Chromosome number, karyotype and DNA C-value of the Wollemi Pine (Wollernia nobilis, Araucariaceae)

The Wollemi Pine ( Wollemia nobilis , Araucariaceae) was discovered in 1994 in a remote area of the Wollemi National Park (New South Wales, Australia). With only around 40 adult trees known to be growing in the wild, it is one of the worlds rarest plant species. The results of the first cytological study are reported, including a chromosome count (2n = 2x = 26), karyotype illustration and nuclear DNA C-value (4C = 55.74 pg), obtained using Feulgen microdensitometry. The results are compared with data available on species in the other two genera of the Araucariaceae, Araucaria and Agathis , and with other gymnosperms     

A MOLECULAR PHYLOGENY OF THE GELIDIALES (RHODOPHYTA) BASED ON ANALYSIS OF PLASTID rbcL NUCLEOTIDE SEQUENCES1

Parsimony analyses of rbcL nucleotide. sequences were used to develop hypotheses of relationships among taxa in the taxonomically difficult order Celidiales including species from seven currently recognized genera: Capreolia, Gelidiella, Gelidium, Onikusa, Pterocladia, Ptilophora, and Suhria. Nucleotide. sequences of rbcL from red algae are variable and provide a large number of informative characters for phylogenetic analysis, yet the absence of insertion/deletion mutations allows for the unambiguous alignment of sequences. Species were resolved into 10 well-.supported major clades representing genera and species complexes. The topological positions of these 10 clades within trees are also well supported and indicate that Gelidium and Pterocladia as currently circumscribed are not monophyletic. These results call for a revision of the classification of the Gelidiales .     

Systematics of Nothofagus (Nothofagaceae) based on rDNA spacer sequences (ITS): taxonomic congruence with morphology and plastid sequences

Phylogenetic relationships were examined within the southern beech family Nothofagaceae using 22 species representing the four currently recognized subgenera and related outgroups. Nuclear ribosomal DNA sequences encoding the 5.8s rRNA and two flanking internal transcribed spacers (ITS) provided 95 phylogenetically informative nucleotide sites from a single alignment of ~588 bases per species. Parsimony analysis of this variation produced two equally parsimonious trees supporting four monophyletic groups, which correspond to groups designated by pollen type. These topologies were compared to trees from reanalyses of previously reported rbcL sequences and a modified morphological data set. Results from parsimony analysis of the three data sets were highly congruent, with topological differences restricted to the placement of a few terminal taxa. Combined analysis of molecular and morphological data produced six equally parsimonious trees. The consensus of these trees suggests two basal clades within Nothofagus. Within the larger of the two clades, tropical Nothofagus (subgenus Brassospora) of New Guinea and New Caledonia are strongly supported as sister to cool-temperate species of South America (subgenus Nothofagus). Most of the morphological apomorphies of the cupule, fruit, and pollen of Nothofagus are distributed within this larger clade. An area cladogram based on the consensus of combined data supports three trans-Antarctic relationships, two within pollen groups and one between pollen groups. Fossil data support continuous ancestral distributions for all four pollen groups prior to continental drift; therefore, vicariance adequately explains two of these disjunctions. Extinction of trans-Antarctic sister taxa within formerly widespread pollen groups explains the third disjunction; this results in a biogeographic pattern indicative of phylogenetic relationship not vicariance. For the biogeographically informative vicariant clades, area relationships based on total evidence support the recently advanced hypothesis that New Zealand and Australia share a unique common ancestry. Contrary to previous thought, the distribution of extant Nothofagus is informative on the area relationships of the Southern Hemisphere, once precise phylogenetic relationships are placed in the context of fossil data.     

A multigene phylogeny of the Gelidiales including nuclear large-subunit rRNA sequence data

Partial sequences (1032 bp) of the nuclear-encoded large ribosomal RNA gene (LSU) were determined for 16 gelidialean species, and analyzed separately and in combination with plastid rbcL and nuclear SSU gene sequences. The number of informative characters and levels of sequence divergence among taxa are intermediate in LSU sequences as compared to that for rbcL and SSU. Analyses of the separate LSU, and a combined LSU, SSU, and rbcL data sets have identified early-diverging lineages within the Gelidiales including Gelidiella, Pterocladia, Pterocladiella, and a lineage including Gelidium and species classified in other genera. The relationships among most gelidialean taxa are well-resolved and well-supported by analyses of the combined data; however, the relationships of Ptilophora and Capreolia remain unclear. It is speculated that these two lineages have diverged from a common ancestor over an evolutionarily short period of time. This revised version was published online in June 2006 with corrections to the Cover Date.     

