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     

中国桫椤科植物叶绿体trnL内含子和trnL-trnF基因间隔区序列的系统发育分析

运用对PCR产物直接测序和克隆后测序的方法测定了蚌壳蕨科1种和桫椤科11种(其中桫椤分别测定19株：小羽桫椤测定2株)植物的叶绿体trnL基因内含子和trnL-trnF基因间隔区序列。12种植物相应的长度介亍l004-l082之间,A T平均含量60．9％,G C平均含量39．1％。计算了不同种间以及种内不同个体间序列的碱基差别(转换值／颠换值)和Kimura遗传距离。序列数据经排列后分别进行最简约法、最大似然法和邻接法分析,结果显示：(1)白桫椤、海南白桫椤和大羽桫椤构成的分支最早和该科内其余植物组成的另一分支分歧,而后者又进一步分为刃个亚分支,分别和桫椤亚属、黑桫椤亚属对应,支持夏群的分类处理：(2)大桫椤～狭羽桫椤～毛轴桫椤～篦齿桫椤、多羽桫椤一白桫椤～海南白桫椤以及小羽桫椤一桫椤各自构成独立、自然的末端分支,再参照分支内植物间的遗传距蔼取值,建议将此3个末端分支依次归并为3种：大桫椤、白桫椤和桫椤;(3)白桫椤属在科内处于基部位置,桫椤属奇桫椤亚属和黑桫椤亚属为衍生分支,赞同Tryon关于桫椤科进化和囊群盖起源的假说。     

堇菜属组间的系统发育与亲缘关系：基于trnL-trnF、psbA-trnH、rpL16、ITS序列,细胞学以及形态学证据

以鼠鞭草（Hybanthus enneaspermus）、鳞隔堇（Scyphellandra pierrei）、雷诺木（Rinorea benga-lensis）作为外类群,对堇菜属（Viola）20个类群的trnL-trnF序列,17个类群的psbA-trnH、rpL16序列以及1个类群的nrDNAITS序列进行了测定,并从GenBank下载相应的序列,运用最大简约法以及贝叶斯推论法进行系统分析,构建系统发育树。结果表明：堇菜亚属（subgen. Viola）不是一个单系类群,并明确了堇菜属部分组间类群的亲缘关系。本文还结合形态与细胞学证据对堇菜属进行性状演化的推测。结果表明：1）直立茎较匍匐茎、莲座状茎（叶基生）原始;2）托叶边缘长流苏状与托叶1/2～3/4合生分别是鸟嘴柱头堇菜组（sect. Trigonocarpae）和合生托叶组（sect. Adnatae）演化路线的重要性状标志;3）花柱样式从柱头无喙演化至柱头有喙,并由柱头简单演化至柱头复杂,再趋向于柱头简化。     

Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence

Intra and interspecific nucleotide sequence variation of rDNA first internal transcribed spacer (ITS1) was analysed using all eight species of the genus Thunnus plus two out‐group species within the same family, skipjack tuna Katsuwonus pelamis and striped bonito Sarda orientalis . Intraspecific nucleotide sequence variation in ITS1, including intra‐genomic variation, was low, ranging from 0·003 to 0·014 [Kimura's two parameter distance (K2P)], whereas variation between species within the genus Thunnus ranged from 0·009 to 0·05. The Atlantic and Pacific northern bluefin tunas Thunnus thynnus thynnus and Thunnus thynnus orientalis , recently proposed to be distinct species, were found to share nearly identical ITS1 sequences (mean K2P = 0·006) well within the range of intraspecific variation. The northern bluefin tuna appeared to be a sister group to albacore Thunnus alalunga , with all other Thunnus species in a distinct clade. The ITS1 phylogeny was consistent with mtDNA phylogeny in clustering the three tropical Thunnus species ( T. albacares , T. atlanticus and T. tonggol ). Southern bluefin Thunnus maccoyii and bigeye Thunnus obesus tunas showed a closer affinity to this tropical tuna group than to the northern bluefin tuna and albacore. The molecular data supported mitochondrial introgression between species and contradicted morphological subdivision of the genus into two subgenera Neothunnus and Thunnus .     

