Wax plants disentangled: a phylogeny of Hoya (Marsdenieae, Apocynaceae) inferred from nuclear and chloroplast DNA sequences

Hoya (Marsdenieae, Apocynaceae) includes at least 200 species distributed from India to the Pacific Islands. We here infer major species groups in the genus based on combined sequences from the chloroplast atpB-rbcL spacer, the trnL region, and nuclear ribosomal DNA ITS region for 42 taxa of Hoya and close relatives. To assess levels of ITS polymorphism, ITS sequences for a third of the accessions were obtained by cloning. Most ITS clones grouped by species, indicating that speciation in Hoya usually predates ITS duplication. One ITS sequence of H. carnosa, however, grouped with a sequence of the morphologically similar H. pubicalyx, pointing to recent hybridization or the persistence of paralogous copies through a speciation event. The topology resulting from the combined chloroplast and nuclear data recovers some morphology-based sections, such as Acanthostemma and Eriostemma, as well as a well-supported Australian/New Guinean clade. The combined data also suggest that morphological adaptations for ant-symbiosis evolved at least three times within Hoya.     

Phylogeny of the Malus (apple tree) species,inferred from its morphological traits and molecular DNA analysis

Some debated issues of the genus Malus (apple) taxonomy were examined using a variety of species from the collection of the Maikop Experimental Station, Vavilon Research Institute of Plant Industry (Krasnodar krai). Phylogenetic relationships among these species were studied using traditional analysis of morphological traits, RAPD, and complete sequencing of the 5'-internal transcribed spacer (ITS1), 5.8S rRNA, 3'-internal transcribed spacer (ITS2) (constituting a cluster of the rRNA genes), and the terminal fragment of the matK gene encoding chloroplast maturase. The results showed that the Sorbomalus section was polyphyletic; the American apple M. fusca was closely related to the species contributing to the East Asian center of the genus origin, and the American species M. angustifolia, M. coronaria, and M. ioensis were closely related to the M. trilobata relict species, whose assignment to the genus Malus is debated by some authors. Molecular analysis of the species relationships showed that the Middle Asian apple M. sieversii is the species from which apple domestication started.     

串珠藻目分子系统学研究进展

串珠藻目(Batrachospermales)是淡水红藻中最主要的类群。近年来, 应用DNA序列分析探讨串珠藻目的系统发育, 并与传统的形态学和生态学特征相结合, 为串珠藻目系统学研究拓展了新的思路。本文回顾了串珠藻目的建立及其所含类群的研究历史, 归纳了目前在串珠藻目系统发育与进化研究中常用的分子标记方法, 其中包括核基因组的18S rDNA、26S rDNA和ITS序列, 叶绿体基因组的rbcL序列, 线粒体基因组的cox2-3序列, 以及新兴的ISSR技术, 并对各种分子标记的特点及适用范围做了评述。结果表明, ITS序列多适用于种群分化及相近种间遗传分析, ISSR标记适用于种下分类群间及同一种群不同个体间基因多态性分析, cox2-3序列在一定程度上也可用于同一种群不同个体间的基因多态性分析, 而18S rDNA 与rbcL序列既可用于种间关系分析, 又可用于更高水平分析的构建系统树。这些分子标记已被证明在研究串珠藻目系统地理、物种起源和散布机制方面有着广泛的应用前景。同时, 本文对串珠藻目分子系统学研究的最新进展也进行了概述,并对今后的研究方向做了展望。     