Stand structure of the emergent conifer Agathis ovata in forest and maquis, Province Sud, New Caledonia

Abstract. The size structure of the endemic New Caledonian conifer Agathis ovata is reported for sample stands in forest and maquis from three areas on ultramafic substrates in the south of the main island (Grand Terre). In closed forest Agathis ovata is typically represented by a low density of emergent adult trees with only limited evidence of seedling recruitment. In maquis, Agathis ovata is represented by individuals of all sizes, with seedlings and saplings abundant in most sample stands. Preliminary evidence from tree-ring studies indicates that rings may be annual. Estimated diameter growth rate is about 2 mm y^?1 for trees ≥ 10 cm d.b.h., and ring counts suggest tree ages of up to 400 years in maquis and 500 years in forest. Agathis ovata, and three other members of the Araucariaceae found in New Caledonia (Araucaria laubenfelsii, A. montana and A. rulei), are the only tree species which regularly occur scattered in maquis in this way, creating an unusual structural assemblage. No angiosperm tree species show this behaviour. The circumstances under which the Agathis ovata– maquis stands arise and are maintained are the subject of further investigation. Preliminary evidence for tree ages indicates that these stands predate European arrival in New Caledonia and so are not the result of recent increases in the frequency and intensity of human disturbances. The presence of fire scars on many individuals, and location of most stands on slopes and spurs with outcropping laterite (cuirasse), suggests that this assemblage may owe its existence to the interplay of fire regime, topography and rockiness, and a resistance to fire in Agathis ovata which increases with plant size and age.     

基于叶绿体基因rbcL和psbA-trnH间区探讨石杉科植物系统关系

关于石杉科Huperziaceae植物的分类,一直存在一些争议。在旧的分类体系中石杉科植物被包含在一个混合的石松科Lycopodiaceae和多谱系的石松属Lycopodium中。本文利用叶绿体rbcL基因和psbA-trnH基因间区序列探讨石杉科植物的系统位置及石杉科内部的分类关系,用最大简约法和邻接法对自测序列结合由GenBank下载的rbcL及psbA-trnH基因间区序列进行系统发育分析。结果显示,石杉科与Phylloglossum属关系较近,与石松科关系较疏远。在石杉科中热带石杉属Huperzia植物和马尾杉属Phlegmariurus植物的关系要比它们与其他石杉属植物更近。所以,我们的rbcL基因数据不支持秦仁昌关于石杉科分为石杉属和马尾杉属的分类处理。但是,因为我们的psbA-trnH序列没有包括热带种类,对石杉属植物和马尾杉属植物的关系无验证。因此需要更多的样品和序列数据进一步探讨石杉科的演化关系。     

The phylogenetic history of Selaginellaceae based on DNA sequences from the plastid and nucleus: extreme substitution rates and rate heterogeneity

Molecular phylogenetic research on Selaginellaceae has focused on the plastid gene rbcL, which in this family has unusually high substitution rates. Here we develop a molecular data set from the nuclear 26S ribosomal DNA gene with the aim of evaluating and extending the results of previous phylogenetic research. The 26S rDNA and the rbcL regions were sequenced for a sample of 23 species, which represent the main elements of species diversity in the family. The data were analysed independently and in combination using both maximum parsimony and Bayesian inference. Although several between genome differences were found, the general pattern of relationships uncovered by all analyses was very similar. Results corroborate the previous study supporting new groupings not previously recognised on morphological grounds. Substitution rates in the 26S rDNA were also found to be high (26% informative) for the region analysed, but lower than for rbcL (37% informative). These data indicate that high substitution rates might be widespread in all three genomes (i.e., plastid, mitochondrion, and nucleus).     

Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for members of Cornales, a well-supported monophyletic group comprising Cornaceae and close relatives. The shortest trees resulting from this analysis were highly concordant with those based on previous phylogenetic analysis of rbcL sequences. Analysis of a combined matK and rbcL sequence data set (a total of 2652 bp [base pairs]) provided greater resolution of relationships and higher internal support for clades compared to the individual data sets. Four major clades (most inclusive monophyletic groups) of Cornales are indicated by both sets of genes: (1) Cornus-Alangium, (2) nyssoids (Nyssa-Davidia-Camptotheca)- mastixioids (Mastixia, Diplopanax), (3) Curtisia, and (4) Hydrangeaceae-Loasaceae. The combined evidence indicates that clades 2 and 3 are sisters, with clade 4 sister to the remainder of Cornales. These relationships are also supported by other lines of evidence, including synapomorphies in fruit and pollen morphology and gynoecial vasculature. Comparisons of matK and rbcL sequences based on one of the most parsimonious rbcL-matK trees indicate that matK has a much higher A-T content (66.9% in matK vs. 55.8% in rbcL) and a lower transition:transversion ratio (1.23 in matK vs. 2.21 in rbcL). The total number of nucleotide substitutions per site for matK is 2.1 times that of rbcL in Cornales. These findings are similar to recent comparisons of matK and rbcL in other dicots. Variable sites of matK are almost evenly distributed among the three codon positions (1.0:1.0:1.3), whereas variable sites of rbcL are mostly at the third position (1.8:1.0 :7.5). Among- lineages rates of nucleotide substitutions in rbcL are basically homogeneous throughout Cornales, but are more heterogeneous in matK.     

Characterization of nuclear microsatellite loci in South American Araucariaceae species

The Araucariaceae family has only two species in South America: Araucaria angustifolia and Araucaria araucana. Both species are mainly used for timber and have been overexploited in the past. Currently, they are found as fragmented populations and are classified under the International Union for Conservation of Nature and Natural Resources (IUCN) guidelines as vulnerable species. Population fragmentation may seriously affect the genetic diversity of these two species of Araucariaceae and can consequently lead to decreased survival. To better understand the genetic structure of these South American Araucaria species, eight nuclear microsatellites are reported: six new microsatellites loci developed based on a membrane enrichment procedure and two microsatellites loci transferred from the related species, Araucaria cunninghamii.     

Phylogenetic analyses of "higher" Hamamelididae based on plastid sequence data

Phylogenetic relationships were examined within the "higher" Hamamelididae using 21 species representing eight families and related outgroups. Chloroplast DNA sequences encoding the matK gene (/1 kilobase) provided 258 informative nucleotide sites. Phylogenetic analysis of this variation produced one most parsimonious tree supporting three monophyletic groups. In this tree, Nothofagus was basal to a well supported clade of remaining "higher" hamamelids, in which Fagaceae, including Fagus, were sister to a clade of core "higher" hamamelids that share wind-pollination, bicarpellate flowers, granular pollen walls, and reduced pollen apertures. Within the core "higher" hamamelids three subclades were resolved, Myricaceae, (Casuarina-(Ticodendron-(Betulaceae))), and (Rhoiptelea-Juglandaceae). Each subclade was well supported but relationships among them were not. The basal position of Nothofagus within the matK tree is consistent with the fossil record of "higher" hamamelids in which Nothofagus pollen appears earlier than microfossils with affinities to other modern "higher" hamamelids. This placement supports the exclusion of Nothofagus from Fagaceae and suggests two hypotheses for the origin of the cupule. The cupule may be ancestral within "higher" hamamelids and subsequently lost in core members of the clade or there may have been two independent origins. It is suggested that the three clades (1) Nothofagaceae, (2) Fagaceae, and (3) Juglandaceae, Rhoiptelea, Myricaceae, Casuarina, Ticodendron, and Betulaceae be considered at the ordinal level and that traditional orders, such as Fagales sensu Cronquist (Fagaceae, Nothofagaceae, and Betulaceae) be abandoned. Comparative analyses of matK sequences with previously published rbcL sequences demonstrate that for the taxa considered here matK sequences produced trees with greater phylogenetic resolution and a higher consistency index.     