Phylogenetic relationships of the Aurantioideae inferred from chloroplast DNA sequence data

The tribes and subtribes of Aurantioideae, an economically important subfamily of the Rutaceae, have a controversial taxonomic history because of the lack of a phylogenetic framework. The rps16 and trnL-trnF sequences of the chloroplast were analyzed phylogenetically to construct an evolutionary history and evaluate the most recent classification system of Swingle and Reece (The Citrus Industry, volume 1 [1967]). Taxa representing tribes Citreae and Clauseneae and five of the six subtribes were sampled. Conflicts in the positions of some taxa between the rps16 and trnL-trnF trees are poorly supported. In all analyses, the Aurantioideae are monophyletic. The strict consensus tree of the combined analysis indicates that the two tribes along with the subtribes sampled are not monophyletic. The combined topology is not congruent with the widely used classification of Aurantioideae by Swingle and Reece. The tribes and subtribes are in need of revision.     

报春花属藏报春组、毛茛叶报春组的界定和系统发育关系:核糖体DNA ITS序列证据

报春花属(Primula L.)藏报春组(sect. Auganthus Pax ex Balf. f.)和毛茛叶报春组(sect. Ranunculoides Chen et C. M. Hu)的界定一直是没有解决的问题.应用核糖体DNA ITS序列数据探讨其系统发育关系.取样包括藏报春组和毛茛叶报春组的全部5个种以及其他一些相关组的代表种.ITS系统树表明,陕西羽叶报春(P.filchnerae Knuth)应与藏报春(P. sinensis Sabine ex Lindl.)和野藏报春(P. rupestris Balf. f. et Farrer)一起置于藏报春组;毛茛叶报春组只含两种:毛茛叶报春(P. cicutariifolia Pax)和安徽羽叶报春(P. merrilliana Schltr.).这两组并不具密切亲缘关系,它们在报春花属中与其他组的关系还需进一步研究.研究也表明ITS序列可以为报春花属的系统发育重建提供大量可靠资料.     

应用ITS序列分析探讨偏花报春的系统位置

对于偏花报春Primula secundiflora Franch. 的系统位置,主要有两种意见,一种认为偏花报春具有典型的钟状花冠,应置于钟花报春组Sect．Sikkimensis;而另一种意见则依据其他特征将其置于灯台报春组sect．Proliferae。通过对偏花报春、灯台报春组4种植物和钟花报春组3种植物核糖体DNA中的内转录间隔区(ITS)的序列测定及分析,并结合形态学及染色体特征的比较论证,认为偏花报春应置于灯台报春组。     

Phylogenetic relations of Rhizoplaca Zopf. from Anatolia inferred from ITS sequence data

Like many lichen-forming fungi, species of the genus Rhizoplaca have wide geographical distributions, but studies of their genetic variability are limited. The information about the ITS rDNA sequences of three species of Rhizoplaca from Anatolia was generated and aligned with other species from other countries and also with the data belonging to Lecanora species. The examined species were collected from the volcanic rocks of Mount Erciyes which is located in the middle of Anatolia (Turkey). The sequence data aligned with eight other samples of Rhizoplaca and six different species of Lecanora were obtained from GenBank. The results support the concept maintained by Arup and Grube (2000) that Rhizoplaca may not be a genus separate from Lecanora. According to the phylogenetic tree, Rhizoplaca melanopthalma from Turkey with two different samples of R. melanopthalma from Arizona (AF159929, AF159934) and a sample from Austria formed a group under the same branch. R. peltata and R. chrysoleuca samples from Anatolia located in two other branches of the tree formed sister groups with the samples of the same species from different countries. Although R. peltata remained on the same branch with other samples of the same species from other countries it was placed in a different branch within the group. When the three species from Anatolia were considered alone, it was noticed that Rhizoplaca melanopthalma and Rhizoplaca peltata are phylogenetically closer to each other than Rhizoplaca chrysoleuca; the morphological characteristics also support this result.     