串珠藻目分子系统学研究进展

串珠藻目（Batrachospermales）是淡水红藻中最主要的类群。近年来,应用DNA序列分析探讨串珠藻目的系统发育,并与传统的形态学和生态学特征相结合,为串珠藻目系统学研究拓展了新的思路。本文回顾了串珠藻目的建立及其所含类群的研究历史,归纳了目前在串珠藻目系统发育与进化研究中常用的分子标记方法,其中包括核基因组的18SrDNA、26SrDNA和ITS序列,叶绿体基因组的rbcL序列,线粒体基因组的cox9．-3序列,以及新兴的ISSR技术,并对各种分子标记的特点及适用范围做了评述。结果表明,ITS序列多适用于种群分化及相近种间遗传分析,ISSR标记适用于种下分类群间及同一种群不同个体间基因多态性分析,cox2-3序列在一定程度上也可用于同一种群不同个体间的基因多态性分析,而18SrDNA与rbcLFF列既可用于种问关系分析,又可用于更高水平分析的构建系统树。这些分子枥对己已被证明在研究串珠藻目系统地理、物种起源和散布机制方面有着广泛的应用前景。同时,本文对串珠藻目分子系统学研究的最新进展也进行了概述,并对今后的研究方向做了展望。     

Molecular characterization of Ephedra species found in Pakistan

Ephedra, also known as "ma huang", is a dioecious, drought- and frost-resistant, perennial, evergreen shrub with compelling medicinal value. The genus is represented by 42 species around the world, 9 of which were provisionally reported from Pakistan. Species of the genus have a controversial taxonomy due to their overlapping morphological features. Conventional tools alone are not sufficient for characterizing the species. The objective of present study was to assess the genetic variability present in different biotypes of Ephedra growing in Pakistan using molecular markers. A total of six genotypes collected from diverse geographic zones of Pakistan were used. The DNA of all genotypes was amplified using nine randomly amplified polymorphic DNA (RAPD) primers to study genetic variability at the molecular level. The dissimilarity coefficient matrix based on the data of 9 RAPD primers was used to construct a dendrogram which was then used to group the genotypes in clusters. Based on the dendrogram and dissimilarity coefficient matrix, the RAPD markers used here revealed a moderate to high level of genetic polymorphism (6 to 49%) among the genotypes. It was found that the collection of genotype accessions from Swat Valley in northwestern Pakistan was most distantly related to the other five collections. More molecular markers including functional genes and ribosomal spacer regions are suggested to find a better estimate of the genetic diversity present in Ephedra growing in Pakistan. The information provided here is useful for identifying valuable Ephedra variants which will be used for medicinal purposes and earning foreign currency.     

Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves

Regional distribution of genetic diversity in widespread species may be influenced by hybridization with locally restricted, closely related species. Previous studies have shown that Central American East Pacific populations of the wide-ranged Avicennia germinans , the black mangrove, harbour higher genetic diversity than the rest of its range. Genetic diversity in this region might be enhanced by introgression with the locally restricted Avicennia bicolor . We tested the hypotheses of ancient hybridization using phylogenetic analysis of the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA and intergenic chloroplast DNA; we also tested for current hybridization by population level analysis of nuclear microsatellites. Our results unveiled ancient ITS introgression between a northern Pacific Central American A. germinans lineage and A. bicolor . However, microsatellite data revealed contemporary isolation between the two species. Polymorphic ITS sequences from Costa Rica and Panama are consistent with a zone of admixture between the introgressant ITS A. germinans lineage and a southern Central American lineage of A. germinans . Interspecific introgression influenced lineage diversity and divergence at the nuclear ribosomal DNA; intraspecific population differentiation and secondary contact are more likely to have enhanced regional genetic diversity in Pacific Central American populations of the widespread A. germinans .     

泡桐属植物种类的RFLP分析

对我国泡桐属15 个植物种类作了叶绿体DNA 的RFLP 分析, 根据估算的相似系数, 用平均链锁聚类方法构建树状图, 结果可将研究材料分为南方泡桐组、毛泡桐组和白花泡桐组。种间相似系数多在0.70 以上, 说明各种类间亲缘关系较近, 尤其是台湾泡桐和海岛泡桐, 相似系数接近1.00。最后讨论了一些泡桐种类的分类问题。     

Phylogenetic relationships and biogeographic patterns in North American members of Carex section Acrocystis (Cyperaceae) using nrDNA ITS and ETS sequence data

