Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)

The olive genus Olea includes c. 30–40 taxa in three subgenera (Olea, Tetrapilus, and Paniculatae) within the family Oleaceae. Historically, the Olea genus was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus Tetrapilus and poor resolution within clades. These analyses also showed that the genus was not monophyletic. Reliable identification of Olea species is important for both their conservation and utilization of this economically important genus. In this study, we used phylogenomic data from genome skimming to resolve relationships within Olea and to identify molecular markers for species identification. We assembled the complete plastomes, and nrDNA of 26 individuals representing 13 species using next-generation sequencing and added 18 publicly available accessions of Olea. We also developed nuclear SNPs using the genome skimming data to infer the phylogenetic relationships of Olea. Large-scale phylogenomic analyses of 138 samples of tribe Oleeae supported the polyphyly of Olea, with Olea caudatilimba and Olea subgenus Tetrapilus not sharing their most recent common ancestor with the main Olea clade (subgenus Paniculatae and subgenus Olea). The interspecific phylogenetic resolution was poor owing to a possible rapid radiation. By comparing with the plastome data, we identified the markers ycf1b and psbE-petL as the best Olea-specific chloroplast DNA barcodes. Compared with universal barcodes, specific DNA barcodes and super-barcode exhibited higher discriminatory power. Our results demonstrated the power of phylogenomics to improve phylogenetic relationships of intricate groups and provided new insights into barcodes that allow for accurate identification of Olea species.     

Genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum-Brucella group by recA and 16S rRNA gene-based comparative sequence analysis

The genetic diversity and phylogenetic interrelationships among 106 Ochrobactrum strains (O. anthropi: 72, O. intermedium: 22, O. tritici: 5, O. oryzae: 2, O. grignonense: 2, O. gallinifaecis: 1, O. lupini: 2), the type strains of the eight Brucella species and other closely related taxa were studied by recA and rrs gene (16S rRNA) comparative sequence analysis. Both markers correctly delineated the various Ochrobactrum species; however, resolution at the subspecies level was considerably higher in the recA gene-based approach. Phylogenetic analyses using neighbor-joining, parsimony, and maximum likelihood algorithms generated trees with similar topologies but the overall branching order, and also the order of the subclades, were not stable in either assay, which could be explained by generally high recA and rrs sequence similarities. Ochrobactrum and Pseudochrobactrum formed separate clades distinct from other Alphaproteobacteria with Bartonella, Agrobacterium, and Rhizobium as the closest relatives. O. gallinifaecis was the most distinct member, when compared to the type species O. anthropi, with rrs and recA similarities of 96.2% and 81.4%. Brucella species were indistinguishable, exhibiting high rrs and recA gene similarities of 98.6% and 85.5% compared with Ochrobactrum intermedium. At the protein level, all RecA sequences among the various Ochrobactrum species and between Ochrobactrum and Brucella were highly similar with only a few amino acid substitutions. O. anthropi and O. tritici were indistinguishable by means of their RecA proteins. A set of initially biochemically classified strains did not cluster within their assigned species and they either grouped within other known species or grouped as potential novel Ochrobactrum species. In further investigations, these strains were reclassified and described as novel species. In summary, Ochrobactrum is a highly diverse genus comprising several novel species. We recommend recA- in addition to rrs gene-analysis for correct species allocation and subtyping of novel Ochrobactrum isolates.     

后蕊苣苔属的花粉形态

本文用光学显微镜和扫描电子显微镜系统观察了苦苣苔科后蕊苣苔属的花粉形态,本属花粉粒为近球形,稍长或稍扁,具三拟孔沟,个别种具四拟孔沟的萌发孔类型,外壁表面具网状纹饰,网脊光滑或具小刺。根据网脊宽度。网眼形状以及网纹明显程度而将本属花粉分为三个类群.1.网脊较宽,宽度不均匀,网脊宽度大于网眼直径,包括的植物种类有Opithandra sinohenryi,O.primoloides和O.fargesii等三种;2.网脊较窄,宽度均匀,包括的种类是O.dalzielii,O.obtusidentata,O.dinghushnnensis和O.cinerea等4种;3.网不明显,小刺突出,具这种纹饰的植物只有O.acaulis一种。     

Fossil pinnae,sporangia, and spores of Osmunda from the Eocene of South China and their implications for biogeography and paleoecology