Phylogenetic relationships of Australian strongyloid nematodes inferred from ribosomal DNA sequence data

The sequence of the second internal transcribed spacer of the ribosomal DNA was determined for the following strongyloid nematodes: Cylicocyclus insignis, Chabertia ovina, Oesophagostomum venulosum, Cloacina communis, Cloacina hydriformis, Labiostrongylus labiostrongylus, Parazoniolaimus collaris, Macropostrongylus macropostrongylus, Macropostrongylus yorkei, Rugopharynx australis, Rugopharynx rosemariae, Macropostrongyloides baylisi, Oesophagostomoides longispicularis and Paramacropostrongylus toraliformis, and compared with published sequences for species of Strongylus and for Hypodontus macropi. The resultant phylogenetic trees supported current hypotheses based on morphological evidence for the separation of the families Strongylidae and Chabertiidae, but did not support the separation of the endemic Australian genera as a distinctive clade within the Chabertiidae. The implications of this finding for the phylogenetic origins of the Australian strongyloids are discussed.     

Phylogeny of Rhaponticum (Asteraceae, Cardueae-Centaureinae) and related genera inferred from nuclear and chloroplast DNA sequence data: taxonomic and biogeographic implications

BACKGROUND AND AIMS: The precise generic delimitation of the Rhaponticum group is not totally resolved. The lack of knowledge of the relationships between the basal genera of Centaureinae could imply that genera whose position is as yet unresolved could belong to the Rhaponticum group. On the other hand, the affinities among the genera that are considered as members of this group are not well known. The aim of the study is to contribute to the phylogenetic and generic delineation of the Rhaponticum group on the basis of molecular data. METHODS: Parsimony and Bayesian analyses of the combined sequences of one plastid (trnL-trnF) and two nuclear (ITS region and ETS) molecular markers were carried out. The results of these analyses are discussed in the light of the biogeographic history. KEY RESULTS: The Rhaponticum group appears as monophyletic, and closely related to the genus Klasea. The results confirm the preliminary generic delimitation of the Rhaponticum group, with the new incorporation of the genus Centaurothamnus. Ochrocephala is supported as a separate genus from Rhaponticum and, contrary to this, Acroptilon and Leuzea appear as merged into the genus Rhaponticum. Several nomenclatural rearrangements are made in Klasea and Rhaponticum. CONCLUSIONS: The new molecular evidence is consistent with the morphological and karyological data, and suggests particularly coherent biogeographic routes of migration and speciation processes for the genus Rhaponticum. The biogeographic inference proposes a Near East and/or Caucasian origin for the genus. Furthermore, representatives of Rhaponticum could have reached Europe in two different ways: (1) expansion across central Asia to eastern Europe, and (2) expansion through the Near East, North Africa and then to the Iberian Peninsula and the Alps.     

基于rDNA ITS序列探讨中国栽培灵芝菌株的亲缘关系

利用ITS序列分析技术对中国栽培灵芝菌株进行了亲缘关系分析。结果发现中国栽培灵芝菌株分布于5个聚类组,其中树舌亚属、紫芝组的菌株各自聚成一组,灵芝组的菌株分成3组,85·7%灵芝组菌株均聚于同一组,表明树舌亚属、紫芝组和灵芝组间的遗传差异较大,灵芝组内虽然存在着一定的遗传差异,但总体上亲缘关系比较近,遗传多样性并不丰富。聚类结果也表明仅仅根据形态学特征并不能将灵芝属菌株进行有效的分类,利用分子生物学的技术手段对灵芝菌种进行分类是一种更有效的方法。     

Phylogeny of calcareous dinoflagellates as inferred from ITS and ribosomal sequence data