Phylogenetic relationships of the enigmatic angiosperm family Podostemaceae inferred from 18S rDNA and rbcL sequence data

The phylogenetic relationships of some angiosperm families have remained enigmatic despite broad phylogenetic analyses of rbcL sequences. One example is the aquatic family Podostemaceae, the relationships of which have long been controversial because of major morphological modifications associated with their aquatic habit. Podostemaceae have variously been associated with Piperaceae, Nepenthaceae, Polygonaceae, Caryophyllaceae, Scrophulariaceae, Rosaceae, Crassulaceae, and Saxifragaceae. Two recent analyses of rbcL sequences suggest a possible sister-group relationship of Podostemaceae to Crassulaceae (Saxifragales). However, the branch leading to Podostemaceae was long, and use of different outgroups resulted in alternative placements. We explored the phylogenetic relationships of Podostemaceae using 18S rDNA sequences and a combined rbcL + 18S rDNA matrix representing over 250 angiosperms. In analyses based on 18S rDNA data, Podostemaceae are not characterized by a long branch; the family consistently appears as part of a Malpighiales clade that also includes Malpighiaceae, Turneraceae, Passifloraceae, Salicaceae, Euphorbiaceae, Violaceae, Linaceae, Chrysobalanaceae, Trigoniaceae, Humiriaceae, and Ochnaceae. Phylogenetic analyses based on a combined 18S rDNA + rbcL data set (223 ingroup taxa) with basal angiosperms as the outgroup also suggest that Podostemaceae are part of a Malpighiales clade. These searches swapped to completion, and the shortest trees showed enhanced resolution and increased internal support compared to those based on 18S rDNA or rbcL alone. However, when Gnetales are used as the outgroup, Podostemaceae appear with members of the nitrogen fixing clade (e.g., Elaeagnaceae, Ulmaceae, Rhamnaceae, Cannabaceae, Moraceae, and Urticaceae). None of the relationships suggested here for Podostemaceae receives strong bootstrap support. Our analyses indicate that Podostemaceae are not closely allied with Crassulaceae or with other members of the Saxifragales clade; their closest relatives, although still uncertain, appear to lie elsewhere in the rosids.     

Gene phylogenies and the endosymbiotic origin of plastids.

The endosymbiotic origin of chloroplasts from cyanobacteria has long been suspected and has been confirmed in recent years by many lines of evidence. Debate now is centered on whether plastids are derived from a single endosymbiotic event or from multiple events involving several photosynthetic prokaryotes and/or eukaryotes. Phylogenetic analysis was undertaken using the inferred amino acid sequences from the genes psbA, rbcL, rbcS, tufA and atpB and a published analysis (Douglas and Turner, 1991) of nucleotide sequences of small subunit (SSU) rRNA to examine the relationships among purple bacteria, cyanobacteria and the plastids of non-green algae (including rhodophytes, chromophytes, a cryptophyte and a glaucophyte), green algae, euglenoids and land plants. Relationships within and among groups are generally consistent among all the trees; for example, prochlorophytes cluster with cyanobacteria (and not with green plastids) in each of the trees and rhodophytes are ancestral to or the sister group of the chromophyte algae. One notable exception is that Euglenophytes are associated with the green plastid lineage in psbA, rbcL, rbcS and tufA trees and with the non-green plastid lineage in SSU rRNA trees. Analysis of psbA, tufA, atpB and SSU rRNA sequences suggests that only a single bacterial endosympbiotic event occurred leading to plastids in the various algal and plant lineages. In contrast, analysis of rbcL and rbcS sequences strongly suggests that plastids are polyphyletic in origin, with plastids being derived independently from both purple bacteria and cyanobacteria. A hypothesis consistent with these discordant trees is that a single bacterial endosymbiotic event occurred leading to all plastids, followed by the lateral transfer of the rbcLS operon from a purple bacterium to a rhodophyte.     