The genus Osmunda L. contains approximately 10 extant species widely distributed in tropical and temperate regions, with the greatest concentration of species in East and Southeast Asia. Osmunda is characterized by dimorphic or commonly hemidimorphic fronds with dimorphic pinnae. Its geological history has been traced back to the Triassic. Most records of the genus are based on rhizomes and rarely on pinnae bearing sporangia and spores. Here, we describe fossil pinnae, sporangia, and spores of Osmunda lignitum (Giebel) Stur recovered from the middle Eocene of the Changchang Formation in the Changchang Basin, Hainan Island and the Youganwo Formation in the Maoming Basin, Guangdong, South China. The fossils closely resemble the extant Osmunda banksiifolia (C. Presl) Kuhn of the subgenus Plenasium on the basis of their morphological and anatomical structures. The present occurrence of O. lignitum indicates subg. Plenasium flourished and extended from the high latitude regions such as Northeast China to the low latitude areas of South China during the middle Eocene. Large numbers of specimens described here also indicate that Osmunda was the dominant understory fern element beneath mixed evergreen broad-leaf angiosperm and gymnosperm forests living in a warm and humid environment.     

中国鼠兔属(Ochotona)的研究——分类与分布

现生鼠兔主要分布在亚洲,次在欧洲东缘和北美洲,其中我国种类最多。就鼠兔属动物的分类而言,以往学者的观点不尽相同,因为许多种类在形态上均相近似。笔者据国内外标本和文献资料,拟对我国鼠兔的分类与分布作一初步整理,并阐述作者的分类意见。 本篇内容包括:几种鼠兔分类地位的讨论,亚属暨种类名录与分布。现记述于后。     

云南疣粒野生稻稻瘟病抗性

野生稻(Oryza rufipogo)保存有许多栽培稻(O. sativa)不具备或已经消失的优异基因资源, 是扩大栽培稻遗传背景、改良产量与品质、提高抗病虫害及抗逆境能力的重要基因库。疣粒野生稻(O. meyeriana)是中国3种野生稻资源之一, 主要分布在云南。为进一步了解其稻瘟病抗性, 首先利用来自不同稻作区的稻瘟病菌株, 通过注射接种法对疣粒野生稻进行系统的稻瘟病抗性鉴定, 发现疣粒野生稻对接种的所有稻瘟病菌株都感病。进一步采用3'/5' RACE方法, 从疣粒野生稻中克隆了水稻同源基因Pid2和Pid3, 并构建过表达转基因株系对基因功能进行了研究。结果表明, Pid2和Pid3与疣粒野生稻中同源基因间在DNA和氨基酸水平上有较大的序列差异, 过表达转基因的日本晴植株对稻瘟病菌的敏感性与对照相似。推测疣粒野生稻在自然接种条件下, 表现出的抗稻瘟病表型很可能是其旱生叶片结构特征形成了对稻瘟病菌侵染的天然屏障。对控制疣粒野生稻这一类性状基因资源的挖掘和利用, 有利于优良抗性水稻品种的培育。研究结果为疣粒野生稻的研究利用提供了新信息和新思路。     

Molecular phylogenetic studies show Omphalina giovanellae represents a new section of Clitopilus (Agaricomycetes)

After reconsidering the specific characters of Omphalia giovanellae and applying data from the sequences of the D1–D2 domain of the 28S rRNA gene and the ITS region of material collected in Italy and Spain, the species is ascribed to the genus Clitopilus. Considering the rather peculiar characters, especially the smooth spores, C. giovanellae is ascribed to the new section Omphaloidei sect. nov. The species is illustrated with drawings of fresh basidiomata observed in situ, as well as with SEM micrographs of the spores. Also based on DNA sequence data, O. farinolens, recently described from Spain, is shown to be a synonym of C. giovanellae.     

Analysis of phylogenetic relationships of Potamogeton species in China based on chloroplast trnT-trnF sequences

Sequences of the chloroplast trnT-trnF region were analyzed for species of the genus Potamogeton distributed in China to reconstruct phylogenetic relationships. The phylogenetic analyses showed that the genus Potamogeton could be divided into two clades. Eighteen species formed a monophyletic clade while the remaining four formed a second, distinguishable one, supporting the conventional treatment that the genus Potamogeton contains the submerged linear-leaved group and the submerged broad-leaved group. The first clade, which represented the subgenus Potamogeton, could be further divided into two subclades. The second clade, which represented the subgenus Coleogeton, displayed a close phylogenetic relationship with the subgenus Potamogeton and occupied a unique position within the genus Potamogeton. This finding suggested that the treatment of the subgenus Coleogeton, which was once regarded as the genus Stuckenia Börner, may need to be reconsidered. Furthermore, identification of maternal donors of some hybrids was successfully applied based on sequence of maternally inherited chloroplast genome. The female parents of three putative hybrids, P. × malainoides, P. × anguillanus, and P. × orientalis, were proved to be accordant with previous morphological conclusions.     

Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov

The genus Chlamydomonas (including Chloromonas) is one of the largest green algal genera comprising more than 600 species. To initiate a comprehensive analysis of the phylogeny and systematics of the genus, we determined nuclear-encoded SSU rRNA sequences from 32 strains of Chlamydomonas, Chloromonas and Chlorogonium with emphasis on oogamous taxa and related strains, and incorporated these into global molecular phylogenetic analyses of 132 strains of Chlorophyceae. In addition, we studied the morphology and reproduction of oogamous and related strains by light microscopy. We recognize and designate 18 monophyletic lineages (clades) within the Chlorophyceae, 11 of which are confined to the CW (basal bodies displaced clockwise) subgroup. The majority of clades recognized within the Chlorophyceae do not correspond to any of the traditional classification systems, which are still largely based on the organization level. Strains assigned to Chlamydomonas and Chloromonas were found in seven different clades confirming the polyphyly of the two genera as presently conceived. To initiate the taxonomic revision of Chlamydomonas, C. reinhardtii is proposed as the conserved type of the genus. In consequence, species in clades other than the clade containing C. reinhardtii must be transferred to other genera, a process initiated in this contribution. The oogamous strains studied represent a monophyletic lineage, which is described as Oogamochlamys gen. nov. comprising three species (O. gigantea, O. zimbabwiensis and O. ettlii spec. nov.). The sister clade to Oogamochlamys consists of isogamous strains characterized by chloroplasts with incisions and is described as Lobochlamys gen. nov. with two species (L. culleus and L. segnis). Another clade is characterized by asteroid or perforated, parietal chloroplasts and contains the type species of Chloromonas (C. reticulata). Thus, the polyphyletic Chloromonas (traditionally defined as “Chlamydomonas without pyrenoids”) can be legitimized as a monophyletic genus by restriction to this clade and is here emended on the basis of chloroplast characters (the clade contains strains with or without pyrenoids thus rejecting the character “absence of pyrenoids”).     

尖塘鳢属鱼类线粒体12SrRNA基因序列分析

利用PCR技术扩增和测序了线纹尖塘鳢、云斑尖塘鳢和海丰沙塘鳢线粒体12SrRNA基因,结合从GenBank中下载的部分同源序列,共分析了5种鱼类的系统发育关系。在Kimura2-parameter模型构建的邻接树中,原产泰国的云斑尖塘鳢与原产澳州线纹尖塘鳢均为单系类群,二者为亲缘关系最为密切的姐妹群,海丰沙塘鳢与其它群体的亲缘关系较远,支持将尖塘鳢属从塘鳢属中分出的传统分类处理。尖塘鳢属内云斑尖塘鳢和线纹尖塘鳢鱼类种内DNA序列无差异,而种间差异明显,表明线粒体12SrRNA基因可作为塘鳢科鱼类种类鉴定的良好分子标记。     

Molecular identification and phylogenetic analysis of nuclear rDNA sequences among three opisthorchid liver fluke species (Opisthorchiidae: Trematoda)

In this study, we describe the development of a fast and accurate molecular identification system for human-associated liver fluke species (Opisthorchis viverrini, Opisthorchis felineus, and Clonorchis sinensis) using the PCR-RFLP analysis of the 18S-ITS1-5.8S nuclear ribosomal DNA region. Based on sequence variation in the target rDNA region, we selected three species-specific restriction enzymes within the ITS1 regions, generating different restriction profiles among the species: MunI for O. viverrini, NheI for O. felineus, and XhoI for C. sinensis, respectively. Each restriction enzyme generated different-sized fragments specific to the species examined, but no intraspecific polymorphism or cross-reaction between the species was detected in their restriction pattern. These results indicate that PCR-linked restriction analysis of the ITS1 region allows for the rapid and reliable molecular identification among these opisthorchid taxa. In addition, phylogenetic analysis of rDNA sequences using different methods (MP, ML, NJ, and Bayesian inference) displayed O. viverrini and O. felineus as a sister group, but this relationship was not strongly supported. The failure of recovering a robust phylogeny may be due to the relatively small number of synapomorphic characters shared among the species, yielding weak phylogenetic signal. Alternatively, rapid speciation within a very short period time could be another explanation for the relatively poorly resolved relationships among these species. Our data are insufficient for discriminating between sudden cladogenesis and other potential causes of poor resolution. Further information from independent loci might help resolve this phylogeny.     