Carex section Acrocystis currently includes 27 taxa in North America. Recent phylogenetic studies have suggested that the North American and some but not all of the Eurasian species form a clade. Relationships and biogeographic patterns among species in this core-Acrocystis group are explored here using nuclear ribosomal (nrDNA) internal transcribed spacer region (ITS) and nrDNA external transcribed spacer region (ETS) sequence data. While maximum parsimony analysis of the ITS and ETS data provides only a moderately resolved branching structure for species relationships within the core-Acrocystis clade, maximum likelihood analysis provides a more resolved hypothesis of relationships in the section. The core-Acrocystis clade consists of a grade of Eurasian and primarily western North American species, with a well-supported clade of only eastern North American species nested within this grade. ITS and ETS types do not coalesce within many species or species complexes. Possible explanations for the non-coalescent nature of ITS and ETS copies in Acrocystis are explored, including lineage sorting, hybridization, and cryptic species.     

A floristic survey of marine tube-forming diatoms reveals unexpected diversity and extensive co-habitation among genetic lines of the Berkeleya rutilans complex (Bacillariophyceae)

Limited molecular data for marine tube-forming diatoms are available currently and this study provides the first molecular survey of these taxa. To conduct this survey, we used a molecular-assisted alpha taxonomy (MAAT) approach that utilizes DNA barcode data. We used three DNA barcode markers: the 3´ end of the large subunit of RUBISCO (rbcL-3P); the variable D2/D3 region of the nuclear large subunit ribosomal DNA (LSU D2/D3); and the internal transcribed spacer 2 (ITS2) to assign marine tube-forming diatoms from Canada to genetic species groups. The rbcL-3P analysis uncovered 29 genetic groups including representatives of Haslea crucigera, Navicula bottnica, N. brunelii, N. ramosissima, Nitzschia fontifuga, N. tubicola, Parlibellus berkeleya and P. delognei f. elliptica, as well as a complex of 14 closely related groups morphologically consistent with Berkeleya rutilans. We sequenced ITS2 for representatives of the B. rutilans complex; these data were consistent with the rbcL-3P genetic clusters for 86% of the colonies tested. The remaining 14% were in conflict, possibly indicating that more than a single Berkeleya genetic species was present in each colony. To investigate this hypothesis further, we developed ‘species-specific’ ITS2 primers and confirmed heterogeneity of Berkeleya genetic species in 64% of the colonies tested (N = 91). Therefore, a taxonomic assessment of tube-forming species that were originally described on the basis of colony morphology (e.g. Berkeleya rutilans) can only proceed using clonal cultures or single-cell analysis.     

Relationships of Anagallis foemina and A. arvensis (Myrsinaceae): new insights inferred from DNA sequence data

We investigated the relationship between Anagallis arvensis and A. foemina using nuclear and plastid molecular data. Information from the nuclear rDNA internal transcribed spacer (ITS) region and four different chloroplast loci; ndhF, trnL-F, rpl16, and rps16 was analysed using both parsimony and Bayesian inference. Anagallis foemina was found to be most closely related to the perennial A. monelli, and not to A. arvensis. The existence of two different cpDNA haplotypes was revealed; one shared by Anagallis foemina, A. monelli, A. platyphylla, and one A. arvensis individual, while all other investigated A. arvensis individuals shared the second haplotype. Ancestral cpDNA polymorphism within Anagallis arvensis or hybridization are possible explanations, however, information in ITS data is too scarce to falsify any of these hypotheses.     

A phylogenetic analysis of Doronicum (Asteraceae, Senecioneae) based on morphological, nuclear ribosomal (ITS), and chloroplast (trnL-F) evidence.

A phylogenetic analysis of the Old World genus Doronicum (26 species, 4 subspecies) based on sequence data of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA, the chloroplast spacer trnL-F, and morphology is presented. Congruence among the three data sets was explored by the computing of several indices, all of which suggest homogeneity between only the two molecular matrices. We argue that the morphological data set contains poor phylogenetic signal and advocate simultaneous analysis of the three data sets (total evidence approach) so that morphological characters are tested for homology by congruence with molecular data. The resulting phylogenetic hypothesis allows several well-supported conclusions including the placement of a Corsican endemic (D. corsicum), sister to the remainder of the genus, and the inference that an early southern European or Mediterranean diversification took place in the genus. Shifts in morphological characters (e.g., homocarpy to heterocarpy) are confirmed to have evolved several times. Results from comparative studies of sequence data of the chloroplast gene ndhF support inclusion of Doronicum in tribe Senecioneae.     

