球状绿藻的隐性生物多样性及其分类学进展

球状绿藻主要指绿藻门中多为单细胞, 形状为球形、近球形, 或由球形衍生出来的其他形状的藻类。球状绿藻分布广泛, 遍布全球, 生活于淡水、海水和亚气生等生境中, 其相似的简单形态下隐藏着复杂的物种多样性。球状绿藻分类学上主要位于绿藻门的两纲四目及其一些独立支系的类群。球状绿藻分类学正由传统的基于形态特征向基于分子信息的复合分类方法转变。球状绿藻隐性的物种多样性涉及约40属, 其中15属是依据新标本材料而建立的新属, 12个属是依据新证据建立的新组合。本文重点介绍了1998年以后在共球藻纲和绿藻纲中新发现和命名的单细胞球状绿藻, 介绍了它们的形态特征、分类学迁移及理由, 特别对常见的小球藻属和栅藻属的分类学概念变迁作了详细介绍, 对一些尚没有中文名的拉丁学名给出了中文命名。另外, 本文讨论了基于DNA的分类学方法在球状绿藻分类学中的应用, 目前系统发育位置的不同已经成为球状绿藻分类的主要依据。目前球状绿藻分类面临的问题是大多分类位置未用分子系统发育方法的验证。 未来, 球状绿藻分类学家应用系统发育研究结合形态学研究探索单细胞球状绿藻的生物多样性。     

Convergent evolution of shell shape in freshwater limpets: the African genus Burnupia

Convergent evolution of shell shape is a well known phenomenon in gastropods that has caused much confusion in taxonomic and systematic studies. A paradigm is the patelliform shell shape in several taxa of the order Basommatophora. Historically, most freshwater limpets were assigned to the family Ancylidae. Based on anatomical data, some taxa were subsequently moved to different families. However, there are still doubts about the monophyly of the remaining ancylids. This is also true for the African limpets and particularly for species of the genus Burnupia Walker, 1912. In the present paper, two independent molecular markers (COI, 18S rRNA) are used to (a) infer the position of Burnupia within the Basommatophora and (b) to test whether the shell shape of Burnupia evolved independently. Bayesian and maximum likelihood analyses of 12 genera of limnic Basommatophora indicate that Burnupia not only appears to be distinct from the Ancylidae, but also from all other representatives of the superfamily Planorboidea studied here. Based on a generally well-supported phylogeny and preliminary anatomical data, it is concluded that patelliform shell shapes evolved at least three times in the taxa studied here and that the shell shape of Burnupia represents another case of convergent evolution. Previously proposed functional and evolutionary scenarios for the evolution of patelliform shell and their relevance for freshwater limpets are discussed.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 577–586.     

Physiological studies on a coccoid marine blue-green alga (Cyanobacterium)

A coccoid marine cyanobacterium assignable to the genus Synechococcus has been isolated in axenic culture. This organism appears not to be a nitrogen fixer as it failed to reduce acetylene under either aerobic or anaerobic conditions. The specific growth rate was determined at six irradiance levels (5-, 15-, 30-, 50-, 100- and 150 μmol m^-2 s^-1) under continuous illumination and controlled temperature (20°C). The growth vs. incident irradiance curve and estimated light energy absorbed showed that growth saturates at a relatively low photon flux density and photosynthesis has a low compensation point. It attained its maximum division rate (1·4 divisions d^-1 = generation time, 18 h) at 30 μmol m^-2 s^-1. Such a low light-requiring planktonic cyanobacterium may be of importance in terms of both biomass and productivity towards the bottom of the photic zone.     

