivated watermelon. Similarly, a nucleotide substitution at an intergenic spacer region of the trnC-trnD region resulted in a diagnostic haplotype for citron, C. lanatus var. citroides. Several C. lanatus var. citroides accessions showed the var. lanatus haplotype. C. rehmii showed almost the same haplotype as C. lanatus var. citroides with the exception of a unique insertion at a cpSSR site. Since C. ecirrhosus lacks the derived diagnostic nucleotide substitutions of C. lanatus, it is probably the progenitor of the cultivated watermelon. Intraspecific haplotypes detected within C. colocynthis were associated with geographic origin.Communicated by J. Dvorak     

Molecular analyses suggest a need for a significant rearrangement of Rutaceae subfamilies and a minor reassessment of species relationships withinFlindersia

DNA sequencing has been used to construct two molecular phylogenies at the intrafamily and intrageneric level within the Rutaceae. Analysis oftrnL-trnF sequence data for five Rutaceae subfamilies has shown that there is no molecular support for the current subfamily classifications within the Rutaceae. The Dictyolomatoideae and Spathelioideae belong to a clade separate from the clades containing the remaining Rutaceae subfamilies. Rutoideae and Citroideae do not form discrete clades which suggests a reassessment of the subfamily classification is necessary, particularly asRuta falls within the majority Citroideae clade. Flindersioideae forms a clade within the Rutaceae and does not form a separate family or form a clade with Meliaceae.Sequencing of 17Flindersia species produces a similar phylogeny to that proposed by other authors using morphological methods with two exceptions. The molecular phylogeny indicatesF. amboinensis is associated withF. fournieri andF. laevicarpa and, in addition,F. oppositifolia andF. pimenteliana were found to be genetically identical.     

Relationships in theAcanthaceae and related families as suggested by cladistic analysis ofrbcL nucleotide sequences

A parsimony analysis of DNA sequences of the chloroplast-encoded generbcL from twelve members of theAcanthaceae s.l., including members of the sometimes segregateThunbergioideae andNelsonioideae, and other families in theBignoniales sensuThorne (1992) is presented. The results largely agree with the classification of theAcanthaceae presented byBremekamp (1965) andThorne (1992) and supportNelsonioideae as a sister group to the rest of theAcanthaceae. Thunbergioideae are placed as a sister toAcanthaceae s.str.Acanthus andAphelandra, both representatives ofAcanthoideae, form a sister group toRuellioideae. An analysis of branch support found that many branches throughout theBignoniales are weakly upheld. This points to the need for further studies in the group using more sequences ofrbcL as well as other data. None of the families ofBignoniales as presently circumscribed (includingAcanthaceae s.l.) were strongly supported, although the larger clade containing the families of theBignoniales was robust.     

A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences

The systematics of the mainly yellow flowered Gagea species complex (Liliaceae) has long been considered difficult because only a few phenotypic features within this genus and as a result of hypothesized interspecific hybridisation. A molecular phylogenetic study of seven Gagea species (G. bohemica, G. lutea, G. minima, G. pomeranica, G. pratenis, G. spathacea and G. villosa) from Germany has been undertaken, based on plastid DNA sequences (trnL(UAA)-trnF(GAA), psbA-trnH) and on the nuclear ribosomal internal transcribed spacer (ITS). Sequence divergence within the Gagea species ranges up to 15.5% for psbA-trnH, 22.0% for trnL-trnF and 23.7% for ITS (ITS1 + 5.8S rRNA + ITS2). Two subspecies of Gagea bohemica: G. bohemica subsp. saxatilis and G. bohemica subsp. bohemica are characterized by trnL-trnF data and morphological features. Analysis of the ITS region shows that G. pomeranica represents a hybrid of G. pratensis and G. lutea. Lloydia serotina was initially used as an outgroup species, but it was placed within the investigated Gagea species in the psbA-trnH and the trnL-trnF phylogenetic tree.     

Implications ofrbcL sequence data for higher order relationships of theLoasaceae and the anomalous aquatic plantHydrostachys (Hydrostachyaceae)

Subclass and ordinal relationships ofLoasaceae, a small predominately New World family, are examined usingrbcL sequence data. Sequences were examined for eight of the fifteen genera of theLoasaceae and the morphologically anomalous aquatic genusHydrostachys (Hydrostachyaceae). Parsimony analyses of these sequences, combined with previously publishedrcbL data, indicate thatLoasaceae belong in theCornales, and are the sister group ofHydrangeaceae. This agrees with phylogenies based on chloroplast DNA inverted repeat restriction site, morphological and chemical data. TherbcL trees support the monophyly of theLoasaceae and most generic relationships correspond to current subfamily divisions. TherbcL phylogeny also provides the first suggestion thatHydrostachys is allied with theHydrangeaceae in theCornales.     