Molecular systematics of Trilliaceae II. Phylogenetic analyses of Trillium and its allies using sequences of rbcL and matK genes of cpDNA and internal transcribed spacers of 18S–26S nrDNA

Coding regions of the rbcL and matK genes of cp DNA and internal transcribed spacers (ITS) of nuclear ribosomal DNA were sequenced to study phylogenetic relationships within and among all four genera of Trilliaceae: Trillium, Paris, Daiswa and Kinugasa . The rbcL gene has evolved much slower than matK and in particular ITS; hence the phylogenetic trees based on the rbcL gene show a much lower resolution than trees based on either matK or ITS. The general topology of phylogenetic trees resulting from separate parsimony analyses of the matK and ITS sequences are relatively congruent, with the exception of the placement of T. pusillum . Both matK and ITS phylogenies reveal that T. rivale diverges at the base of the trees. In both trees, Paris, Daiswa and Kinugasa form a relatively weakly supported group. Within this group, the allo-octaploid Kinugasa japonica is the sister group of Daiswa species. The Paris–Daiswa – Kinugasa group, the major Trillium group, and T. undulatum and T. govanianum showed a loosely related topology, but their affinities are not evident according to these two molecular markers. However, phylogenetic analysis of amino acid sequences derived from matK shows that T. rivale together with clades T. undulatum–T. govanianum, Daiswa–Kinugasa and Paris is basally diverged as a sister group to the remainder of Trillium .     

Molecular systematics of Malpighiaceae: evidence from plastid rbcL and matK sequences

Phylogenetic analyses of DNA nucleotide sequences from the plastid genes rbcL and matK were employed to investigate intergeneric relationships within Malpighiaceae. Cladistic relationships generated from the independent data matrices for the family are generally in agreement with those from the combined matrix. At the base of Malpighiaceae are several clades mostly representing genera from a paraphyletic subfamily Byrsonimoideae. Intergeneric relationships among these byrsonimoid malpighs are well supported by the bootstrap, and the tribe Galphimeae is monophyletic. There is also a well-supported clade of genera corresponding to tribes Banisterieae plus Gaudichaudieae present in all trees, and many of the relationships among these banisterioid malpighs are well supported by the bootstrap. However, tribes Hiraeae and Tricomarieae (the hiraeoid malpighs) are paraphyletic and largely unresolved. Species of Mascagnia are distributed throughout these hiraeoid clades, confirming the suspected polyphyly of this large genus. Optimization of selected morphological characters on these trees demonstrates clear phylogenetic trends such as the evolution of globally symmetrical from radially symmetrical pollen, increased modification and sterilization of stamens, and switch from base chromosome number n = 6 to n = 10.     

Molecular phylogenetics of Meliaceae (Sapindales) based on nuclear and plastid DNA sequences

Phylogenetic analyses of Meliaceae, including representatives of all four currently recognized subfamilies and all but two tribes (32 genera and 35 species, respectively), were carried out using DNA sequence data from three regions: plastid genes rbcL, matK (partial), and nuclear 26S rDNA (partial). Individual and combined phylogenetic analyses were performed for the rbcL, matK, and 26S rDNA data sets. Although the percentage of informative characters is highest in the segment of matK sequenced, rbcL provides the greatest number of informative characters of the three regions, resulting in the best resolved trees. Results of parsimony analyses support the recognition of only two subfamilies (Melioideae and Swietenioideae), which are sister groups. Melieae are the only tribe recognized previously that are strongly supported as monophyletic. The members of the two small monogeneric subfamilies, Quivisianthe and Capuronianthus, fall within Melioideae and Swietenioideae, respectively, supporting their taxonomic inclusion in these groups. Furthermore, the data indicate a close relationship between Aglaieae and Guareeae and a possible monophyletic origin of Cedreleae of Swietenioideae. For Trichilieae (Melioideae) and Swietenieae (Swietenioideae) lack of monophyly is indicated.     