The phylogenetic relationships of calcareous dinoflagellates (i.e., Calciodinellaceae and Thoracosphaera) are investigated. Molecular data from the ribosomal 5.8S rRNA and highly conserved motifs of the ITS1 show Calciodinellaceae s.l. to be monophyletic when few non-calcareous taxa are included. They segregate into three monophyletic assemblages in a molecular analysis that considers the 5.8S rRNA and both the Internal Transcribed Spacer regions ITS1 and ITS2: a clade comprising species of Ensiculifera and Pentapharsodinium (E/P-clade), Scrippsiella s.l. (including fossil-based taxa such as Calciodinellum and Calcigonellum), and a heterogeneous group (T/P-clade) of calcareous (e.g., Thoracosphaera) and non-calcareous taxa (e.g., the highly toxic Pfiesteria). The potential to produce calcareous structures is considered as apomorphic within alveolates, and non-calcareous taxa nesting with calcareous dinoflagellates may have reduced calcification secondarily. Molecular results do not contradict general evolutionary scenarios provided by previous morphological (mainly paleontological) investigations.     

用叶绿体ndhF和核核糖体ITS序列推断李属(蔷薇科)的系统发育

Sequences of the chloroplast ndhF gene and the nuclear ribosomal ITS regions are employed to reconstruct the phylogeny of Prunus (Rosaceae), and evaluate the classification schemes of this genus. The two data sets are congruent in that the genera Prunus s.l. and Maddenia form a monophyletic group, with Maddenia nested within Prunus. However, the ndhF data set is incongruent with the ITS data supporting two major groups within Prunus one consisting of subgenera Laurocerasus (including Pygeum) and Padus as well as the genus Maddenia and another of subgenera Amygdalus, Cerasus, and Prunus. The ITS data, on the other hand, support a clade composed of subgenera Amygdalus and Prunus and Prunus sect. Microcerasus in addition to a paraphyletic grade of subgenera Laurocerasus and Padus (and the genus Maddenia) taxa. In general, the subgeneric classifications of Prunus s.l. are not supported. The ITS and ndhF phylogenies differ mainly in interspecific relationships and the relative position of the Padus/Laurocerasus group. Both ITS and ndhF data sets suggest that the formerly recognized genus Pygeum is polyphyletic and that the distinction of the subgenera Padus and Laurocerasus is not supported. The biogeographic interactions of the temperate and tropical members in the Padus/Laurocera- sus/Maddenia alliance including Pygeum are shown to be highly dynamic and complex.     

Phylogenetic relationships and natural hybridization in Triadica inferred from nuclear and chloroplast DNA analyses

Triadica (Euphorbiaceae) is a small genus endemic to East Asia and Southeast Asia, consisting of three species differentially adapted to heterogeneous habitats. To date, the phylogenetic relationships of this genus have not been resolved, and there has been no evidence for interspecific hybridization in Triadica. In this study, we sequenced the nrITS regions, two nuclear genes and a chloroplast gene to reconstruct the molecular phylogeny of Triadica and to test the hypothesis of natural hybridization between Triadica sebifera and Triadica cochinchinensis, and between T. sebifera and Tridica rotundifolia. Phylogenetic analysis showed that T. sebifera diverged first within this genus, and T. cochinchinensis and T. rotundifolia were sister species. Both of the two putative hybrids show chromatogram additivity at each of the two nuclear genes, providing convincing evidence for natural hybridization between T. sebifera and T. cochinchinensis, and between T. sebifera and T. rotundifolia. The chloroplast gene sequences of both hybrids were identical with that of T. sebifera, suggesting that T. sebifera was the maternal parent of the two hybrids. This is the first report of natural hybridization in Triadica, and the hybrids identified in this study should be a good starting point for further hybridization-based breeding in T. sebifera.     