Pinguiococcus pyrenoidosus gen. et sp. nov. (Pinguiophyceae), a new marine coccoid alga

A coccoid marine alga, collected from an aquaculture tank and maintained in culture as CCMP1144, was examined using light and electron microscopy. Young, rapidly growing cells were mostly spherical in shape, approximately 4–6 μm in diameter. Older cells often produced protrusions and pseudopodia‐like extensions, giving cells an amoeboid‐like appearance, but no amoeboid movement was observed and the pseudopodia‐like extensions exhibited no active movement. The single chloroplast had a typical photosynthetic stramenopile ultrastructure. A large stalked pyrenoid was easily observed by light microscopy. Ultrastructurally, the granular portion of the pyrenoid was divided into sections by a penetrating chloroplast envelope. A mitochondrion was often, but not always, adjacent to the pyrenoid, and in some cases the mitochondrion formed a ‘cap’ over the protruding pyrenoid. The Golgi cisternae were (when viewed in cross‐section) curved toward the nucleus. A peripheral network of anastomosing tube‐like membranes was located immediately beneath the plasmalemma. Two centrioles were located adjacent to the nuclear envelope. Lipid‐like and electron transparent vacuoles were present. Based on this investigation and data published elsewhere (large percentage of eicosapentaenoic acid, 18S rRNA and rbcL genes), this alga was described as Pinguiococcus pyrenoidosus gen. et sp. nov.     

双壳纲贝类18S rRNA基因序列变异及系统发生

双壳纲贝类栖息于环境多变的海域,是一个形态学和生态学都具有多样性的类群,清晰而可靠的进化关系对于养殖与相关种类的管理具重要意义。然而,目前对双壳类宏观分子系统学研究的报道较少。研究用18S rRNA基因(18S)分析了双壳类3个亚纲贝类的系统发育关系。从GenBank下载帘蛤目、海螂目、贻贝目、胡桃蛤目、蚶目、珍珠贝目6个目94个种类的18S全/部分序列107个,通过ClustalX软件进行序列比对, 用MEGA4.1软件和PHyML软件计算遗传距离, 构建系统发育树, 研究了双壳类18S变异规律及其在系统发生研究中的应用。结果显示18S有插入/缺失序列, 存在长度多态性。序列比对显示有5段约30 70bp的保守区, 4段约130 550bp的高变区。碱基组成平均为T:24.4%, C:23.6%, A:24.5%, G:27.5%。G+C含量为51.1%。在1796个比对位点中, 变异位点占31.7%, 简约信息位点占24.0%。目内科间遗传距离为0.003 0.043, 目间遗传距离为0.026 0.093。NJ树和ML树显示贻贝目、珍珠贝目、胡桃蛤目、蚶目和海螂目的缝栖蛤科先分别聚为支持率很高(BPN=94 100)的单系支, 后聚为一大支(BPN=100)。蛤蜊科与帘蛤目的其他科分离形成一置信度很高的单系支(BPN=93)。帘蛤科种类聚为置信度较低(BPN=60)的一支。海螂目、帘蛤目的种类没能完全聚到所属支系, 彼此嵌套,缝栖蛤科的种类从海螂目中分离出来。18S资料揭示帘蛤目的蛤蜊科、海螂目的缝栖蛤科已经进化为独立的支系。     

Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA

In order to study the phylogenetic relationships within the stramenopiles, and particularly among the heterokont algae, we have determined complete or nearly complete large-subunit ribosomal RNA sequences for different species of raphidophytes, phaeophytes, xanthophytes, chrysophytes, synurophytes and pinguiophytes. With the small- and large-subunit ribosomal RNA sequences of representatives for nearly all known groups of heterokont algae, phylogenetic trees were constructed from a concatenated alignment of both ribosomal RNAs, including more than 5,000 positions. By using different tree construction methods, inferred phylogenies showed phaeophytes and xanthophytes as sister taxa, as well as the pelagophytes and dictyochophytes, and the chrysophytes/synurophytes and eustigmatophytes. All these relationships are highly supported by bootstrap analysis. However, apart from these sister group relationships, very few other internodes are well resolved and most groups of heterokont algae seem to have diverged within a relatively short time frame.     

