ITS rDNA sequence comparisons resolve phylogenetic relationships in <Emphasis Type="Italic">Orostachys</Emphasis> subsection <Emphasis Type="Italic">Appendiculatae</Emphasis> (Crassulaceae)

Orostachys (Crassulaceae) is a small genus of succulent plants having a predominantly East Asian distribution. Recent DNA sequence comparisons revealed polyphyletic nature of the genus and found distant relationship between its infrageneric taxa. Here we present the first molecular phylogeny of Orostachys subsection Appendiculatae based on a large number of ITS rDNA sequences representing most currently recognized members of the subsection and utilizing secondary structure information. Ribosomal spacer was a highly informative marker and provided a phylogenetic signal sufficient to resolve relationships at different scales, from affinities between species to a fine geographic structure in broadly sampled species. It was also conservative enough to allow unambiguous alignment and construction of consensus secondary structure models for ITS1 and ITS2. These models displayed a number of molecular synapomorphies defining most lineages established in our analyses. We revealed a major split in the subsection placing three species, O. spinosa, O. japonica and O. chanetii, into a strongly supported clade to the exclusion of O. thyrsiflora. Phenotypically distinct monotypic genus Meterostachys was also resolved as a part of the subsection’s clade and showed affinity to O. thyrsiflora. Our data suggested that morphology-based species concept for O. thyrsiflora requires reassessment.     

Phylogenetic relationships among members of the subfamily sedoideae (Crassulaceae) inferred from the ITS region sequences of nuclear rDNA

Nucleotide sequences of the nuclear rDNA ITS regions were determined in 20 species of the subfamily Sedoideae (Crassulaceae). The phylogenetic relationships of these species with other members of the subfamily, occurring mainly in Southeast Asia, were analyzed. It was shown that the genus Orostachys was not monophyletic; its typical subsection was reliably included into the clade of the genus Hylotelephium. Synapomorphic substitutions and indels, specific for the subsection Orostachys, were detected in ITS1. Sister relationships were established between clades Aizopsis and Phedimus, based on which they can be recognized as isolated genera.     

Systematics of the subfamily Haplorchiinae (Trematoda: Heterphyidae), based on nuclear ribosomal DNA genes and ITS2 region

Phylogenetic relationships of 6 species in the trematode subfamily Haplorchiinae were analyzed using small and large subunit of ribosomal DNA genes (18S rDNA and 28S rDNA) and internal transcribed spacer subunit II (ITS2) region as molecular markers. Maximum Likelihood and Bayesian inference analyses of combined rDNAs and ITS2 indicated a close relationship between the genera Haplorchis and Procerovum, while these two genera were distinct from Stellantchasmus falcatus. These phylogenetic relationships were consistent with the number of testes but not with the characters of the modification of the seminal vesicle or of the ventral sucker. Although three Haplorchis spp. were, together with Procerovum, in the same cluster, their mutual topology was incongruent between rDNA and ITS2 trees. Phylogenetic analyses using other molecular markers with more species are necessary to work out solid phylogenetic relationships among the species in this subfamily.     

A Molecular Phylogeny of Lilium in the Internal Transcribed Spacer Region of Nuclear Ribosomal DNA

Phylogenetic relationships among 55 species of Lilium, Cardiocrinum giganteum, and Nomocharis saluenensis were inferred from nucleotide sequence variations in the internal transcribed spacer (ITS) regions of 18S–25S nuclear ribosomal DNA. The phylogeny derived from ITS sequences estimated using maximum-likelihood methods indicated that (1) most of the species construct their own clade according to the classification based on morphological features at the section level; (2) section Daurolirion is not independent of Sinomartagon, and it is appropriate to integrate two sections as Sinomartagon; (3) it is appropriate that L. henryi and L. bulbiferum are classified into subsection 6a and Sinomartagon–Daurolirion, respectively; (4) subsection 6b is much closer to Sinomartagon than subsection 6a and Archelirion, and it arose directly from Sinomartagon; and (5) Lilium is much closer to Nomocharis than Cardiocrinum. Phylogenetic estimation using sequences of the ITS region is suitable at the levels of genus, section, and most of subsection. Received: 18 December 1998 / Accepted: 14 March 1999     

Polyphyletic origin in <Emphasis Type="Italic">Pimpinella</Emphasis> (Apiaceae): evidence in Western Europe

The genus Pimpinella L. comprises about 150 species, being one of the largest genera within the family Apiaceae (subfamily Apioideae). Previous molecular phylogenetic studies have shown that Pimpinella is a taxonomically complex group. In this study, evolutionary relationships among representatives from Western Europe have been inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer (ITS 1 and ITS 2) and plastid sequences (trnL intron and the trnL-F spacer), with a representative sampling included (168 accessions in the ITS analysis, representing 158 species; and 42 accessions in the cpDNA analysis representing 35 taxa of Pimpinella and closely related species). All analyses resolved that Pimpinella is a non-monophyletic group, and Pimpinella’s taxa that grow in Western Europe are part of phylogenetically independent groups that correspond to three different tribes of the subfamily Apioideae: Pimpinelleae (core group), Pyramidoptereae and Smyrnieae.     

