两栖蓼的分子系统学研究

两栖蓼是一种水陆两栖植物,植株在不同生态环境下外部形态差异较大,同时两栖蓼的系统位置存在争议,被归入春蓼组(sect.Persicaria)或提升为两栖蓼组(sect.Amphibium)。该文选取两栖蓼及春蓼组植物12种,以及刺蓼组、头状蓼组、神血宁组、拳参组、萹蓄组和外类群掌叶大黄共23种植物进行研究。植物总DNA的提取采用改进的CTAB法,所测序列以及从Genbank数据库下载的序列,以掌叶大黄为外类群,采用最大简约法和贝叶斯法对核糖体ITS序列和叶绿体trn L-F序列进行了系统发育分析。ITS序列对位排列的长度为735 bp,包括489个可变位点,272个位点是信息位点。简约法得到9个简约树,步长为1 084,CI指数为0.680,RI指数为0.614。trn L-F序列对位排列的长度为1 121 bp,包括427个可变位点,239个位点是信息位点。简约法寻找到9个简约树,步长为551(CI=0.911,RI=0.910)。贝叶斯法和简约法得到的树基本一致。分子序列分析结果显示,trn L-F序列树类似于ITS序列树。ITS序列构建的发育树上,两栖蓼与刺蓼组植物、春蓼组其他植物形成3个并列的分支;在trn L-F序列树上,两栖蓼则与其他春蓼组植物形成两个并列的分支。由此可见,两栖蓼与春蓼组其他植物的亲缘关系较远,成一独立的分支。两个分子证据支持将两栖蓼提升为两栖蓼组的处理意见。此外,两栖蓼的花粉具散沟,与典型的春蓼组的具散孔花粉不一致。再加上两栖蓼水陆两栖的特性,因此支持把两栖蓼提升为两栖蓼组的观点。两栖蓼组的界定为多年生草本,水陆两栖,根状茎横生,生于水中茎漂浮,叶长圆形或椭圆形,生于陆地茎直立,叶披针形或长圆状披针形,托叶鞘为筒状、薄膜质,总状花序穗状,瘦果近圆形,花粉具散沟。     

Hybridization between the threatened plant, <Emphasis Type="Italic">Lespedeza leptostachya</Emphasis> Englem. and its co-occurring congener <Emphasis Type="Italic">Lespedeza capitata</Emphasis> Michx.: morphological and molecular evidence

Natural hybridization is common in the genus Lespedeza. No hybrids between Lespedeza leptostachya Englem. and Lespedeza capitata Michx. are formally recognized in any of the current floras, however observations in the field suggest that hybridization might occur in many of their shared habitats. Putative hybrids were compared to L. leptostachya and L. capitata using morphological measurements and screened for the presence of species-specific trnL-F gene region (cpDNA) and the ITS gene region (nrDNA). A discriminate analysis of 10 morphological measurements identified the hybrids as intermediate to both parents with two PCA axes explaining 99% of the variation between taxa. The presence of hybrids was confirmed by genetic markers with individuals morphologically identified as hybrids having cpDNA trnL-F genotypes identical to L. leptostachya and the ITS (nrDNA) phenotypes in most cases contain the ITS genotype of both parents, however, some putative hybrid individuals contained the ITS genotype of only one parents. Those individuals with L. leptostachya ITS and trnL-F could be a case of misclassification, but the presence of both L. capitata ITS genotypes and L. leptostachya trnL-F genotypes suggest segregation has occurred, which may result from either selfing or backcrossing.     

Phylogenetic relationships within Pappophoreae s.l. (Poaceae: Chloridoideae): Additional evidence based on ITS and trnL-F sequence data

Historically, Pappophoreae included the genera Cottea, Enneapogon, Kaokochloa, Pappophorum and Schmidtia. Some authors consider this tribe as a well-supported monophyletic group; while other evidences reveals Pappophoreae as polyphyletic, with Pappophorum separated from the rest of the tribe. When the latter happens, it can form a clade with Tridens flavus. Molecular phylogenetic analyses of the subfamily Chloridoideae have included few species of Pappophoreae; therefore, further research involving more representatives of this tribe is needed. With the aim of providing new evidence to help clarify the phylogenetic position of Pappophorum and its relationships with other genera of the tribe and the subfamily Chloridoideae, eight new sequences of ITS and trnL-F regions of Pappophoreae species were generated. These sequences were analyzed together with other available sequence data obtained from GenBank, using maximum parsimony and Bayesian inference, for individual (trnL-F or ITS) or combined trnL-F/ITS data sets. All analyses reveal that Pappophoreae is polyphyletic, with Pappophorum separated from the rest of the tribe forming a well-supported clade sister to Tridens flavus.     

