香港红山茶个体内ITS多态性及物种鉴定的应用

核糖体DNA的内转录间隔区(ITS)一直被作为一种重要的分子标记,却很难用于山茶物种中。通过对1个疑似香港红山茶(Camellia hongkongensis)的样本进行ITS区域的扩增、克隆和测序,从中获得74种不同序列。研究结果表明,其ITS区域具有高度的多态性,其中76%的序列为假基因。系统发育分析显示,超过半数的假基因源自同一祖先。这些假基因在经历多次基因重复后分化成至少5个谱系,且每个谱系中的序列非常相似,这表明一些假基因不但未被剔除,反而通过快速复制事件幸存下来。由于山茶物种个体内ITS的高度多态,使用这个区域区分山茶物种可能导致错误。然而,通过比较香港红山茶中的1个种间特异性r DNA假基因,确定该样本属于香港红山茶。     

Agonistic behavior of the crayfish Euastacus armatus and Cherax destructor

The intra- and interspecific agonistic behavior of Euastacus armatus and Cherax destructor from northeastern Victoria were examined. While the agonistic patterns of E. armatus appeared similar to those shown by most crayfish, individuals of C. destructor execute an unusual, highly stylized cheliped “punch” behavior during strong interactions, along with the other behaviors seen in many species. Juvenile C. destructor exhibited gregarious behavior, tending to co-occupy burrows and being physically near each other. Tests showed that the white chelipeds which are characteristic of mature E. armatus affect the outcome of aggressive interactions. When individuals had their chelipeds whitened, they won agonistic interactions more often. This result held for both intraspecific pairings and size-matched pairings with individuals of C. destructor. Individuals of C. destructor won the majority of size-matched pairings with non-whitened individuals of E. armatus.     

Relative effects of elevated grazing pressure and competition from a red algal turf on two post-settlement stages of Fucusevanescens C. Ag.

In Nova Scotia, Canada, the lower shore of wave-exposed and semi-sheltered portions of the coast is dominated by a dense turf of the red alga Chondrus crispus C. Ag. The mid shore is dominated by three species of rockweed belonging to the genus Fucus, which are also physiologically competent in the low zone, but may be inhibited by pre-emptive competitive exclusion by red algal turf and/or increased grazing pressure from abundant mesoherbivores. A grazer assay showed that herbivore pressure is >50% higher in the Chondrus zone than in the rockweed zone. Fucus can colonize the low shore only through microrecruits which develop from planktonic zygotes. A main objective of this study was to test the hypothesis that early post-settlement stages represent a critical phase for successful recruitment. We, therefore, tested the relative effects of competitive pressure from Chondrus and grazing on small (2 mm) and larger (6 cm) Fucus evanescens plants in a three-way factorial experiment. Red algal turf and grazers independently depressed F. evanescens growth, but only a combination of factors resulted in a significant weight loss in the rockweeds. The effect size of grazing was more than double that of competition from the turf. Small and larger individuals of F. evanescens were equally affected by grazing and competition. The results showed that colonization by rockweeds may only occur where there are gaps in the Chondrus canopy. We hypothesized that grazer effects may decrease with increasing gap size. However, a controlled experiment showed no differences in Fucus recruitment among the range of naturally occurring gap sizes. That is, larger gaps do not promote rockweed recruitment. In concordance with this observation, we found that grazer abundances were similar among gap sizes. Chondrus was shown to be highly resistant to intense physical and herbivore-induced disturbance. This combination ensures the persistence of a dense canopy which largely excludes rockweed recruitment from zygotes. Competitive dominance of Chondrus on the low shore is not obviously related to individual growth rates or canopy height. A positive correlation between growth rate and competitive ability may be expressed only in morphologically similar species which are likely to compete as germlings.     