西江中下游鳤的遗传多样性与种群动态历史

鳤(Ochetobius elongatus)曾经是我国许多河流的重要经济鱼类, 然而由于环境污染和人为干扰等原因, 鳤的资源量萎缩严重, 种群处于极度濒危的境地。目前, 常规采样方法获得鳤样本的难度较大, 致使相关研究难以开展。本研究通过仔鱼采集和成鱼采集的手段, 测定两个线粒体基因和两个核基因, 对西江中下游鳤的遗传多样性和种群动态历史进行研究。结果显示, 西江中下游鳤的遗传多样性处于较低水平并且出现了衰退的迹象, 可能经历了遗传瓶颈效应。此外, 种群动态历史分析发现, 西江中下游鳤在后更新世期间(0.06和0.13百万年前)经历了种群扩张, 刚好处于中更新世(0.78-0.126百万年前)冰期褪去之后, 表明更新世气候的波动影响了西江中下游鳤的种群动态。作为鳤可能的重要产卵场, 西江中下游部分江段可以考虑建立鳤的自然保护区, 用于保育和修复鳤的种质资源。     

三种鼠兔血清蛋白和血红蛋白的电泳比较——高原鼠兔分类地位的探讨

鼠兔属(Ochotona)为青藏高原兽类的重要类群之一,近年来对它的研究较多,不仅发现了若干新种,而且作了一些分类订正。不少学者,将高原鼠兔(O.cvrzoniae Hodgson)独立为一个种(Rypeeb 1964,钱燕文、冯祚建1974;郑昌琳1979)。亦有一些学者把它作为达乌尔鼠兔亚种的如Allen、Банников张荣祖以及持怀疑态度的Ellerman等（转引自郑昌琳,1979）。而二者形态上的差别,主要为高原鼠兔的头骨额部显著隆起,顶骨后部向下倾斜,故头骨背面弧度较大,另外唇部四周和鼻端为黑褐色。这些差别多为量的差别,终究是否达到了种的水平,抑或是亚种水平,实难完全肯定。     

Isoenzyme diversity and phylogenetic relationships among the American beans of the genus Vigna Savi (Fabaceae)

Electrophoretic variation of 13 isoenzyme systems encoded by 25 gene loci has been studied among the 12 American bean species of the genus Vigna, subgenera Sigmoidotropis and Lasiospron, in comparison with the two pantropical species Vigna luteola and V. vexillata of the subgenera Vigna and Plectrotropis, respectively. Of the 202 electromorphs (putative allozymes) discovered, 106 were phylogenetically informative, i.e. shared by at least two taxa, and 96 were taxon-specific. Parsimony, neighbour-joining and UPGMA analyses of the isozyme data as unordered presence–absence characters revealed the division of the American Vigna species into six clades which mostly correspond to the grouping of species into subgenera and sections in the traditional morphology-based systems, except in the placement of species V. gentryi and V. caracalla. The type species of the section Caracallae, V. caracalla, appears on the cladogram as basally paraphyletic in the subgenus Sigmoidotropis, but apart from the V. linearis group of the same section which forms a separate subclade. Vigna gentryi is not linked to other species of the section Sigmoidotropis, but appears in a distant subclade as a sister species to V. adenantha s. l. of the section Leptospron. The subgenus Lasiospron is sister to the pantropical V. vexillata of the African subgenus Plectrotropis.     

Trap architecture in carnivorous Utricularia (Lentibulariaceae)

Within carnivorous plants, the bladderworts (Utricularia) possess the most complicated traps whose mechanisms are not yet completely understood. For the first time, a representative survey of different traps from both subgenera (Utricularia and Polypompholyx) is presented.