Phylogeny of Crocus (Iridaceae) based on one chloroplast and two nuclear loci: Ancient hybridization and chromosome number evolution

Crocus consists of about 100 species distributed from western Europe and northern Africa to western China, with the center of diversity on the Balkan Peninsula and in Asia Minor. Our study focuses on clarifying phylogenetic relationships and chromosome number evolution within the genus using sequences of the chloroplast trnL-F region, the nuclear ribosomal DNA internal transcribed spacer (ITS) region, and a part of the nuclear single-copy gene pCOSAt103.In a combined dataset of ITS and trnL-F sequences, 115 individuals representing 110 taxa from both subgenera and all sections and series of Crocus were analyzed with Bayesian phylogenetic inference. For pCOSAt103 79 individuals representing 74 Crocus taxa were included, and for the majority of them PCR amplicons were cloned and up to eight clones per individual were sequenced to detect allopolyploidization events. Romulea species were included as outgroup in both analyses. Characteristics of seed surface structures were evaluated by scanning electron microscopy.Phylogenetic analysis of ITS/trnL-F data resulted in a monophyletic genus Crocus, probably monophyletic sections Crocus and Nudiscapus, and inferred monophyly for eight of the 15 series of the genus. The C. biflorus aggregate, thought to be consisting of closely related subspecies, was found to be polyphyletic, the taxa occurring within three major clades in the phylogenetic tree. Cloning of pCOSAt103 resulted in the detection of homoeologous copies in about one third of the taxa of section Nudiscapus, indicating an allotetraploid origin of this section. Reconstruction of chromosome number evolution along the phylogenetic tree using a probabilistic and a parsimony approach arrived at partly contradictory results. Both analyses agreed however on the occurrence of multiple polyploidization and dysploidy events. B chromosomes evolved at least five times independently within the genus, preferentially in clades characterized by karyotype changes.     

Epidermal micromorphology of the genus Festuca L. subgenus Festuca (Poaceae)

Qualitative and some quantitative micromorphological characters of leaf blades, lemmas and paleas were examined using scanning electron microscopy for 29 species of Festuca subgenus Festuca, including the first observations on members of sections Amphigenes, Dimorphae and Cataphyllophorae. The aim of this study was to survey these features in the subgenus Festuca, to assess their taxonomical value. The observed patterns are compared with current taxonomic proposals based on molecular studies. The characters show important taxonomic value, mainly of the abaxial lemma. Characters showing the greatest variation are shape of long cells, shape of the periclinal walls, thickness of anticlinal walls, presence of prickles and abundance of silica bodies. The principal characters of the leaf-blade surfaces include the type and shape of short cells. Two different surface patterns were observed on the lemma, one, long cells rectangular to elongated, with flat to slightly convex periclinal walls and thickened anticlinal walls, for the sections Amphigenes and Dimorphae, and another, long cells rectangular to square, with concave periclinal walls and unthickened anticlinal walls, for the remaining sections. This study confirms the taxonomic value of micromorphological characters in the subgenus Festuca, and that abaxial lemma surface appears to be the most useful.     

Phylogenetic status of Vavilovia formosa (Fabaceae-Fabeae) based on nrDNA ITS and cpDNA sequences

The phylogenetic status of the monotypic genus Vavilovia was studied using nrDNA ITS and cpDNA trnL-F and trnS-G regions. The results from the analysis of each dataset and the combined dataset, revealed that Vavilovia is closely related to Pisum, forming a group that is sister to Lathyrus. The molecular data and some morphological and biological characteristics strongly indicate that Vavilovia should be subsumed under Pisum, as Pisum formosum.     

