DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus

Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p‐distance, 0.115–0.235; k2p, 0.128–0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity.     

Molecular taxonomy of members of the Anopheles hyrcanus group from Thailand and Indonesia

During studies of malaria vectors in Indonesia and Thailand, several specimens identified by field staff as members of the Anopheles barbirostris group (Diptera: Culicidae) were found to belong to the Anopheles hyrcanus group, as shown by marked differences in the size of the nuclear rDNA second internal transcribed spacer (ITS2) between the barbirostris (~1500 bp) and hyrcanus (~600 bp) groups. Identification of the species concerned required a more detailed study of ITS2 sequences and subunit I of the mitochondrial DNA cytochrome oxidase gene (COI). A phylogenetic analysis, based on Bayesian methods, revealed that the hyrcanus group specimens comprised five distinct clades, two of which corresponded with known species, Anopheles peditaeniatus and Anopheles sinensis. The remaining specimens formed three additional clades, for which there are no similar sequences in GenBank and which cannot be linked to previously described species. The misidentification of hyrcanus group species has important implications for malaria vector control; more comprehensive studies employing gene sequences are required to clarify the number of species in the group, their distribution and vector status.     

Primary structure of histone H2A from nucleated erythrocyte of the marine worm Sipunculus nudus. Presence of two forms of H2A in the sipunculid chromatin

The complete amino acid sequence (123 residues) of histone H2A from erythrocytes of the marine worm Sipunculus nudus, has been established from data provided by automated sequence analysis of large fragments generated by V8 staphylococcal protease digestion of histone H2A and by limited hydrolysis of the protein with alpha-chymotrypsin and from structural studies of tryptic peptides of the protein. By comparison with calf homologous histone, the sipunculid histone H2A shows 6 deletions and 13 substitutions. Six of the substitutions are non-conservative. Most of the evolutionary changes are mainly observed in the basic amino-terminal and carboxy-terminal regions of the molecule, which are the primary DNA-binding sites. Few conservative point changes are observed in the central region (residues 18-118) which interacts strongly with histone H2B to form the dimer H2A-H2B. 60% of the H2A molecules were found phosphorylated on the amino-terminal residue, N-acetyl-serine. The high content of phosphorylated histone H2A in the sipunculid erythrocyte chromatin could probably be related to smaller repeat length (177 +/- 5 base pairs) of nucleosomal DNA and to nuclear inactivation and chromatin condensation.     

Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper.     

Was there a second adaptive radiation of giant tortoises in the Indian Ocean? Using mitochondrial DNA to investigate speciation and biogeography of Aldabrachelys (Reptilia,Testudinidae)

A radiation of five species of giant tortoises (Cylindraspis) existed in the southwest Indian Ocean, on the Mascarene islands, and another (of Aldabrachelys) has been postulated on small islands north of Madagascar, from where at least eight nominal species have been named and up to five have been recently recognized. Of 37 specimens of Madagascan and small-island Aldabrachelys investigated by us, 23 yielded significant portions of a 428-base-pair (bp) fragment of mitochondrial (cytochrome b and tRNA-Glu), including type material of seven nominal species (A. arnoldi, A. dussumieri, A. hololissa, A. daudinii, A. sumierei, A. ponderosa and A. gouffei). These and nearly all the remaining specimens, including 15 additional captive individuals sequenced previously, show little variation. Thirty-three exhibit no differences and the remainder diverge by only 1-4 bp (0.23-0.93%). This contrasts with more widely accepted tortoise species which show much greater inter- and intraspecific differences. The non-Madagascan material examined may therefore only represent a single species and all specimens may come from Aldabra where the common haplotype is known to occur. The present study provides no evidence against the Madagascan origin for Aldabra tortoises suggested by a previous molecular phylogenetic analysis, the direction of marine currents and phylogeography of other reptiles in the area. Ancient mitochondrial DNA from the extinct subfossil A. grandidieri of Madagascar differs at 25 sites (5.8%) from all other Aldabrachelys samples examined here.     