Evolutionary and Biogeographic Insights on the Macaronesian Beta-Patellifolia Species (Amaranthaceae) from a Time-Scaled Molecular Phylogeny

The Western Mediterranean Region and Macaronesian Islands are one of the top biodiversity hotspots of Europe, containing a significant native genetic diversity of global value among the Crop Wild Relatives (CWR). Sugar beet is the primary crop of the genus Beta (subfamily Betoideae, Amaranthaceae) and despite the great economic importance of this genus, and of the close relative Patellifolia species, a reconstruction of their evolutionary history is still lacking. We analyzed nrDNA (ITS) and cpDNA gene (matK, trnH-psbA, trnL intron, rbcL) sequences to: (i) investigate the phylogenetic relationships within the Betoideae subfamily, and (ii) elucidate the historical biogeography of wild beet species in the Western Mediterranean Region, including the Macaronesian Islands. The results support the Betoideae as a monophyletic group (excluding the Acroglochin genus) and provide a detailed inference of relationships within this subfamily, revealing: (i) a deep genetic differentiation between Beta and Patellifolia species, which may have occurred in Late Oligocene; and (ii) the occurrence of a West-East genetic divergence within Beta, indicating that the Mediterranean species probably differentiated by the end of the Miocene. This was interpreted as a signature of species radiation induced by dramatic habitat changes during the Messinian Salinity Crisis (MSC, 5.96–5.33 Mya). Moreover, colonization events during the Pleistocene also played a role in shaping the current diversity patterns among and within the Macaronesian Islands. The origin and number of these events could not be revealed due to insufficient phylogenetic resolution, suggesting that the diversification was quite recent in these archipelagos, and unravelling potential complex biogeographic patterns with hybridization and gene flow playing an important role. Finally, three evolutionary lineages were identified corresponding to major gene pools of sugar beet wild relatives, which provide useful information for establishing in situ and ex situ conservation priorities in the hotspot area of the Macaronesian Islands.     

Favolaschia in remnants of the Atlantic Forest,Brazil

The examination of recent collections of Favolaschia from remnants of the Atlantic Forest, Brazil, resulted in the identification of F. aurantiaca, F. cinnabarina and F. luteoaurantiaca sp. nov. Internal transcribed spacer (ITS) sequences obtained from these collections were introduced into the previously published phylogenetic tree of the genus to assess the position of these species within the Favolaschia clade. A maximum likelihood analysis generated a phylogenetic tree with a better resolution, especially for the clade that contains species belonging to section Favolaschia subsection Auriscalpium, where the three specimens collected in Brazil also were clustered in.     

Phylogeny of the Archiborborinae (Diptera: Sphaeroceridae) Based on Combined Morphological and Molecular Analysis

The Archiborborinae is a diverse Neotropical subfamily of Sphaeroceridae, with many undescribed species. The existing generic classification includes three genera consisting of brachypterous species, with all other species placed in the genus Archiborborus. We present the first phylogenetic hypothesis for the subfamily based on morphological, molecular, and combined datasets. Morphological data include 53 characters and cover all valid described taxa (33 species in 4 genera) in the subfamily, as well as 83 undescribed species. Molecular data for five genes (mitochondrial 12S rDNA, cytochrome c oxidase subunit I, and cytochrome B, and nuclear alanyl-tRNA synthetase and 28S rDNA) were obtained for 21 ingroup taxa. Data support the separation of the Archiborborinae from the Copromyzinae, with which they were formerly combined. Analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. The validity of the brachypterous genera Penola Richards and Frutillaria Richards is supported. The former genus Archiborborus Duda is paraphyletic, and will be divided into monophyletic genera on the basis of this work. Aptery and brachyptery have evolved multiple times in the subfamily. Antrops Enderlein, previously including a single brachypterous species, is a senior synonym of Archiborborus.     