四种野生苔草属植物的耐寒性评价

以采自泰山的白颖苔草、披针叶苔草、青绿苔草和低矮苔草为材料,观察越冬期间田间适应性并测定低温胁迫下抗寒相关的生理指标,计算半致死温度(LT₅₀),利用模糊隶属函数法对耐寒性进行综合评价.结果表明: 4种野生苔草属植物均能安全越冬,且翌春恢复生长良好,年绿期达到260～310 d,越冬期间枯叶率为12%～95%;LT₅₀为-18.65～-11.74 ℃.随着低温胁迫的加剧,4种苔草的丙二醛(MDA)含量、游离脯氨酸(Pro)和可溶性蛋白含量总体呈先上升后下降的趋势,可溶性糖含量呈上升趋势.除披针叶苔草表现为整体呈下降趋势外,其他3种苔草的超氧化物歧化酶(SOD)活性均呈先上升后下降的趋势.耐寒性相对较弱的白颖苔草较早地积累MDA、Pro和可溶性糖.可溶性蛋白含量在低温处理后期达到最大值,且苔草的耐寒性越强其峰值越小.在低温处理初期披针叶苔草SOD活性显著高于其他3种苔草.4种苔草属植物的耐寒性强弱为:披针叶苔草>青绿苔草>低矮苔草>白颖苔草.     

Monogenea of Arabian Gulf fishes. 1. Descriptions of three Capsala spp. (Capsalidae) including Capsala naffari n. sp. infecting mackerel tuna Euthynnus affinis from coasts of Emirates

Three species of the genus Capsala including Capsala naffari n. sp., C. neothunni (Yamaguti, 1968) and C. nozawae (Goto, 1894) are recorded and described from the buccal cavity of mackerel tuna Euthynnus affinis caught from Emirate coasts. Capsala naffari can be differentiated by its lateral spiniform teeth, which extend posteriorly, small measurements compared with the closely resembled C. gotoi and relatively large testes. This is the first record of the genus Capsala from Arabian Gulf fishes and E. affinis is a new host record.     

Phylogenetic relationships within Pyrenodesmia sensu lato and the role of pigments in its taxonomic interpretation

Most lichens of the family Teloschistaceae (Ascomycota) produce yellow-orange-red anthraquinone pigments. However, the genus Pyrenodesmia encompasses species in which anthraquinones are absent and replaced by a gray pigment Sedifolia-gray. It was shown recently that these species are related to taxa with both anthraquinones and Sedifolia-gray (Caloplaca xerica group, C. haematites group, and C. cretensis) and to species with a brown pigment instead of both anthraquinones and Sedifolia-gray (C. demissa, C. obscurella, and C. reptans). Nevertheless, relationships between mentioned anthraquinone-containing and anthraquinone-lacking species remained unclear. In total, 8 DNA loci from 41 species were used here to resolve these uncertainties. We concluded that C. demissa, C. obscurella, and C. reptans are rather distant from the core of Pyrenodesmia, and we place them outside of Pyrenodesmia sensu lato. Within Pyrenodesmia sensu lato, three lineages were revealed and recognized on a generic level: the genus Pyrenodesmia sensu stricto (21 species), the genus Kuettlingeria (14 species), which is resurrected here, and the genus Sanguineodiscus (4 species), which is newly described here. The genus Pyrenodesmia includes taxa that never contain anthraquinones, but Sedifolia-gray. It matches with the former C. variabilis group. Taxa of the genera Kuettlingeria and Sanguineodiscus have anthraquinones in their apothecia and Sedifolia-gray in their thalli. The genus Kuettlingeria includes the former C. xerica group plus C. cretensis and C. diphyodes. The genus Sanguineodiscus includes the former C. haematites group and C. bicolor. The identity of Kuettlingeria (Caloplaca) diphyodes was clarified and the name Pyrenodesmia helygeoides was resurrected. Twenty-four new combinations were proposed.     

Cryptococcus zeae, a new yeast species associated with Zea mays

A new yeast, Cryptococcus zeae (type strain HB 1207^T) is described. Six strains were isolated from corn and pests of corn in Austria. Microsatellite-primed polymerase chain reaction (MSP-PCR) fingerprints showed that the strains are members of the same species. Phylogenetical analyses of domains D1/D2 26S rDNA and ITS 1-5,8S–ITS 2 sequences showed C. zeae to have the closest relationship to C. luteolus. The D1/D2 sequences of C. zeae fit with three Korean Cryptococcus sp. strains (AF459690, AF459691, AF459692). The new species is separable from the closest relative C. luteolus using only two physiological tests.     