里白科植物的系统发育和分歧时间估计——基于叶绿体三个基因序列的证据

里白科(Gleicheniaceae)是古老的真蕨类植物,最早的化石记录可追溯到石炭纪。现存类群的属级分类和系统演化关系一直存在很大的分歧,为了进一步探讨该类群的起源演化,文中运用最大简约法和贝叶斯演绎方法对18种代表现存里白科植物全部6属(包括新测的12种)的叶绿体3个编码基因序列(atpB,rbcL和rps4)进行分析,探讨其主要分类群(属级)的系统演化关系。结果显示,里白科植物为一个单系群,由3个分支构成:里白属(Diplopterygium Nakai)和Gleichenia japonica构成一个分支;芒萁属(Dicranopteris Bernh.)和Gleichenella pec-tinata构成另一个分支;假芒萁属(Sticherus C.Presl)与单种属Stromatopteris Mettenius及Gleichenia dicarpa构成第三个分支。用宽松分子钟方法推测里白科主要类群的起源时间为:现代里白科植物起源于早白垩世(111—140Ma),其主要分支类群随后发生多样性分化,里白属和芒萁属的快速辐射演化均发生在古近纪(40—64Ma,36—50Ma)。起源时间的估算结果暗示化石种三叠里白Diplopterygium triassica不应归入现代里白属,其归属需要重新考虑。     

Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data

Nucleotide sequences of the chloroplast-encoded rbcL gene were used to examine phylogenetic relationships of the genus Salix together with other allied genera of the family Salicaceae. Phylogenetic analyses of rbcL sequences strongly suggest the monophyly of three commonly recognized genera (Chosenia, Salix, and Toisusu). Two monophyletic groups are recognized within the larger monophyletic group. They do not correspond with any infrageneric taxa proposed so far. With regard to character evolution, it is thought that the reduction of stamen number from more than two stamens to two might occur in at least three lineages and that fused bud scales evolved several times and/or the reverse evolution occurred from fused to free. Some types of pollen surfaces are considered to have evolved independently.     

利用分子标记18S rDNA对天牛高阶元进化关系的研究

【目的】构建天牛总科高阶元的进化关系,为解决天牛各亚科之间进化关系和归属提供依据。【方法】本研究采用18S rDNA(V4、V7区)分子标记,分析和测定了49种天牛基因序列,并结合GenBank数据库中3科2亚科21种天牛的18S rDNA基因序列,采用邻近法(Neighbor Jointing,NJ)、贝叶斯推论法(Bayesian Inference,BI)和最大似然法(Maximum Likelihood),对天牛总科3科6亚科的70种天牛基因序列构建进化树,探讨天牛高阶元类群的进化关系。【结果】研究表明:序列分析比对后得到序列为703 bp,碱基A、T、C、G的含量分别为21.1%、26.3%、23.6%和28.9%;变异位点(Variable sites)98个占全部位点的13.9%,简约信息位点(Parsimony informative sites)45个占全部位点的6.4%;转换(Transition)/颠换(Transversion)的平均值R值为2.79,转换大于颠换。进化树结果显示沟胫天牛亚科Lamiinae、天牛亚科Cerambycinae、锯天牛亚科Prioninae和瘦天牛科Disteniidae为单系性进化群,这与传统形态学分类结果相似。【结论】本研究成功构建了天牛总科高阶元的系统发育树,研究证明18S rDNA(V4、V7区)是探讨天牛高级阶元分类有效的分子标记。     

Molecular evolution of rbcL in the mycoheterotrophic coralroot orchids (Corallorhiza Gagnebin, Orchidaceae)

The RuBisCO large subunit gene (rbcL) has been the focus of numerous plant phylogenetic studies and studies on molecular evolution in parasitic plants. However, there has been a lack of investigation of photosynthesis gene molecular evolution in fully mycoheterotrophic plants. These plants invade pre-existing mutualistic associations between ectomycorrhizal trees and fungi, from which they obtain fixed carbon and nutrients. The mycoheterotrophic orchid Corallorhiza contains both green (photosynthetic) and non-green (putatively nonphotosynthetic) species. We sequenced rbcL from 31 accessions of eight species of Corallorhiza and hypothesized that some lineages would have pseudogenes resulting from relaxation of purifying selection on RuBisCO's carboxylase function. Phylogenetic analysis of rbcL+ITS gave high jackknife support for relationships among species. We found evidence of pseudogene formation in all lineages of the Corallorhiza striata complex and in some lineages of the C. maculata complex. Evidence includes: stop codons, frameshifts, decreased d(S)/d(N) ratios, replacements not observed in photosynthetic species, rate heterogeneity, and high likelihood of neutral evolution. The evolution of rbcL in Corallorhiza may serve as an exemplary system in which to study the effects of relaxed evolutionary constraints on photosynthesis genes for >400 documented fully mycoheterotrophic plant species.