A new aerial alga, Stichococcus ampulliformis sp. nov. (Trebouxiophyceae, Chlorophyta) from Japan

A new aerial alga, Stichococcus ampulliformis S. Handa sp. nov. (Trebouxiophyceae, Chlorophyta) is described based on a clone isolated from the bark of Cephalotaxus harringtonia (Knight ex Forbes) K. Koch collected from Taishaku‐kyo Gorge, Hiroshima Prefecture, south‐west Japan. This alga was examined by light microscopy and transmission electron microscopy and subjected to molecular phylogenetic analysis. Based on its morphological features and life‐cycle, especially short filament formation, the alga was assigned to the genus Stichococcus Nägeli. However, this alga differs from other described Stichococcus species in that it reproduces by a form of ‘budding’, producing two daughter cells of different sizes. The larger cell, enclosed within the mother cell wall, soon reaches the size of a normal vegetative cell. The smaller cell is extruded and takes longer to reach full vegetative size. A phylogenetic tree constructed using 18S rRNA sequences indicated that, within the Trebouxiophyceae, S. ampulliformis is closely related to S. bacillaris Nägeli and some species of Prasiola Meneghini.     

Kalinella bambusicola gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel coccoid Chlorella-like subaerial alga from Southeast Asia

The traditional green algal genus Chlorella , which comprised coccoid algae surrounded by a smooth cell wall and reproducing solely by autosporulation, has proved to be polyphyletic and extremely diverse in phylogenetic terms. We studied a new subaerial Chlorella -like strain CAUP H7901 and morphological, ultrastructural, and molecular phylogenetic investigations indicated that it represents a new lineage of the trebouxiophycean Watanabea clade, dissimilar from other members of this group. The alga has globular coccoid cells with a single parietal pyrenoid-bearing chloroplast. The pyrenoid is transected by multiple radial thylakoid bands. The alga reproduces exclusively by means of asexual autospores of unequal size. In 18S rDNA sequence phylogenies, it was nested within the Watanabea clade close to lineages containing Chlorella saccharophila , Chlorella luteoviridis , Heveochlorella hainangensis , and two uncharacterized strains, but alternative positions within the Watanabea clade could not be rejected by an approximately unbiased (AU) test. Here we describe this organism as a new genus and species Kalinella bambusicola gen. et sp. nov. Furthermore, we describe Heterochlorella gen. nov. to accommodate a species previously referred to as Chlorella luteoviridis .     

基于18S rRNA基因序列的直翅目主要类群系统发育关系研究

基于78种直翅目昆虫的18S rRNA基因全序列构建了直翅目各主要类群间的系统发育关系。本研究的结果支持直翅目的单系性,但不支持蝗亚目和螽亚目各自的单系性;直翅目下除蜢总科和蝗总科外各总科的划分多数与Otte系统相一致;蜢总科的单系性得不到支持;蝗总科的剑角蝗科、斑腿蝗科、斑翅蝗科、网翅蝗科和槌角蝗科5科均不是单系群,各物种间的遗传距离差异不大,应合并为一科,即蝗科;本研究支持将Otte系统中蚱总科和螽蟖总科下各亚科级阶元提升为科级阶元;18S rRNA基因全序列可以作为划分科级阶元的工具,当位于同一分支上互成姐妹群的类群间的遗传距离超过1%时,这几个类群属于不同的科;但由于其在进化上的保守性,18S rRNA基因只能用于纲目等高级阶元间关系的研究,而由其获得的总科以下阶元间的关系并不可靠。     

New phagotrophic euglenoid species (new genus Decastava; Scytomonas saepesedens; Entosiphon oblongum), Hsp90 introns,and putative euglenoid Hsp90 pre-mRNA insertional editing