秦巴山区漆树nrDNAITS和cpDNA序列分子进化特点的分析

应用PCR产物直接测序法分析漆树种群nrDNA （核糖体DNA） ITS序列和cpDNA序列（matK、rbcL、psbA-trnH）的碱基差异,初步研究两套植物基因组的变异速率。结果表明：nrDNA ITS序列共有518 bp,有变异位点15处,变异位点百分率为2.9%,（G+C）含量为61.8%。cpDNA序列合并后长度1 907 bp,有变异位点20处,变异位点百分率为1.05%,（G+C）含量为36.1%。通过对ITS序列核糖型（Ribotype）和叶绿体序列单倍型（Haploype）进行分析发现,秦巴山区漆树区域性分布明显,不同区域拥有自己独特的单倍型,漆树居群历史近期没有扩张。nrDNA ITS序列较叶绿体序列进化较快,变异速率较快。nrDNA ITS序列及叶绿体matK、psbA-trnH适合漆树的亲缘地理学研究。     

锁阳ITS序列遗传多样性分析

为阐明锁阳(Cynomorium songaricum)的遗传结构与遗传多样性, 以甘肃省河西走廊地区及青海省共18个居群的188个锁阳个体为研究对象, 利用现代分子生物学技术, 采用序列分析方法从核-质基因方面对遗传结构进行了分析。结果显示, 锁阳ITS序列总长度为687 bp, 含有7个变异位点, 定义9个单倍型, 整体单倍型多态性H_d=0.294 20, 核苷酸多样性π=0.000 49。在整个单倍型网络中介图中, 单倍型H1位于中心位置, 并在所有的居群中均有分布, 为核心的古老单倍型。分子方差分析结果显示, 锁阳种群变异主要来源于种群内。根据ITS序列得到的群体间遗传分化系数以及Mantel检验结果, 锁阳种群间的遗传距离与地理距离之间不存在相关性, 表明现存的锁阳居群是相对近期发生生境片段化的产物。中性检验结果表明, 锁阳拒绝中性进化, 群体历经扩张或者基因座位受到负选择作用, 其中性零假说不能被排除。该研究为锁阳的系统分类、资源鉴定以及保护措施的制定提供了分子证据。     

A molecular analysis of relationships and biogeography within a species complex of Holarctic fish (genus Osmerus)

Episodes of trans-Arctic faunal exchange and isolation between the north Pacific and Atlantic ocean basins have been implicated as important historic geological events contributing to extant patterns of genetic diversity and structure in Holarctic faunas. We made a further test of the significance of such biogeographic events by examining mitochondrial DNA (mtDNA) restriction fragment length and cytochrome b sequence polymorphism among north Pacific and Arctic, north-western Atlantic (north-eastern North American), and north-eastern Atlantic (European) regional forms of the boreal smelt, genus Osmerus. Our analyses also assessed whether the regional forms within this ‘species complex’: (i) represent a single widely distributed and polytypic species, or is composed of three geographically distinct species, and (ii) resulted from a single split from north Pacific ancestral Osmerus or two independent Pacific-Atlantic divergences. MtDNA sequence divergence estimates among forms ranged from 5.6–8.9% and from 6.1–8.5% based on restriction fragment and 300 base pairs of cytochrome b sequencing, respectively. Divergence within forms averaged less than 0.5% for fragment analysis and no differences were detected from sequence analysis. Provisional dating of lineage separations in Osmerus based on our sequence divergence estimates suggested a mid-Pliocene to early Pleistocene time frame for diversification among the forms. These estimated lineage separation dates support the idea that geological events in ‘Beringia’ and the surrounding trans-Arctic area (e.g. opening of the Bering Seaway, Pleistocene glacial advances), occurring over a similar time frame, have influenced radiation in Osmerus. Phenetic and parsimony analyses of the sequence divergence estimates and of sequence polymorphisms suggested that the north Pacific/Arctic form and the northwestern Atlantic form shared a common ancestor more recently than either has with the north-eastern Atlantic form, thus supporting the hypothesis that the species complex has arisen from two independent Pacific-Atlantic divergences probably beginning during the mid-Pliocene.     