丝瓜藓属(Pohlia Hedw.)的系统位置及属内种间关系探讨

丝瓜藓属的系统地位及属内种间关系存在争议。本研究首次利用核糖体DNA内转录间区(ITS)序列数据对丝瓜藓属及相关科属植物进行系统发育分析。最大简约法,最大似然法及贝叶斯推论法构建的系统树均表明,ITS序列数据不支持将丝瓜藓属划归提灯藓科。丝瓜藓属植物与缺齿藓属植物构成一个单系分支。Brotherus(1903),Ochi(1959),Shaw(1984)及Hill等(2006)等学者提出的丝瓜藓属属下分类均不是单系类群。     

Analysis of the genus Petagnaea Caruel (Apiaceae), using new molecular and literature data

In Southern Italy, an endemic monotypic genus belonging to family Apiaceae occurs: Petagnaea (P. gussonei), relict of Tertiary flora, belonging to subfamily Saniculoideae. At present, P. gussonei is an endangered species and is included in various lists of species deserving special protection. The genus belongs to scapose hemicryptophytes and shares a sciaphilous habitat (hygrophilous woodland). This study is aimed at doing a complete contribution about the evolutionary history of Petagnaea, using molecular markers as plastidial DNA (cpDNA), nuclear ribosomal DNA (rDNA) and data present in literature. We used nucleotide sequences from four regions of the chloroplast genome (rps16 intron, trnL^(UAA) intron, atpB-rbcL intergenic spacer, and partial matK gene) to investigate possible haplotypes in Petagnaea populations. To have an idea of the molecular relationships of all populations of P. gussonei, the internal transcribed spacer (ITS) sequences, already employed in recent studies, were obtained for 18 populations. These sequences in combination with other Saniculoideae ITS sequences available from GenBank have been used for a further phylogenetic analysis. The results agree with the current classification of Saniculoideae in placing P. gussonei in tribe Saniculeae, since P. gussonei is in basal position to Sanicula. According to intraspecific chloroplast DNA diversity, no different haplotypes were detected. In addition to molecular data, morphology, cytology, phytochemistry and conservation status have been considered in the discussion.     

Towards a species level tree of the globally diverse genus Chenopodium (Chenopodiaceae)

Chenopodium is a large and morphologically variable genus of annual and perennial herbs with an almost global distribution. All subgenera and most sections of Chenopodium were sampled along with other genera of Chenopodieae, Atripliceae and Axyrideae across the subfamily Chenopodioideae (Chenopodiaceae), totalling to 140 taxa. Using Maximum parsimony and Bayesian analyses of the non-coding trnL-F (cpDNA) and nuclear ITS regions, we provide a comprehensive picture of relationships of Chenopodium sensu lato. The genus as broadly classified is highly paraphyletic within Chenopodioideae, consisting of five major clades. Compared to previous studies, the tribe Dysphanieae with three genera Dysphania, Teloxys and Suckleya (comprising the aromatic species of Chenopodium s.l.) is now shown to form one of the early branches in the tree of Chenopodioideae. We further recognize the tribe Spinacieae to include Spinacia, several species of Chenopodium, and the genera Monolepis and Scleroblitum. The Chenopodium rubrum and the Ch. murale-clades were newly discovered as distinct major lineages but their relationships within Chenopodioideae will need further evaluation. Based on our results, we suggest the delimitation of Chenopodium to include Einadia and Rhagodia because these are part of the crown group composed of species of subg. Chenopodium that appear sister to the Atripliceae. The tetraploid crops such as Ch. berlandieri subsp. nuttalliae and Ch. quinoa also belong to Chenopodium sensu stricto. Trees derived from trnL-F and ITS were incongruent within this shallow crown group clade. Possible biological causes are discussed, including allopolyploidization.     

A settled sub-family for the orphan tree: The phylogenetic position of the endemic Colombian genus <Emphasis Type="Italic">Orphanodendron</Emphasis> in the Leguminosae

Orphanodendron is a taxonomically and geographically isolated South American genus of two species. When first described by Barneby and Grimes in 1990, the genus was placed in Leguminosae subfamily Caesalpinioideae, but that placement was doubted and the name Orphanodendron (Gr. orphanos, orphan + dendron, tree) was chosen to reflect the uncertain subfamilial relationship of the genus. In this study, nucleotide sequence data from five Orphanodendron specimens were added to 662 other, previously sampled, Leguminosae taxa representing all three currently recognized subfamilies (Caesalpinioideae, Mimosoideae and Papilionoideae) in a matK maximum parsimony analysis that resolved Orphanodendron as a member of the genistoid s.l. clade of subfamily Papilionoideae. Two additional Bayesian phylogenetic analyses with reduced taxon sampling of plastid (matK combined with trnL-F) and nuclear (ITS) loci strongly support the monophyly of Orphanodendron and unambiguously establish Orphanodendron as a member of the genistoid sensu lato clade. Although our plastid phylogenetic analysis finds relatively low support for a sister-group relationship with the African genus Camoensia, the nuclear-encoded ITS resolves Orphanodendron as sister to the Bowdichia clade with strong support and Camoensia as sister to other core genistoids. The phylogenetic resolution of Orphanodendron as a member of the genistoid s.l. legumes based on nuclear and plastid sequences will undoubtedly advance future evolutionary investigations of this Colombian endemic tropical tree genus.     