We describe three new phagotrophic euglenoid species by light microscopy and 18S rDNA and Hsp90 sequencing: Scytomonas saepesedens; Decastava edaphica; Entosiphon oblongum. We studied Scytomonas and Decastava ultrastructure. Scytomonas saepesedens feeds when sessile with actively beating cilium, and has five pellicular strips with flush joints and Calycimonas-like microtubule-supported cytopharynx. Decastava, sister to Keelungia forming new clade Decastavida on 18S rDNA trees, has 10 broad strips with cusp-like joints, not bifurcate ridges like Ploeotia and Serpenomonas (phylogenetically and cytologically distinct genera), and Serpenomonas-like feeding apparatus (8–9 unreinforced microtubule pairs loop from dorsal jaw support to cytostome). Hsp90 and 18S rDNA trees group Scytomonas with Petalomonas and show Entosiphon as the earliest euglenoid branch. Basal euglenoids have rigid longitudinal strips; derived clade Spirocuta has spiral often slideable strips. Decastava Hsp90 genes have introns. Decastava/Entosiphon Hsp90 frameshifts imply insertional RNA editing. Petalomonas is too heterogeneous in pellicle structure for one genus; we retain Scytomonas (sometimes lumped with it) and segregate four former Petalomonas as new genus Biundula with pellicle cross section showing 2–8 smooth undulations and typified by Biundula (=Petalomonas) sphagnophila comb. n. Our taxon-rich site-heterogeneous rDNA trees confirm that Heteronema is excessively heterogeneous; therefore we establish new genus Teloprocta for Heteronema scaphurum.     

Relationship of the genusCordyceps and related genera, based on parsimony and spectral analysis of partial 18S and 28S ribosomal gene sequences

A molecular phylogenetic study of selected species of three sub-genera of the genusCordyceps was undertaken, along with representatives of the generaAkanthomyces, Aschersonia, Gibellula, Hymenostilbe, Hypocrella, Nomuraea andTorrubiella, to examine their inter-relationship. Phylogenetic analyses of the data indicated that the Clavicipitaceae form a monophyletic group within the Hypocreales, while the monophyly ofCordyceps was not supported. Four clades were identified:Cor. militaris/Cor. pseudomilitaris; Cor. iranginesis/Cor. sphecocephala; Cor. intermedia/Cor. capitata; andCor. cylindrica/Nom. atypicola. The sub-genusNeocordyceps was shown to be monophyletic while the sub-generaEucordyceps andOphiocordyceps do not form monophyletic groups. The genusHypocrella appeared monophyletic, and radiated after the formation of the generaCordyceps, andTorrubiella. Akanthomyces arachnophilus andGi. pulchra, anamorphs ofTorrubiella species, formed a distinct clade that was separate from one formed by the scale insect pathogens,To. luteorostrata andPaecilomyces cinnamomeus, suggesting that this genus may be polyphyletic.     

DNA barcodes for marine fungal identification and discovery

We employed DNA barcodes for identification of fungal species in marine sediments. Sediments were collected seasonally along the Southeast coast of India from which a culturable fungal library was constructed. All cultured species were morphologically documented using microscopical analysis. A maximum population density of 19.3 × 10³ CFU/g was recorded in monsoon and minimum of 3 × 10³ CFU/g in premonsoon season. Two-way analysis of variance suggests that the fungal community varied significantly between the seasons (F = 9.543, P < 0.001) and at various depths sampled (F = 4.655, P < 0.05). In total, 54 fungal species belonging to 13 different families were documented and all species were sequenced for internal transcribed spacer genes. Each species was represented by at least two specimens constituting a total of 171 specimens for DNA barcoding. Twelve species of a marine fungi were sequenced for the first time. Branching patterns of phylogenetic tree strongly supported the sequence variations within and between all species barcoded. Based on the pairwise distance model we suggest barcode gaps of 15 %, 21 %, 30 %, 35 % and 51 % for genera, family, order, class and phyla respectively.     