多基因联合揭示海南鲌的遗传结构与遗传多样性

海南鲌(Culter recurviceps)是我国华南地区重要经济鱼类, 由于受到近些年水利开发、过度捕捞、环境污染等诸多因素的影响, 其资源量快速下降, 亟需得到更多的关注和保护。为保护和合理开发海南鲌种质资源, 本研究采集了华南地区23个地理群体207尾海南鲌样本, 测定了2个线粒体基因(Cytb和ND2)并从Barcode of Life Data System数据库获得相对应线粒体COI基因, 结合多种分析方法(系统发育分析、分化时间估算、单倍型网状图、群体遗传分析和Mantel检验)对海南鲌的遗传结构和遗传多样性展开研究。系统发育分析和单倍型网状图表明华南地区海南鲌群体被分成3个谱系(I、II和III), 其中谱系I和III由珠江的群体组成, 谱系II由海南岛的群体组成。分化时间估算发现3个谱系之间的分化时间介于0.028-0.251 Ma之间, 表明华南地区更新世气候变化可能是造成海南鲌谱系分化的重要原因。群体遗传分析发现海南鲌群体之间存在极显著的遗传分化(F_ST = 0.511, P < 0.001), 并且符合距离隔离模式(R = 0.348, P = 0.0010)。群体动态历史分析表明, 海南鲌群体可能在0.010-0.025 Ma经历了群体扩张, 表明更新世的气候波动也影响了海南鲌的群体大小和分布。综上所述, 海南鲌群体由3个谱系组成, 更新世气候变化是导致3个谱系分化和影响海南鲌群体动态历史的重要因素。此外, 海南鲌群体之间的遗传分化也可能受到了空间距离的影响。     

Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes)

The Teloschistaceae is a widespread family with considerable morphological and ecological heterogeneity across genera and species groups. In order to provide a comprehensive molecular phylogeny for this family, phylogenetic analyses were carried out on sequences from the nuclear ribosomal ITS region obtained from 114 individuals that represent virtually all main lineages of Teloschistaceae. Our study confirmed the polyphyly of Caloplaca, Fulgensia and Xanthoria, and revealed that Teloschistes is probably non-monophyletic. We also confirm here that species traditionally included in Caloplaca subgenus Gasparrinia do not form a monophyletic entity. Caloplaca aurantia, C. carphinea and C. saxicola s. str. groups were recovered as monophyletic. The subgenera Caloplaca and Pyrenodesmia were also polyphyletic. In the subgenus Caloplaca, the traditionally recognized C. cerina group was recovered as monophyletic. Because this study is based solely on ITS, to maximize taxon sampling, the inclusion of phylogenetic signal from ambiguously aligned regions in MP (recoded INAASE and arc characters) resulted in the most highly supported phylogenetic reconstruction, compared with Bayesian inference restricted to alignable sites.     

西北太平洋亚热带海域浮游动物种类组成与分布

为了解西北太平洋亚热带海域浮游动物群落结构,根据2019年3月"淞航号"调查船在西北太平洋(28°--35° N,147°--154° E)44个站点进行渔业资源调查期间采集的浮游动物样本,分析了浮游动物的种类组成与分布.结果 表明:该海域共鉴定出浮游动物456种(含浮游幼体和未定种),属于14个类群8个门类,其中桡足...     