AGLAOTHAMNION HALLIAE COMB. NOV. AND A. COLLINSII SP. NOV. (CERAMIALES, RHODOPHYTA): RESOLUTION OF NOMENCLATURAL AND TAXONOMIC CONFUSION

Specimens from the exsiccatae Phycotheca BorealiAmericana number 698 are shown to represent two distinct species. One of them, formerly known as Callithamnion halliae, is transferred to Aglaothamnion on the basis of its uninucleate cells. The specimens exhibit distichous branching and are ecorticate. A lectotype is proposed for one of the P.B.-A. #698 specimens displaying these characters . Aglaothamnion halliae ( Collins) comb. nov. is an earlier name for Aglaothamnion westbrookiae Rueness et L'Hardy-Halos. The second species, together with specimens of P.B.-A. #1896, has radial branching and corticated axes and is described herein as a new species , Aglaothamnion collinsii. The binomial Aglaothamnion boergesenii ( Aponte et Ballantine ) L'Hardy-Halos et Rueness in Aponte, Ballantine, et J. Norris is validated. A key to the tropical and warm-temperate western Atlantic species of Aglaothamnion is presented .     

Did vicariance and adaptation drive cryptic speciation and evolution of brooding in Ophioderma longicauda (Echinodermata: Ophiuroidea), a common Atlanto‐Mediterranean ophiuroid?

Over the last decade, cryptic speciation has been discovered in an increasing number of taxa. Species complexes are useful models for the understanding of speciation processes. Motivated by the discovery of brooding specimens in the common Atlanto-Mediterranean broadcast spawning brittle star, Ophioderma longicauda, a recent study revealed the occurrence of divergent mitochondrial lineages. We analysed 218 specimens from 23 locations spread over the geographic range of the species with partial Cytochrome c Oxidase subunit I (COI) sequences. A subset of this sample was also surveyed with the internal transcribed spacer of the ribosomal DNA cluster (nuclear ITS-1). Our study revealed six highly divergent mitochondrial lineages, and the ITS-1 data confirmed that they most likely represent a species complex. Geographic ranges, abundances and genetic structures are contrasted among the putative cryptic species. Lineages in which brooding specimens have been found form a monophyletic group and are restricted to the Eastern Mediterranean basin, an oligotrophic zone. A phylogeny-trait association analysis revealed a phylogenetic signal for low 'chlorophyll a' values (our proxy for oligotrophy). An ecological shift related to the hyper oligotrophy of the Eastern Mediterranean region is therefore likely to have played a role in the evolution of brooding. This study revealed that a complex mixture of vicariance, population expansion, adaptive divergence and possibly high local diversification rates resulting from brooding has shaped the evolution of this species complex. The dating analysis showed that these events probably occurred in the Pleistocene epoch.     

ACACIA CONSTRICTA (FABACEAE: MIMOSOIDEAE) AND RELATED SPECIES FROM THE SOUTHWESTERN U.S. AND MEXICO

Vegetative, fruit, and floral characters of more than 200 herbarium specimens of Acacia constricta and closely related species from the Southwestern U.S. and Mexico were scored and analyzed by principal components analysis (PCA) and stepwise discriminant analysis (SDA). The results show that all of the 5 species of this group are distinct and form nonoverlapping groups in plots of the first three principal components. All taxa were found to be quite homogeneous as indicated by the tight clusters formed in the PCA plots. Acacia pacensis, whose relationship to the species of this group has been questioned, is confirmed to be more closely related to A. farnesiana and related species. Some specimens with a combination of characters from A. constricta, A. neovernicosa, and A. schottii were positioned intermediate to the putative parental species groups in the PCA and SDA plots, suggesting hybridization among these taxa.     

甘肃南部及秦岭林区姬小蜂区系调查(膜翅目,小蜂总科)

对甘肃省南部及秦岭林区的姬小蜂区系进行了调查.根据1998～2000年作者在甘肃省南部山区所采集的标本和中国科学院动物研究所的馆藏标本,报道了该科4个亚科25属中的73种昆虫.其中,3属为中国新纪录属,41种为中国新纪录种.另外,作者对该地区的姬小蜂区系进行了初步的成分分析.     

黑带艾尤飞虱的重新描记及美伽飞虱属中国一新纪录种记述(半翅目,蜡蝉总科)(英文)

重新描记了采自宁夏六盘山自然保护区的艾尤飞虱属模式种:黑带艾尤飞虱E.nigrolineata Scott,1875,该种国外学者曾报道在我国新疆有分布,但目前未见国内学者的研究报道;同时记述美伽飞虱属Megadelphax一中国新纪录种:科尼美伽飞虱M.cornigera(Kusnezov,1929),提供了美伽飞虱属中国已知种的检索表.所有研究标本均保存在西北农林科技大学昆虫博物馆.     