Evolutionary classification: A case study on the diverse plant genus Ranunculus L. (Ranunculaceae)

Evolutionary classification attempts to integrate information on shared ancestry, evolutionary process and phenetic information into the taxonomic concept. Here we exemplify this concept on the monophyletic, species-rich and cosmopolitan plant genus Ranunculus. Previous classifications have rendered almost all traditional sections as polyphyletic, and a modern revision based on phylogenetic principles was so far lacking. Maximum parsimony and Bayesian inference analysis of a combined nuclear (ITS of nrDNA) and plastid DNA dataset (matK/trnK, and psbJ–petA) provided a phylogenetic framework for the genus with nine well-supported subclades. Neighbor Net analysis revealed a reticulate data structure within two subclades with frequent polyploidy and/or hybridization. Character evolution was studied by McClade reconstructions of morphological data mapped on to the molecular tree topology. Morphological characters show a mosaic-like distribution, but express several shared states congruent to molecular clades. A total evidence approach (TE) based on the combined morphological and molecular dataset suggests a subdivision of Ranunculus into a paraphyletic, temperate to arctic group of five subclades (subg. Auricomus), and a temperate to subtropical clade with four subclades (subg. Ranunculus). Infrageneric classification of two subgenera and 17 sections is based on both monophyly s.l. as evident from TE and a minimum of shared morphological characters. Six subclades have shared morphological or karyological features (sects. Auricomus, Flammula, Oreophili, Polyanthemos, Ranunculus, Thora, and Trisecti). One subclade was subdivided into three smaller clades according to morphological data (sects. Epirotes, Leucoranunculus, Ranuncella, Aconitifolii). In the case of reticulate evolution and uncertain ancestry we accept well-supported genetic clusters with shared morphological features, as revealed by Neighbor Net analysis (sections Batrachium, Hecatonia, Pseudadonis). Character evolution connected to ecological shifts characterizes the paraphyletic section Ranunculastrum, the holophyletic section Euromontani (sect. nov.), and the monotypic sect. Echinella. The information content of our classification is compared to alternative concepts.     

Molecular phylogenetic analysis of key <Emphasis Type="Italic">Jatropha</Emphasis> species inferred from nrDNA ITS and chloroplast (<Emphasis Type="Italic">trn</Emphasis>L-F and <Emphasis Type="Italic">rbc</Emphasis>L) sequences

The genus Jatropha (Euphorbiaceae) contains species that are of significant economic and ornamental value. However, Jatropha breeding material is rather limited due to incomplete information regarding phylogenetic relationships among germplasm resources. Phylogenetic analyses were performed based on the internal transcribed spacer of nuclear ribosomal DNA (nrDNA ITS), two chloroplast regions (trnL-F and rbcL), and the combined (ITS+trnL-F+rbcL) dataset among twenty-five specimens representing six key Jatropha species. Phylogenetic relationships of Jatropha were well resolved between subgenus Curcas and subgenus Jatropha, and demonstrated the intermediate position of section Polymorphae among sections of both subgenera. Jatropha curcas and J. integerrima demonstrated a close phylogenetic relationship. The molecular data agreed with the morphological classification that recognized J. multifida and J. podagrica in sec. Peltatae. The distinct intraspecific divergence that occurred in J. curcas could be attributed to restricted gene flow caused by geographical isolation and different ecological conditions. Phylograms produced with trnL-F and rbcL sequence data suggested slow rates of sequence divergence among Jatropha spp., while the ITS gene tree had good resolution suggesting high genetic variation of ITS among Jatropha species.     

Five molecular markers reveal extensive morphological homoplasy and reticulate evolution in the Malva alliance (Malvaceae)

The Malva alliance is a well-defined group with extensive morphological homoplasy. As a result, the relationships among the taxa as well as the evolution of morphological traits have remained elusive and the traditional classifications are highly artificial. Using five molecular markers (nuclear ITS, plastid matK plus trnK, ndhF, trnL-trnF, psbA-trnH), we arrived at a phylogenetic hypothesis of this group, the genera Alcea, Althaea and Malvalthaea being studied here for the first time with molecular data. Althaea and, in particular, Lavatera and Malva are highly polyphyletic as currently circumscribed, because their diagnostic characters, the number and degree of fusion of the epicalyx bracts, evolve in a highly homoplasious manner. In contrast, fruit morphology largely agrees with the molecularly delimited groups. Hybrid origins confirmed for the genus Malvalthaea and for Lavatera mauritanica and hybridization in the group of ruderal small-flowered mallows underline the importance of reticulate evolution in shaping the history of this group and complicating the interpretation of morphological evolution.     