Evolution of the 5.8S nrDNA gene and internal transcribed spacers in Carapichea ipecacuanha (Rubiaceae) within a phylogeographic context

Nuclear ribosomal DNA (nrDNA) constitutes a multicopy gene family that is used widely to test evolutionary hypotheses across a broad range of organisms. It is presumed that, as a result of concerted evolution, tandem nrDNA repeats are homogeneous within species and different between species. We sampled 77 specimens of a disjunct species (Carapichea ipecacuanha) from throughout its three geographic ranges and obtained 266 nrDNA sequences, of which 26 were obtained by direct sequencing and 240 by cloning of PCR products. Complementary sequence analyses, which included analyses of secondary structure stability, the pattern of base substitutions, GC content, and the presence of conserved motifs, were used to characterize the internal transcribed spacer (ITS) region (ITS1-5.8S nrDNA-ITS2). Our results showed that concerted evolution of the ITS region was incomplete in C. ipecacuanha, particularly in the Atlantic range. In the highly polymorphic populations of the Atlantic range, intraindividual variation was observed and involved 56 functional paralogs and 15 pseudogenes from two highly divergent ribogroups. The Amazonian range (with 12 functional paralogs) and the Central-American range (with five functional paralogs) were genetically depauperate and exhibited no pseudogenes. In the two latter ranges, almost complete homogenization of the ITS sequences had occurred. We argue that it is important to consider past evolutionary history when making inferences about the efficiency with which concerted evolution homogenizes tandem nrDNA repeats a single sequence.     

A yeast clade near Candida kruisii uncovered: nine novel Candida species associated with basidioma-feeding beetles

Yeasts similar to Candida kruisii were isolated repeatedly from the digestive tracts of basidioma-feeding beetles, especially nitidulids inhabiting and feeding on a variety of agarics in the southeastern USA and Barro Colorado Island, Panama. Based on the identical sequences of the D1/D2 domains of the LSU rRNA gene (rDNA) and host beetle information, the isolates were grouped into 19 genotypes which varied from C. kruisii by up to 38 nucleotide differences in the D1/D2 region. Phylogenetic analysis of rDNA sequences and phenotypic traits placed the isolates in C. kruisii and in nine undescribed taxa. The new species and type strains are designated as Candida pallodes (NRRL Y-27653^T), C. tritomae (NRRL Y-27650^T), C. panamensis (NRRL Y-27657^T), C. lycoperdinae (NRRL Y-27658^T), C. atbi (NRRL Y-27651^T), C. barrocoloradensis (NRRL Y-27934^T), C. aglyptinia (NRRL Y-27935^T), C. stri (NRRL Y-48063^T), and C. gatunensis (NRRL Y-48064^T). A phylogeny based on analysis of a combined database of sequences of SSU and LSU rDNA and the ITS region showed that the nine new species formed a novel sister clade to C. kruisii that was strongly supported by bootstrap analysis. Candida pallodes, C. tritomae, C. panamensis, and C. lycoperdinae formed one subclade, while C. atbi, C. barrocoloradensis, C. aglyptinia, C. stri, and C. gatunensis formed a second distinct subclade within the larger clade. Candida pallodes and C. atbi showed a strong host specificity to beetle species in the genus Pallodes (Coleoptera: Nitidulidae) collected from a variety of agarics. On the other hand, C. panamensis, C. tritomae, and C. lycoperdinae were associated with several unrelated beetles in Erotylidae, Scarabaeidae, Tenebrionidae, and Curculionidae as well as Lycoperdina ferruginea (Nitidulidae). Candida pallodes, C. tritomae, C. lycoperdinae, and C. atbi have been isolated repeatedly in the USA, while the other five new species have been found only at Barro Colorado Island, Panama.     

Species of Colletotrichum on Agavaceae

Species of Colletotrichum cause diseases on a wide range of hosts, frequently infecting plants in the Agavaceae (monocotyledons: Liliales). Three species of Colletotrichum restricted to the Agavaceae were detected through morphological studies of specimens and molecular sequence analyses of the LSU of the nu-rDNA and the ITS region of the nu-rDNA from cultures. Colletotrichum agaves on Agave is fully described and illustrated. Colletotrichum dracaenophilum is described as a new species for isolates having long conidia and occurring on Dracaena sanderiana from China. Colletotrichum phormii and Glomerella phormii are determined to be the correct scientific names for the asexual and sexual states, respectively, of a species commonly referred to as C. rhodocyclum and G. phacidiomorpha occurring mainly on Phormium. In addition, C. gloeosporioides and C. boninense were isolated from plants in the Agavaceae. All species of Colletotrichum described on Agavaceae were evaluated based on type specimens. A key to the five species of Colletotrichum on Agavaceae is included. This paper includes one new species, Colletotrichum dracaenophilum, and three new combinations, Colletotrichum phormii, Glomerella phormii, and Phaeosphaeriopsis phacidiomorpha.     