甘草属种间杂交种叶绿体DNA父系遗传的发现及分析

通过对甘草属乌拉尔甘草(Glycyrrhiza uralensis)、光果甘草(G.glabra)、胀果甘草(G.inflata)及其人工杂交种组合G.uralensis♀×G.glabra♂、G.glabra♀×G.uralensis♂、G.uralensis♀×G.inflata♂、G.inflata♀×G.uralensis♂共68份材料的核基因ITS序列、叶绿体rbc L、mat K、trn H-psb A基因的序列分析,探讨了甘草属叶绿体DNA遗传方式。结果表明:(1)亲本种和人工杂交种ITS序列长度均为614 bp,其中34份人工杂交种ITS序列存在4处变异位点,且人工杂交种均检测出来自父本、母本ITS序列相同位点碱基的叠加,检测率为100%。(2)亲本种与人工杂交种的叶绿体基因rbc L、mat K、trn H-psb A序列长度相同,共有4处变异位点,人工杂交种在变异位点处的碱基与其相对应的父本碱基一致率高达97.1%。以上结果说明,该研究获得34份人工杂交种为100%杂交成功的F_1子代,核基因ITS序列可用于甘草属杂交种的遗传鉴定;甘草属叶绿体rbcL、mat K、trn H-psb A基因具有父系遗传特性,推测甘草属质体的遗传方式主要表现为父系遗传,这种质体遗传方式的发现为甘草属杂交种和遗传多样性研究提供了新的认识,也为杂交种的亲本鉴定提供分子依据。     

The molecular phylogeny of the genus Rhizopus based on rDNA sequences

In order to establish the molecular phylogeny of the genus Rhizopus, three molecules of the ribosomal RNA-encoding DNA (rDNA), complete 18S, internal transcribed spacer (ITS)1-5.8S-ITS2, and 28S D1/D2 regions of all the species of the genus were sequenced. Phylogenetic trees showed three major clusters corresponding to the three groups in the current morphological taxonomy, microsporus-group, stolonifer-group, and R. oryzae. R. stolonifer var. lyococcos was clustered independently from the major clusters. R. schipperae clustered differently in all trees. Strains of R. sexualis had multiple ITS sequences. A. rouxii clustered with R. oryzae. These results indicate the possibility of molecular identification of species groups using rDNA sequencing. Reclassification of the genus might be appropriate.     

A REASSESSMENT OF SPECIES BOUNDARIES IN CYSTOSEIRA AND HALIDRYS (PHAEOPHYCEAE,FUCALES) ALONG THE NORTH AMERICAN WEST COAST1

Application of phylogenetic species recognition to morphologically recognized species in the genera Cystoseira Agardh and Halidrys Lyngbye on North American west coasts revealed little genetic variation despite a remarkable degree of morphological variation currently used to recognize and delineate species. Whereas morphological characteristics allow recognition of two genera, four morphological species and three informal forms, maximum genetic variation among them was similar to that characteristic of the intraspecific level in European congeners and other Fucales. Among morphological species and forms, nucleotide variation in a combined 26S (large subunit (LSU)) and internal transcribed spacer (ITS) ribosomal DNA analysis was below 3% while it was 1% or less for the RUBISCO spacer of the chloroplast DNA. Comparison of the LSU data to available data for European congeners showed that the genera Cystoseira and Halidrys are not monophyletic and that the previously recognized Cystoseiraceae should be included within the family Sargassaceae. These observations suggest that the current taxonomy for the Sargassaceae fails to reflect evolutionary history because Atlantic and Pacific Cystoseira and Halidrys appear to have arrived at similar morphologies independently. Our results indicate a comparatively recent establishment on the west coast of North America of a sargassacean progenitor whose descendant taxa have experienced limited genetic divergence and are characterized by a high capacity for phenotypic variation despite their overall genetic similarity.     