Phylogenetic relationships of Empetraceae inferred from sequences of chloroplast gene matK and nuclear ribosomal DNA ITS region

We used sequences of nrDNA ITS and chloroplast gene matK to evaluate the monophyly of Empetrum and Corema and to examine phylogenetic relationships of the Empetraceae. Sequences of these two DNA markers were obtained for 11 plant samples, representing species of Empetrum from both the Southern and Northern Hemispheres, species and subspecies of Corema, and the monotypic Ceratiola. Sequences of four species of Rhododendron were used for rooting purposes. Our results show that species of Empetrum form a clade sister to the clade containing both Corema and Ceratiola. These two clades are strongly supported in both the matK and ITS trees, suggesting that Ceratiola is more closely related to Corema than to Empetrum, and is not of a hybrid origin between the ancestors of the latter two genera. In the matK tree, Corema conradii is more closely related to Ceratiola than to Corema album and C. album subsp. azoricum, whereas in the ITS tree, Ceratiola is allied with Corema album and C. album subsp. azoricum. This suggests that C. conradii might be a hybrid between ancestral populations of Ceratiola and C. album. The monophyly of Empetrum rejects the hypothesis of its independent origin in the two Hemispheres. Our trees also suggest the fact that the modern amphitropical distribution of Empetrum is the result of long distance dispersal, not of the vicarious events.     

Phylogenetic relationships of Loasaceae subfamily Gronovioideae inferred from matK and ITS sequence data

Members of subfamily Gronovioideae are distinctive among Loasaceae in their androecial and gynoecial simplicity. The four genera of the subfamily differ, however, in chromosome number, floral novelties, and pollen exine sculpturing, which led to suggestions that the Gronovioideae were polyphyletic. Phylogenetic analyses based on sequences of the chloroplast gene matK and the internal transcribed spacer region (ITS) of nuclear rDNA have been conducted using parsimony and maximum likelihood methods to assess the monophyly of Gronovioideae and to determine the sister group relationships of gronovioid genera. The results show Gronovioideae are monophyletic and placed as the sister to Mentzelia. Within Gronovioideae, Petalonyx is sister to a clade consisting of Cevallia, Gronovia, and Fuertesia. Among the remaining Loasaceae, subfamily Mentzelioideae, as originally circumscribed, is paraphyletic. Subfamily Loasoideae is placed as the sister to the Gronovioideae-Mentzelia clade.     

Phylogenetic relationship and taxonomic position of Xylanthemum tianschanicum (Krasch.) Muradyan (Compositae,Anthemideae) as inferred from nrDNA ITS data

The central Asian endemic Xylanthemum tianschanicum (Krasch.) Muradyan (Compositae, Anthemideae) is the only species of Xylanthemum Tzvelev with radiate capitula. While the species was formerly found to be closely related to members of the subtribe Handeliinae, other representatives of the genus were considered to be similar to members of Tanacetum. In order to assess its phylogenetic relationships and taxonomic classification, a molecular analysis based on ITS sequences of 13 representatives of the subtribe Handeliinae and 17 species of three other subtribes (Anthemidinae, Artemisiinae and Matricariinae) was performed. Due to the close relationship of the X. tianschanicum to the type species of Richteria (Richteria pyrethroides) in a well supported clade (PP = 1, BS = 100%), which is supported by morphological features concerning the indumentum, capitulum morphology, and pappus structure, the combination Richteria tianschanica (Krasch.) Sonboli & Oberpr. is proposed based on the basionym Pyrethrum tianschanicum Krasch.     

Phylogenetic relationships of Chalara and allied species inferred from ribosomal DNA sequences

The phylogenetic relationships of Chalara and allied taxa are studied based on ribosomal DAN sequences. Partial 28S rDNA and 18S rDNA regions from 26 strains were sequenced in this study. These and related sequences from GenBank were analyzed using parsimony and Bayesian analyses. Most of the Chalara species clustered in a strongly supported monophyletic lineage representing Helotiales. However, a few Chalara species appeared closely related to Xylariales. The phylogenetic significance of morphological characters observed in Chalara species are evaluated based on our sequence analyses. Conidial septation, conidial width and conidiophore pigmentation are thought to be indicative in understanding their evolutionary relationships. Sterile setae, which traditionally have been used to delimitate Chaetochalara from Chalara, are phylogenetically insignificant.