不同海拔的三种杓兰属植物与菌根真菌群落组成相关性

本研究采集了四川黄龙沟沿海拔梯度3 170-3 400m上4个不同杓兰居群中3种杓兰植物根,利用克隆文库方法获得菌根真菌ITS序列,研究同一栖息地（黄龙沟）不同海拔梯度和不同杓兰对菌根真菌多样性和群落结构的影响。共得到18个可操作分类单元（OTU）,其中14个OTU隶属胶膜菌科Tulasnellaceae,为优势类群（99.6%）;2个OTU隶属腊壳菌科Sebacinaceae,2个OTU隶属亡革菌科Thelephoraceae。随着海拔升高,西藏杓兰菌根真菌多样性减少,而黄花杓兰和无苞杓兰没有明显变化;海拔对3种杓兰菌根真菌群落结构均无显著影响。3种杓兰之间菌根真菌群落结构差异显著且指示物种互不相同,说明在同一栖息地,杓兰对菌根真菌的偏好性显著影响其菌根真菌群落结构。这些研究结果利于了解环境变化对杓兰属植物菌根真菌区系组成的影响,为进一步探索菌根真菌与杓兰属植物的互作机制奠定基础。     

Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae.

We report the potential phylogenetic utility of DNA sequence data from the last 700 bp of a ca. 1-kb intron of the MADS-box gene pistillata from a sampling of Sphaerocardamum species and other Brassicaceae. These results are compared with nrDNA ITS and the chloroplast trnL intron for the same taxa to demonstrate the potential phylogenetic utility of this pistillata intron and to identify potential historically independent sequences for an ongoing study of relationships within Sphaerocardamum. Analyses of the DNA sequence data for Brassicaceae indicated that pairwise divergences and potentially informative characters were higher in the pistillata intron (0.6-30.8%, 284 characters) and ITS (0-24%, 94 characters) than in the chloroplast trnL intron (0-4.2%, 17 characters). A comparison of Sphaerocardamum sequences identified low divergences and numbers of informative characters for trnL intron (0-2.4%, 1 character) and nrDNA ITS (0-2.5%, 2 characters) and substantially more variation among the pistillata sequences (0.15-3.7%, 19 characters). Phylogenetic analyses of these pistillata sequences fully resolve ingroup relationships without character conflict. Results of pistillata PCR amplifications from a broader dicot sample showed that some primers may be useful in amplifying orthologous pistillata sequences. Ultimately this pistillata intron may be a valuable source of phylogenetic characters at lower taxonomic levels.     

四照花亚属的nrDNA ITS致同进化不完全

四照花亚属(Cornus subg.Syncarpea)隶属于山茱萸科山茱萸属(Cornus),我国该亚属共有5种8亚种。为探讨四照花亚属nrDNA ITS序列的致同进化不完全现象及假基因产生的可能原因,分析了该亚属4种(每种1~2个居群)共21个个体的nrDNA ITS序列。结果表明,这些类群的nrDNA ITS存在多态性,通过分析这些nrDNA ITS克隆序列的G+C含量、5.8S保守基序和二级结构最小自由能,推测其可能存在假基因。系统发育研究结果显示所有nrDNA ITS序列分成5个分支,同一个体的不同拷贝被分别置于两个甚至多个分支中,且不同分支显示了不同种间关系。四照花亚属物种个体内部存在nrDNA ITS不完全致同进化,可能归咎于不完全的世系分选(incomplete lineage sorting)、种间杂交或多倍化等进化事件,从而导致基因组内nrITS区序列出现多态性,同时也导致难以通过外部形态来划分亚属内种间界限。     

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.