23株不同地理来源嗜酸硫杆菌的系统发育及其遗传差异

【目的】研究不同地理来源嗜酸硫杆菌的系统发育及其遗传差异,以及基因指纹图谱技术聚类与嗜酸硫杆菌地理来源的相关性。【方法】采用16S-23S r RNA间隔区(ITS)序列建立系统发育树,并结合ERIC和BOXAIR两种引物进行rep-PCR,以及rus基因扩增,对不同地理来源嗜酸硫杆菌进行分析。【结果】分离自不同样点的23株嗜酸硫杆菌遗传差异显著,依据ITS序列系统发育树被划分为5个大类群,与rep-PCR指纹图谱的分类结果较为接近,其中Acidithiobacillus ferrooxidans在ITS系统发育和BOXAIR-PCR指纹聚类分析中被划分为2个类群,但在ERIC-PCR中归为1个类群,rus基因分组中,在系统发育和聚类分析中处于同一类群的菌株拥有不同类型的rus基因,说明嗜酸硫杆菌的亚铁氧化途径与系统发育类群无明显相关性;ITS基因拥有区分近缘种或亚种的能力,且BOXAIR-PCR的分辨能力较强,非常适于嗜酸硫杆菌的遗传差异分析。     

The evolution of Dactylorhiza (Orchidaceae) allotetraploid complex: insights from nrDNA sequences and cpDNA PCR-RFLP data

Sequence data from a portion of the external transcribed spacer (ETS) and from the internal transcribed spacers (ITS1 and ITS2) of 18S-26S nuclear ribosomal DNA were used together with chloroplast DNA PCR-RFLP data to unravel patterns of allotetraploid speciation within the Western European Dactylorhiza polyploid complex. A maximum likelihood tree based on combined ETS and ITS sequences suggests that the Western European Dactylorhiza allotetraploids have evolved by hybridization between four main diploid lineages. Cloned sequences and the topology of the ITS plus ETS tree indicate that the allotetraploid species D. elata, D. brennensis, and D. sphagnicola have originated from the autotetraploid D. maculata together with the diploid D. incarnata, while D. majalis, D. traunsteineri, and D. angustata seem to have evolved by hybridization between the D. fuchsii s.str and D. incarnata lineages. Finally, the diploid D. saccifera lineage seems to have been involved together with the D. incarnata lineage in the formation of the allotetraploid D. praetermissa. The observed congruence between the chloroplast tree and the ITS/ETS tree suggests a directional evolution of the nrDNA after polyploidization in favor of the maternal genome. Considered together with morphological, biogeographical, and ecological evidence, the molecular analysis leads us to recognize four species within the investigated allotetraploid complex, namely D. majalis, D. praetermissa, D. elata, and D. sphagnicola.     

Phylogeographically concordant chloroplast DNA divergence in sympatric Nothofagus s.s. How deep can it be?

? Here, we performed phylogenetic analyses and estimated the divergence times on mostly sympatric populations of five species within subgenus Nothofagus. We aimed to investigate whether phylogenetic relationships by nuclear internal transcribed spacer (ITS) and phylogeographic patterns by chloroplast DNA (cpDNA) mirror an ancient evolutionary history that was not erased by glacial eras. Extant species are restricted to Patagonia and share a pollen type that was formerly widespread in all southern land masses. Weak reproductive barriers exist among them. ? Fifteen cpDNA haplotypes resulted from the analysis of three noncoding regions on 330 individuals with a total alignment of 1794 bp. Nuclear ITS data consisted of 822 bp. We found a deep cpDNA divergence dated 32 Ma at mid-latitudes of Patagonia that predates the phylogenetic divergence of extant taxa. Other more recent breaks by cpDNA occurred towards the north. ? Complex paleogeographic features explain the genetic discontinuities. Long-lasting paleobasins and marine ingressions have impeded transoceanic dispersal during range expansion towards lower latitudes under cooler trends since the Oligocene. ? Cycles of hybridization-introgression among extant and extinct taxa have resulted in widespread chloroplast capture events. Our data suggest that Nothofagus biogeography will be resolved only if thorough phylogeographic analyses and molecular dating methods are applied using distinct genetic markers.