Phylogenetic relationships in the genus <Emphasis Type="Italic">Primula</Emphasis> L. (Primulaceae) inferred from the ITS region sequences of nuclear rDNA

The nucleotide sequences of the nuclear rDNA ITS regions were determined for 34 species of the genus Primula L. and one species of the genus Cortusa L., family Primulaceae Vent., and used to infer the phylogenetic relationships among these species. In this analysis species of the Russian flora and the flora of adjacent territories were studied for the first time. The results clarified the taxomic structure of the genus Primula and confirmed the entity of some of its sections; but not the subgenera sensu J.Richards. Our data do not support an independent status of the genus Cortusa, placing it as one of the terminal lineages of the section Cortusoides Balf. f. in the genus Primula.     

Sequence diversification of 45S rRNA ITS, trnH-psbA spacer, and matK genic regions in several Allium species

Allium is a very diverse genus with over 600 species distributed worldwide. Haplotype analyses of 45S rRNA ITS, trnH-psbA spacer, and matK gene sequences in 9 Allium species were carried out, subsequent to which phylogenetic relations of the nine species were also analyzed. Of the three genes, the nuclear 45S rRNA ITS sequences showed the highest variation with one haplotype in each species. The other two chloroplast genes revealed that more than one haplotype was present in each species, and each haplotype was present in several of the species. In the matK gene, EcoRI restriction revealed heteroplasmy in which the functional gene retains the EcoRI recognition site while the nonfunctional, pseudogene does not. Phylogenetic patterns were not consistent among the haplotypes of the 45 rRNA ITS, trnH-psbA spacer, and matK genic regions. This phylogenetic incongruency might be due to the presence of multiple haplotypes in each of the chloroplast genes. However, the inconsistency of the phylogenetic relationships, based on the 45S rRNA ITS sequences makes a strong case for further analysis.     

Analysis of the ITS1/ITS2 nuclear spacers and the secondary structure of <Emphasis Type="Italic">5.8S</Emphasis> rRNA gene in endemic species <Emphasis Type="Italic">Bellevalia sarmatica</Emphasis> (Pall. ex Georgi) Woronow and related species of the subfamily scilloideae

Sequence variability of the ITS spacers and 5.8S rRNA gene was examined in 11 accessions of the subfamily Scilloideae, including seven accessions of rare and endangered species Bellevalia sarmatica from Volgograd region. The intraspecific polymorphism level of the examined ITS1–5.8S–ITS2 sequence of B. sarmatica accessions constituted 1.3%. The phylogenetic position of B. sarmatica within the genus Bellevalia was determined. It was demonstrated that B. sarmatica belonged to the section Nutantes, and the most closely related species were B. webbiana and B. dubia. Nucleotide substitutions in the 5.8S rRNA gene sequence of the analyzed Scilloideae accessions were identified and studied. The predicted secondary structure of 5.8S rRNA gene was constructed. It was demonstrated that in the examined accessions, mutations in the 5.8S rRNA gene were mainly localized in the third hairpin region and had no effect on the secondary structure of the 5.8S rRNA molecule.     

Characterization of Euplotes lynni nov. spec., E. indica nov. spec. and description of E. aediculatus and E. woodruffi (Ciliophora,Euplotidae) using an integrative approach

Four species belonging to the genus Euplotes have been investigated, namely: E. lynni nov. spec., E. indica nov. spec., E. aediculatus, and E. woodruffi. All populations are from India and were investigated using morphological and molecular markers. The phylogenetic relationships were inferred from small subunit ribosomal rRNA gene (SSU rRNA), internal transcribed spacer (ITS) region, and mitochondrial cytochrome c oxidase subunit I (COI) gene. Predicted secondary structure models for two new species using the hypervariable region of the SSU rRNA gene and ITS2 region support the distinctness of both species. Morphological characters were subjected to principal component analysis (PCA) and genetic variations were studied in-depth to analyze the relatedness of the two new species with their congeners. An integrative approach combining morphological features, molecular analysis, and ecological characteristics was carried out to understand the phylogenetic position of the reported species within the different clades of the genus Euplotes.     

Phylogenetic relationships of the Rhizophoraceae in China based on sequences of the chloroplast gene matK and the internal transcribed spacer regions of nuclear ribosomal DNA and combined data set

The chloroplast gene matK and the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced from 17 samples of 13 species representing 6 genera of the angiosperm family Rhizophoraceae from China. Phylogenetic analyses were initially conducted based on sequences of the matK gene and the ITS regions, respectively, using Byrsonima crassifolia and Bunchosia armeniaca (Malpighiaceae) as outgroups. The partition–homogeneity test indicated that the two data sets are homogeneous. A combined analysis of the matK and ITS data generated a well supported phylogeny, which is topologically congruent with the two gene trees based on the Templeton test. The combined phylogeny shows that each genus formed a monophyletic group and the monophyletic relationships of the mangrove genera and of the inland genera were strongly supported.