Based on scanning- and transmission electron microscopy, traps of 14 species of Utricularia (out of 215 species) representing 11 sections (out of 35 sections) and including all life forms (aquatic, epiphytic, and terrestrial) were investigated. Additionally, it was tested whether life forms correlate with trapping mechanisms. Most morphological and anatomical features of the traps vary considerably between the different life forms, e.g. position of trap and trap entrance as well as form and position of trap appendages. Morphological data support the basal position of subgenus Polypompholyx within the genus. Some characteristics of the traps of terrestrial Utricularia multifida (subgenus Polypompholyx) differ remarkably from traps of the other species, e.g. trap-door anatomy and trap walls. This might be an indication for a primordial (non-suction) trapping mechanism in the former species, similar to that of the eel-traps of the closely related genus Genlisea.     

Taxonomy and new bacterial symbioses of gutless marine Tubificidae (Annelida, Oligochaeta) from the Island of Elba (Italy)

In shallow sublittoral sediments of the north-west coast of the Island of Elba, Italy, a new gutless marine oligochaete, Olavius ilvae n. sp., was found together with a congeneric but not closely related species, O. algarvensis Giere et al., 1998. In diagnostic features of the genital organs, the new species differs from other Olavius species in having bipartite atria and very long, often folded spermathecae, but lacking penial chaetae. The Elba form of O. algarvensis has some structural differences from the original type described from the Algarve coast (Portugal). The two species from Elba share characteristics not previously reported for gutless oligochaetes: the lumen of the body cavity is unusually constricted and often filled with chloragocytes, and the symbiotic bacteria are often enclosed in vacuoles of the epidermal cells. Regarding the bacterial ultrastructure, the species share three similar morphotypes as symbionts; additionally, in O. algarvensis a rare fourth type was found. The divergence of the symbioses in O. algarvensis, and the coincidence in structural and bacteria-symbiotic features between the two taxonomically different, but syntopic host species at Elba are discussed.     

Flavonoids in the leaves of Thymus: a chemotaxonomic survey

The flavonoid aglycone analysis of 20 Thymus taxa (most Iberic or Balearic endemics) shows the presence of luteolin, apigenin, acacetin, genkwanin, 6-hydroxyluteolin, xanthomicrol, cirsimaritin; four partially identified flavones, of which three are 6-OR-substituted and one flavonol. The differences observed between T. capitatus (L.) Hoffmanns. et Link (subgenus Coridothymus (Reichenb. fil.) Borbás) and the other species belonging to the subgenus Thymus (L.) Jalas, seem enough to maintain the separation of the two groups, but within the same genus, as proposed in Flora Europaea.     

Genetic analysis by DNA fingerprinting in tsetse fly genomes

Genomic DNA from tsetse flies (Diptera : Glossinidae: Glossina Wiedemann) was analyzed by hybridization using the whole M13 phage as a probe to reveal DNA fingerprinting (DNAfp) profiles. Intrapopulation variablity, measured by comparison of DNAfp profiles of tsetse flies from large colony of G. brevipalpis, showed a high degree of polymorphism similar to that found in other animal species. Different lines of G. m. morsitans, G. m. centralis, G. m. submorsitans, G. p. palpalis and G. p. gambiensis established from small colonies displayed less genetic variability than the G. brevipalpis population. The analysis of pedigree relationships within an inbred line of G. m. centralis conformed to a Mendelian inheritance pattern. In the pedigree presented no mutations were observed, one fragment was linked to the X chromosome, and three fragment sets were linked, but most fragments showed independent segregation. M13 revealed no characteristics DNAfp profile differences between the subgenus Glossina and the subgenus Nemorhina, but a conserved distribution pattern was found in the laboratory colonies within each subspecies. M13 also revealed line specific DNA fragments that may be useful as genetic markers to expand the present linkage map of G. m. morsitans.     

Olencira praegustator (Crustacea, Isopoda, Cymothoidae) parasitic on Brevoortia species (Pisces, Clupeidae) from the southeastern coasts of North America: review and re-description

The cymothoid isopod Olencira praegustator (Latrobe, 1802), the sole species of the genus Olencira Leach, 1818, has been the subject of several previous studies, but has remained incompletely described. This species is re-described and figured from the Atlantic menhaden Brevoortia tyrannus (Latrobe, 1802), the type host from the estuarine systems of the South Carolina coast, USA. The general morphology, mouthparts and appendages of the female, male and other stages of its lifecycle are described.

The geographical distribution and hosts recorded for O. praegustator are reviewed. Biological data are summarized and discussed. Areas that need additional studies include the infection process and the effect of the parasite on its host.