Systematics and evolution of Carex sects. Spirostachyae and Elatae (Cyperaceae)

Carex sect. Spirostachyae comprises 25 species displaying the centre of diversity in Eurasia, while sect. Elatae comprises 22 species displaying the centre of diversity in tropical African mountainous regions. Phylogenetic analysis of the 136 ITS and 108 5′trnK intron sequences of 23 species of sect. Spirostachyae and 20 species of sect. Elatae revealed that neither section is monophyletic. With the exclusion of C. montis-eeka (sect. Spirostachyae) and C. insularis, C. iynx and C. longibrachiata (sect. Elatae), the sects. Spirostachyae and Elatae constitute a monophyletic group of 38 species, 22 of which were previously included in sect. Spirostachyae and 16 of which were in sect. Elatae (considering C. thomasii as C. mannii ssp. thomasii). Two main groups with different edaphic preferences were identified in the core Spirostachyae, in congruence with some morphological features. One group comprises primarily acidophilus species including 11 species of sect. Spirostachyae and 16 species of sect. Elatae. The other group includes 11 basophilic species of sect. Spirostachyae. Incongruence between nuclear and plastid genomes was detected, suggesting hybridization or lineage sorting processes in the evolution of the core Spirostachyae.     

Molecular systematic study of Cardamine glechomifolia Levl. (Brassicaceae) using internal transcribed spacer sequence of nuclear ribosomal DNA (ITS) and chloroplast trnL and trnL-F sequences

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA, trnL and trnL-F genes of Cardamine glechomifolia Levl. (family Brassicaceae) were sequenced and analyzed with the sequence of related Cardamine species retrieved from NCBI GenBank to detect pattern of evolutionary differentiation. All trees resulting from combined sequence analyses data of ITS, trnL and trnL-F gene resolve that C. glechomifolia – an endemic species to South Korea clade with Cardamine microzyga (100% bootstrap support). The evolutionary history was inferred using the Maximum Parsimony method. The consistency index is (0.588235), the retention index is (0.687500), and the composite index is 0.519622 (0.404412) for all sites and parsimony-informative sites (in parentheses). The result of the analysis using Maximum Parsimony was found congruence with Maximum Likelihood method and in Baseyan analysis.     

Phylogenetic reappraisal of Allium subgenus Cyathophora (Amaryllidaceae) and related taxa,with a proposal of two new sections

The phylogeny of subgenus Cyathophora and representatives of its closely related taxa within Allium were reconstructed based on nrDNA ITS and two plastid fragments (trnL-F and rpl32-trnL). The constructed phylogenies indicated that subgenus Cyathophora was not monophyletic and to be split in three parts positioned in different clusters. Allium kingdonii was unequivocally placed within subgenus Amerallium and formed an immediate sister relationship with New World Amerallium clade, suggesting an unexpected intercontinental disjunct distribution. For another, Allium trifurcatum was firmly nested within subgenus Butomissa next to A. tuberosum and A. ramosum, but it is distinctly different morphologically from the latter by thinly leathery bulb tunics, uniovulate locule and obviously 3-cleft stigma. Based on the geographic features, morphological and molecular evidences, two new sections, Kingdonia X.J.He et D.Q.Huang for A. kingdonii and Trifurcatum X.J.He et D.Q.Huang for A. trifurcatum, were proposed. The remaining three species of subgenus Cyathophora formed a well-defined clade, and the phylogenetic relationships among them recovered were consistent with previous findings. In addition, A. weschniakowii and A. subtilissimum were proven to be a member of subgenera Rhizirideum sensu stricto (s. str.) and Cepa, respectively, rather than subgenera Cepa and Polyprason previously proposed. Section Rhizomatosa represented by A. caespitosum should be subsumed within section Caespitosoprason of subgenus Rhizirideum s. str.     