RFLP analysis of cpDNA in the genus <Emphasis Type="Italic">Hypericum</Emphasis>

The chloroplast DNA of 43 species including 16 sections from the genus Hypericum was studied by PCR-RFLP analysis. The PCR-amplified products of four cpDNA regions, trnC-trnD, psbC-trnS, trnL-trnF and rbcL were digested with four restriction endonucleases. A high level of interspecific variation was detected while intraspecific diversity was not observed. The resulting parsimony analysis indicated the monophyletic assemblage of the sections Androsaemum, Olympia, Drosocarpium and Trigynobrathys. Monophyly of Hypericum is weakly supported, but close relationships of H. perforatum and H. maculatum are indicated. The members of Ascyreia are weakly resolved, but clustering of H. kouytchense and H. oblongifolium is well supported, however, H. reptans is nested with Olympia. CpDNA profiles and the positions on the parsimony tree indicate that the chloroplast donor among the putative parents of the hybrid species H. ×inodorum is H. androsaemum.     

Phylogeny of the Madagascan endemic family Didiereaceae

A molecular phylogeny of the Didiereaceae was produced through parsimony analysis of chloroplastrpl16 intron andtrnL-trnF andtrnT-trnL intergenic spacer sequences of all eleven species of the Didiereaceae and several outgroup taxa from the Portulacaceae. Results indicated that: 1) the Didiereaceae were embedded within the Portulacaceae, withCalyptrotheca as the sister group of the family; 2) present generic limits were supported; 3)Alluaudiopsis was the most basal lineage; 4) at least two separate episodes of polyploidization within the genusAlluaudia had occurred, and 5) unusually low amounts of variation were present in rapidly evolving noncoding plastid sequences.     

Sarcostemma R.Br. (Apocynaceae — Asclepiadoideae) — a controversial generic circumscription reconsidered: Evidence fromtrnL-F spacers

The polyphyly ofSarcostemma sensu latu, suspected on morphological and karyological reasons is confirmed by analysis of thetrnL-F spacer region. With the exception ofCynanchum montevidense (subgen.Mellichampia, Sundell 1981), Old World and New World taxa belong to different clades.Sarcostemma sensu stricto andPlatykeleba show a strong affinity to Old WorldCynanchum; the affinities ofOxystelma cannot be determined at present.Philibertia andBlepharodon are sister groups, both are sister toFunastrum, andPentacyphus is basal to the New World clade.     

Characterisation of the enigmatic,endemic red algaGelidium allanii (Gelidiales) from northern New Zealand — morphology,distribution, agar chemistry

Gelidium allanii Chapman is endemic to northern New Zealand with a highly localised distribution. This species has remained little known, having been collected from only one locality for more than 40 years. We compare this species with other New Zealand members of the Gelidiaceae, in particularGelidium caulacantheum andPterocladia capillacea, presenting new data on morphology, distribution and agar chemistry to more fully characteriseG. allanii.G. allanii possesses a very distinctive, highly pyruvated agar. New Zealand records of two Australian speciesG. australe andG. asperum are examined and it is concluded that there is no evidence for their occurrence in New Zealand.Author for correspondence     

Molecular identification of species in Prunus sect. Persica (Rosaceae), with emphasis on evaluation of candidate barcodes for plants

Abstract Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no reliable morphological characters are available. Nowadays, the technique of DNA barcoding has the potential to meet such requirements. In this study, we evaluated the suitability of 11 DNA loci (atpB‐rbcL, trnH‐psbA, trnL‐F, trnS‐G, atpF‐H, rbcL, matK, rpoB, rpoC1, nad1, and internal transcribed spacer [ITS]) as candidate DNA barcodes for peaches, using samples from 38 populations, covering all the species in sect. Persica. On the whole, the primers worked well in this group and sequencing difficulties were met only in the case of ITS locus. Five loci (rbcL, matK, rpoB, rpoC, and nad1) have very low variation rates, whereas atpB‐rbcL, atpF‐H, trnH‐psbA, trnL‐F and trnS‐G show more variability. The most variable loci, atpB‐rbcL and trnH‐psbA, can distinguish three of the five species. Two two‐locus combinations, atpB‐rbcL+trnL‐F and atpB‐rbcL+atpF‐H, can resolve all five species. We also find that identification powers of the loci are method‐dependent. The NeighborNet method shows higher species identification power than maximum parsimony, neighbor joining, and unweighted pair group method with arithmetic mean methods.     