Phylogenetic analyses of various euglenoid taxa (euglenozoa) based on 18s rdna sequence data

18S rRNA genes (SSU rDNA) of five newly sequenced species were used as molecular markers to infer phylogenetic relationships within the euglenoids. Two members of the order Euglenales ( Lepocinclis ovata Playfair , Phacus similis Christen), two of the order Eutreptiales ( Distigma proteus Ehrenberg, , D. curvata Pringsheim) and Gyropaigne lefévrei Bourelly et Georges of the order Rhabdomonadales were used in parsimony, maximum likelihood, and distance analyses. All trees derived from SSU rRNA data strongly supported the monophyletic origin of the Euglenozoa, with kinetoplastids as sister clade to the euglenoids and Petalomonas cantuscygni Cann et Pennick diverging at the base of the monophyletic euglenoid lineage. The data also supported the theory that phagotrophic euglenoids arose prior to osmotrophs and phototrophs. A lineage of Peranema trichophorum Ehrenberg and all sequenced Euglenales formed a sister clade to the osmotrophs. This suggests that the evolution of phototrophy within the euglenoids radiated from a single event.     

苔藓动物18S rRNA基因的分子系统发生初探

本文对我国沿海较为常见的8种唇口目苔藓动物的18SrRNA基因进行了PCR扩增和序列测定。结合已知的其它苔藓动物（包括内肛动物和外肛动物）以及腕足动物和帚虫的相应序列,运用分子系统学方法,研究苔藓动物门的系统发生关系,结果表明,外肛动物和内肛动物构成苔藓动物分子系统树中的二大平行支;本文测定的大室膜孔苔虫与Giribet等测定的膜孔苔虫在系统树中的位置间隔较远。结果也支持外肛动物包含被唇纲和裸唇纲两大类群的形态划分,而关于裸唇纲特别是唇口目内部的系统发生关系。分子数据的分析结果和形态分类之间的分歧有待于进一步研究。     

Lunachloris lukesovae gen. et sp. nov. (Trebouxiophyceae,Chlorophyta), a novel coccoid green alga isolated from soil in South Bohemia,Czech Republic

Culture collections of microorganisms can still hold undiscovered biodiversity; with molecular techniques, considerable progress has been made in characterizing microalgae which were isolated in the past and misidentified due to a lack of morphological features. However, many strains are still awaiting taxonomic reassessment. Here we analysed the phylogenetic position, morphology and ultrastructure of the strain CCALA 307 previously identified as Coccomyxa cf. gloeobotrydiformis Reysigl isolated in 1987 from field soil in South Bohemia, Czech Republic. Molecular phylogenetic analyses based on SSU rDNA and the plastid rbcL gene revealed that the strain CCALA 307 formed a distinct sister lineage to Neocystis and Prasiola clades within the Trebouxiophyceae. We describe this strain as a new genus and species, Lunachloris lukesovae. Multiple conserved nucleotide positions identified in the secondary structures of the highly variable ITS2 rDNA barcoding marker provide further evidence of the phylogenetic position of Lunachloris. Minute vegetative cells of this newly recognized species are spherical or ellipsoid, with a single parietal chloroplast without a pyrenoid. Asexually, it reproduces by the formation of 2–6 autospores. Since the majority of recent attention has been paid to algae from the tropics or extreme habitats, the biodiversity of terrestrial microalgae in temperate regions is still notably unexplored and even a ‘common’ habitat like agricultural soil can contain new, as yet unknown species. Moreover, this study emphasizes the importance of culture collections of microorganisms even in the era of culture-independent biodiversity research, because they may harbour novel and undescribed organisms as well as preserving strains for future studies.     

Phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from three rDNA sequences: implications for morphological evolution and superfamily classification