Phylogeny and genetic diversity of D-genome species of Aegilops and Triticum (Triticeae, Poaceae) from Iran based on microsatellites, ITS, and trnL-F

Cereal species of the grass tribe Triticeae are economically important and provide staple food for large parts of the human population. The Fertile Crescent of Southwest Asia harbors high genetic and morphological diversity of these species. In this study, we analyzed genetic diversity and phylogenetic relationships among D genome-bearing species of the wheat relatives of the genus Aegilops from Iran and adjacent areas using allelic diversity at 25 nuclear microsatellite loci, nuclear rDNA ITS, and chloroplast trnL-F sequences. Our analyses revealed high microsatellite diversity in Aegilops tauschii and the D genomes of Triticum aestivum and Ae. ventricosa, low genetic diversity in Ae. cylindrica, two different Ae. tauschii gene pools, and a close relationship among Ae. crassa, Ae. juvenalis, and Ae. vavilovii. In the latter species group, cloned sequences revealed high diversity at the ITS region, while in most other polyploids, homogenization of the ITS region towards one parental type seems to have taken place. The chloroplast genealogy of the trnL-F haplotypes showed close relationships within the D genome Aegilops species and T. aestivum, the presence of shared haplotypes in up to three species, and up to three different haplotypes within single species, and indicates chloroplast capture from an unidentified species in Ae. markgrafii. The ITS phylogeny revealed Triticum as monophyletic and Aegilops as monophyletic when Amblyopyrum muticum is included.     

Molecular phylogenetic reconstruction of Osmanthus Lour. (Oleaceae) and related genera based on three chloroplast intergenic spacers

Although polyphyly of Osmanthus has been suggested by different authors, the conclusions of previous studies have lacked robust support due to limited sampling or a paucity of phylogenetic characters. In this study, the phylogeny of Osmanthus was explored using sequences of three informative chloroplast regions (psbJ-petA, rpl32-trnL and rps16-trnQ), including all the five sections of the genus and eight closely related genera. The results confirm that Osmanthus, as presently circumscribed, is a polyphyletic group, containing three or four distinct lineages, i.e. sect. Leiolea (lineage I), sect. Notosmanthus (lineage III), sects. Osmanthus (excluding O. decorus), Siphosmanthus and Linocieroides (lineage IV), and an uncertain lineage including only O. decorus (lineage II). These results emphasize that the generic delimitation within subtribe Oleinae is in need of revision. In addition, this study found that the four cultivar groups of sweet osmanthus formed a paraphyletic clade, implying that cultivated sweet osmanthus might originate from several species.     

Tribe Eritrichieae (Boraginaceae s.str.) in West Asia: a molecular phylogenetic perspective

A selection of Boraginaceae genera was used to obtain a framework for the phylogenetic position of some tribes belong to subfamily Boraginoideae and genera within tribe Eritrichieae (Heterocaryum, Rochelia, Eritrichium, Lappula, Lepechiniella, and Asperugo) and related species. Our results were produced on the basis of nrDNA ITS and cpDNAtrnL-F sequences. The combined nrDNA ITS trnL-F data confirm four main clades of Boraginoideae comprising Echiochileae, Boragineae, Lithospermeae, and Cynoglosseae s. l. (including Eritrichieae, Cynoglosseae s. str., and Myosotideae). The tribe Eritrichieae itself at the current status is paraphyletic; some members, for example Asperugo procumbens, Lepechiniella inconspicua, Myosotidium hortensia, and Cryptantha flavoculata are placed out of the core tribe Eritrichieae. The genus Heterocaryum is monophyletic and allied with a subclade of genera Lappula, Lepechiniella, Eritrichium, and Rochelia. Rochelia is monophyletic, but Eritrichium and Lappula are non-monophyletic. Lepechiniella is nested among a group of Lappula species.     