Ballistosporous yeasts found on the surface of plant materials collected in New Zealand

Six new species of ballistosporous yeast, the genusSporobolomyces, were isolated from dead leaves and fruit of plants collected in New Zealand;Sp. novazealandicus, Sp. dimmenae, Sp. coprosmicola, Sp. coprosmae, Sp. dracophyllus, andSp. taupoensis. These species differ from any hitherto known species ofSporobolomyces based on chemotaxonomic characteristics.Abbreviations B. Bullera - Ben. Bensingtonia - Sp. Sporobolomyces - Sporid. Sporidiobolus - T. Tilletiopsis - U. Udeniomyces - G + C guanine plus cytosine     

The systematic identity of Chiloscyphus trichocoleoides,a new liverwort species from New Zealand,uncovered by morphological and molecular evidence

Abstract

A new liverwort species from Western Nelson Ecological Province of New Zealand known from a single sterile specimen is described. It is unusual in having well-developed stem paraphyllia, and the leaves and underleaves are divided with three levels of ciliate division in a pinnate manner. This morphology suggested membership of Trichocoleaceae or Trichotemnomaceae, but other features of the plant made placement in either family seem unnatural. We determined its position by conducting phylogenetic analyses of rbcL, rps4 and trnL–F sequence datasets from 35 exemplars, and further confirmation of the position was carried out by an extended analysis using rbcL sequence dataset of 59 exemplars. The surprising result is that it belongs within the genus Chiloscyphus, where it is unique in these features. We describe this new species as Chiloscyphus trichocoleoides. Placing the new species in Chiloscyphus has broadened the generic concept of Chiloscyphus, and its phylogenetic relationship within and to other genera such as Clasmatocolea and Heteroscyphus needs further investigation. The results also show that the same morphological features seen in Chiloscyphus and in Trichocoleaceae and Trichotemnomaceae have developed independently.     

Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae, Musci). An example of stenoevolution in mosses Studies in austral temperate rain forest bryophytes 2

Evolutionary relationship between disjunct populations of the palaeoaustral moss taxonLopidium concinnum (Hypopterygiaceae) from New Zealand and southern South America were studied using non-coding chloroplast DNA sequences. No or only slight changes could be observed within the sequences oftrnT_UGU —trnL_UAA 5exon intergenic spacer,trnL_UAA intron andtrnL_UAA 3exon —trnF_GAA intergenic spacer. This indicates nearly no genetic divergence between extant New Zealand and Chilean populations, i.e. no significant differing pathways of evolution within the 80–60 million years of disrupted areas with interrupted gene flow. Molecular data support the idea of an old Gondwanan relict species of stenoevolutionary character. Ecological data on short-range dispersal strengthen this assessment.     

TheGunnera symbiosis: DNA restriction fragment length polymorphism and protein comparisons ofNostoc symbionts

Cyanobacteria separated from symbiosis with several species of the angiospermGunnera were comparatively characterized and correlated with the locales and taxonomy of their host plants. All were identified as strains ofNostoc. Protein profiles and DNA restriction fragment length polymorphisms (from hybridizations with heterologousnifH andglnA probes) determined that three of the four cyanobacteria fromGunnera grown at one site in Sweden, each from a different host species, were very similar or identical. Plants of one species,G. manicata, grown in a second location at the site were infected with a different cyanobiont. Among five isolates from two species ofGunnera, collected in the same locale in New Zealand, three subgroups were documented. Isolates from three differentGunnera species grown in separate locations in the United States were each uniquely different. None of the cyanobacteria differed in the molecular weights of their glutamine synthetase and Fe-nitrogenase proteins. The diversity and accessibility of compatibleNostoc populations present in the soil micro-environment, not a critical selective factor required byGunnera, were concluded to be a major determinant in symbiont selection.     

Phylogenetic relationships among tetraploid species of Bellevalia (Asparagaceae) endemic to south-central Mediterranean

In the south-central Mediterranean four tetraploid species of Bellevalia occur: B. dolichophylla, B. galitensis, B. mauritanica, and B. pelagica. Another group of plants, morphologically similar to B. dolichophylla, has been recently recovered in Zembra Island (Tunisia). A phylogenetic reconstruction involving all these tetraploid taxa was performed using both plastidial and nuclear markers (trnL-trnF and ITS, respectively). For all these taxa, an allopolyploid origin involving B. romana and B. dubia is supported. Regarding plants from Zembra, they may fall within the variability of B. dolichophylla.