The infraorder Thalassinidea is a group of cryptic marine burrowing decapods of which the higher taxonomy is often contentious. The present analysis attempts to reconstruct phylogenetic relationship among 12 of the 13 currently recognized families using partial nuclear 18S, 28S rDNA and mitochondrial 16S rDNA sequences. The infraorder is divided into two distinct clades, with the first clade consisting of Thalassinidae, Laomediidae, Axianassidae and Upogebiidae, and the second clade including Axiidae, Calocarididae, Eiconaxiidae, Callianassidae, Ctenochelidae, Micheleidae, Strahlaxiidae and Callianideidae. Within the first clade, the Upogebiidae is the basal family. The Axianassidae shows low affinity to other laomediid genera indicating that it is a valid family. The interfamilial relationships are less well resolved in the second clade. The Axiidae is paraphyletic with respect to Calocarididae and Eiconaxiidae. Thus, the status of these two latter families is not supported if the currently defined Axiidae is maintained. All three families appear to be basal in the thalassinidean clade. The Micheleidae is closely related to the Callianideidae and they form a sister group to the Strahlaxiidae. The monophyletic Callianassidae aligns with the Micheleidae + Callianideidae + Strahlaxiidae clade. The relationship among the Axiidae + Calocarididae + Eiconaxiidae clade, Callianassidae + Micheleidae + Callianideidae + Strahlaxiidae clade and the Ctenochelidae cannot be resolved which might be due to a rapid radiation of the three lineages. Our results do not support the generally used classification scheme of Thalassinidea and suggest that the infraorder might be divided into two superfamilies instead of three as suggested based on larval morphology, second pereiopod morphology in adults and gastric mill structure. The two superfamilies are Thalassinoidea (i.e. Thalassinidae, Laomediidae, Upogebiidae and Axianassidae) and Callianassoidea (i.e. Axioidea + Callianassoidea, as defined in Martin and Davis (2001) but excluding Laomediidae and Upogebiidae). It also appears that gill‐cleaning adaptations are important in thalassinidean evolution while the presence of linea thalassinica is a result of parallel evolution.     

基于18S rRNA基因序列分析唇口目苔藓动物主要类群的系统发生关系

对隶属于3亚目、5次目、20科、23属共25个种类的唇口目(裸唇纲)苔藓虫18S rRNA基因部分序列进行了序列测定.结合从GenBank中获得的该类群其它7个种类的18S rRNA基因同源序列,以序列分析软件对其序列组成和变异进行了比较分析;同时,以羽苔虫(被唇纲)和管孔苔虫(窄唇纲)为外类群,以邻接法和最大简约法重建了它们的系统发生树,分析了该目主要类群系统发生关系.序列分析结果显示:经比对后序列长度为884 bp,其中保守位点241个,可变位点643个,简约信息位点357个;A,T,C和G 4碱基平均含量分别为23.8%、22.8%、24.4%和28.9%.分子系统树表明:本研究所有有囊类构成1个单系群,其中檐胞次目的几种苔虫位于皮壳次目内部;无囊类形成1个多系群,其中的亚目级(新唇口亚目)和次目级分类阶元(枝室次目、假软壁次目和隐壁次目)也都为多系发生,这些结果与前人的分子系统学研究结果大体一致,而与传统的形态分类体系间存在明显的冲突.     

软体动物系统发育研究进展

软体动物是动物界仅次于节肢动物的第二大门类.长期以来,其系统位置及其系统发育关系一直争议颇多.简述了软体动物的分类及系统学研究概况,重点介绍了近年来18SrRNA和28SrRNA基因的分子系统学研究进展.同时就软体动物系统学研究中存在的问题和前景作了分析和展望.     

Phylogenetic relationships within the Mysidae (Crustacea, Peracarida, Mysida) based on nuclear 18S ribosomal RNA sequences

Species of the order Mysida (Crustacea, Peracarida) are shrimp-like animals that occur in vast numbers in coastal regions of the world. The order Mysida comprises 1,053 species and 165 genera. The present study covers 25 species of the well-defined Mysidae, the most speciose family within the order Mysida. 18S rRNA sequence analysis confirms that the subfamily Siriellinae is monophyletic. On the other hand the subfamily Gastrosaccinae is paraphyletic and the subfamily Mysinae, represented in this study by the tribes Mysini and Leptomysini, consistently resolves into three independent clades, and hence is clearly not monophyletic. The tribe Mysini is not monophyletic either, and forms two clades of which one appears to be closely related to the Leptomysini. Our results are concordant with a number of morphological differences urging a taxonomic revision of the Mysidae.