基于ITS序列的中国外来苋属植物系统关系分析

通过ITS序列对21种中国外来苋属植物进行系统进化关系研究。通过ITS序列种间、种内遗传距离分析,发现苋属种间变异为0~0.055 1,种内变异为0~0.009 2。使用TAXON DNA软件分析ITS序列种间、种内变异的分布图看出规律,结果表明苋属ITS序列的种间变异适中,种间变异明显大于种内变异。采用最大似然法(ML)构建的系统树将中国苋属分为5或6个进化支(根据自展支持率取值不同)。异株苋亚属长芒苋和苋亚属刺苋聚类在一起,西部苋和糙果苋单独成为一个进化支。苋亚属中苋组苋亚组反枝苋和绿穗苋亚组鲍氏苋有着更近的亲缘关系,苋组苋亚组尾穗苋和绿穗苋亚组绿穗苋、繁穗苋等亲缘关系更近。白苋亚属分为2或3个类群,根据自展支持率取值不同,合被苋可以和白苋、北美苋并为一支,也可以单独成为一支。综上所述,该文认为苋属经典分类体系中3亚属或2~3组的分类地位不成立,建议中国苋属采取5组2亚组或6组2亚组的分类体系。5组2亚组分别由长芒苋组、糙果苋组、苋组(苋亚组和绿穗苋亚组)、白苋组和凹头苋组组成。其中,合被苋也可从白苋组分出,单独构成1组,形成6组2亚组的分类体系。表明该序列对苋属大部分种类分类效果较好,对西部苋和糙果苋复合群,绿穗苋复合群以及白苋亚属的分类价值不高。     

The genus Gymnospermium (Berberidaceae) in Italy: identity and relationships of the populations at the western limit of the genus range

Abstract

Gymnospermium is a small genus of 7–12 taxa subject to diverging taxonomic treatments and distributed from east China to the Balkans. The recent discovery of Gymnospermium in the S-Apennines posed questions about origin and identity. Accordingly, we performed a systematic investigation by means of morphological, karyological and molecular tools. All populations were diploid with 2n = 14 as for the Balkan G. scipetarum (incl. G. maloi), and also morphology suggested a close affinity to the latter. However, the Italian populations differed from typical G. scipetarum by the lower stamen:petal length and style:carpel length. By including all European and most Asian taxa in a phylogenetic analysis, we shed new light into the species-level relationships in this genus. In the combined ITS-trnL-F phylogeny, two major clades were retrieved. One included the central Asian and eastern European taxa plus the Greek endemic G. peloponnesiacum sister to G. odessanum, and one the Balkan and Apennine populations. Such findings further corroborated that the Apennine plant belong to G. scipetarum. The native status of the Italian population is supported by exclusive SNPs in both ITS1 and trnL-F sequences. Along with morphological evidence, this allows to refer it to the new subspecies G. scipetarum subsp. eddae.     

On polyphyly of the former section Ochlopoa and the hybridogenic section Acroleucae (Poa,Poaceae): insights from molecular phylogenetic analyses

In this study, sequence data from the inert nuclear region ITS1‐5.8S rDNA‐ITS2 and the chloroplast region trnL–F, as well as a few morphological characters, are analysed to the relationships among known annual Poa (bluegrasses). It is shown that all taxa from the Poa annua aggregate distinguished by lemma characters and growth form have identical ITS and trnL–trnF sequences, all ITS sequences of this aggregate are the same as thethose of P. supina, and all trnL–trnF sequences are homologous with those of P. infirma. Furthermore, no differences were found between unusual morphotypes of P. supina with short spinules on their panicle branches and typical plants, but Siberian samples were found to have a slightly differentiated trnL–trnF region. These results suggest a hybrid origin of the Asian annual bluegrasses. Their maternal genome is close to that of P. sect. Homalopoa, but their ITS sequences are different. Some ITS sequences from annual Asian bluegrasses are resolved among representatives of P. sect. Stenopoa while for other (morphologically closely similar) species they fall in a clade with representatives of P. sect. Malacanthae. The latter group is distant from P. sect. Ochlopoa and is better treated as a separate section, viz P. sect. Acroleucae. The American annual bluegrasses are heterogeneous and also rather distant from P. sect. Ochlopoa. Poa chapmaniana, a species with cleistogamic flowers, is nested among the basal Subantarctic sections, far away from the taxa with which it has previously been considered related. It is indeed closer to P. sect. Ochlopoa than to other annual American bluegrasses. Thus, the studied annual species in fact belong to four independent evolutionary lines (or six including the separate genus Eremopoa and the Turkish Poa jubata), one of which, Acroleucae, has gone through three reticulation events. As in previous studies, our analysis did not support the generic status of P. sect. Ochlopoa.