MOTUs, Morphology, and Biodiversity Estimation: A Case Study Using Nematodes of the Suborder Criconematina and a Conserved 18S DNA Barcode

DNA barcodes are increasingly used to provide an estimate of biodiversity for small, cryptic organisms like nematodes. Nucleotide sequences generated by the barcoding process are often grouped, based on similarity, into molecular operational taxonomic units (MOTUs). In order to get a better understanding of the taxonomic resolution of a 3' 592-bp 18S rDNA barcode, we have analyzed 100 MOTUs generated from 214 specimens in the nematode suborder Criconematina. Previous research has demonstrated that the primer set for this barcode reliably amplifies all nematodes in the Phylum Nematoda. Included among the Criconematina specimens were 25 morphologically described species representing 12 genera. Using the most stringent definition of MOTU membership, where a single nucleotide difference is sufficient for the creation of a new MOTU, it was found that an MOTU can represent a subgroup of a species (e.g. Discocriconemella limitanea), a single species (Bakernema inaequale), or a species complex (MOTU 76). A maximum likelihood phylogenetic analysis of the MOTU dataset generated four major clades that were further analyzed by character-based barcode analysis. Fourteen of the 25 morphologically identified species had at least one putative diagnostic nucleotide identified by this character-based approach. These diagnostic nucleotides could be useful in biodiversity assessments when ambiguous results are encountered in database searches that use a distance-based metric for nucleotide sequence comparisons. Information and images regarding specimens examined during this study are available online.     

Patterns and relationships between and within the sections Alchemilla and Ultravulgares of the genus Alchemilla (Rosaceae) in Estonia

Nine Estonian Alchemilla species belonging to the sections Ultravulgares and Alchemilla , or considered being close to them, were analysed. When the analysed specimens were divided into sections, the latter were statistically distinct and formed separable groups in the character space. When the specimens were grouped on a species level, A. cymatophylla, A. subcrenala and A. heptagona were insignificantly distinct, but, in the character space, specimens of A. heptagona were visually well distinguished from the other two. Specimens of A. acutiloba, A. micans , and A. xanthochlora formed confidently distinct (p < 0.01) species-clusters, but at the same time they formed a joint cloud in the character space, indicating the compactness of section Alchemilla. Specimens of A. semilunaris were close to A. lindbergiana , and not, as has previously been supposed, to the section Ultravulgares. A. semilunaris should possibly be kept in a separate section Decumbentes. Specimens of A. lindbergiana were on one hand close to A. semilunaris. on the other hand close to the species of section Alchemilla ; including it in the latter section is still doubtful. A. subglobosa was indistinct from A. subcrenata but could generally be separated from sections Alchemilla and Ultmvulgares. Of the 41 tested characters, 35 were useful for species discrimination; counts, nominal and ratio characters were better than metric ones. According to the cluster analysis, specimens of A. acutiloba and A. micans formed one big cluster, all other specimens belonged to another.     

Agaricus subrufescens, a cultivated edible and medicinal mushroom, and its synonyms

Agaricus subrufescens Peck was cultivated first in the late 1800s in eastern North America. The type consists partly of cultivated material and partly of field-collected specimens. Once a popular market mushroom, the species faded from commerce in the early 20th century. More recently, a mushroom species growing wild in Brazil has been introduced into cultivation in Brazil, Japan and elsewhere. This Brazilian mushroom has been referred to by various names, most commonly as A. blazei Murrill (sensu Heinemann) and most recently as A. brasiliensis Wasser et al. The author first cultivated A. subrufescens in 1981 and has grown and studied Brazilian isolates since 1992. The species has an amphithallic pattern of reproduction. Based on DNA sequence analysis of the rDNA ITS region and on mating studies and genetic analysis of hybrid progeny, there is a strong case for conspecificity of the Brazilian mushrooms with A. subrufescens. Based on a study of the type and other data, the recent lectotypification of A. subrufescens is accepted. Data are presented on mushrooms of diverse geographical origins, including A. rufotegulis Nauta from western Europe, another apparent conspecific. A possible role for interpopulational hybridization in current populations of A. subrufescens is proposed. The agronomic history of the species is reviewed.     

Microphthalmus hamosus sp.n. (Polychaeta, Hesionidae)—an Example of Evolution Leading from the Interstitial Fauna to a Macrofaunal lnterspecific Relationship

Microphthalmus hamosus sp.n. is described from Florida and North Carolina, USA. Striking characters as body shape, parapod construction, setation and shape of the anal plate can be referred to a close interspecific relationship with a macrofauna species: one specimen was found on Sipunculus nudus . The phylogenetic-systematic position of the new species within the genus is discussed. The speciation process leading to a niche outside the interstitial biotope included a secondary increase in body size and number of segments. Dollo's law is applicable on the sctation: setae which have been lost in the previous adaptation to interstitial life do not reappear.     

古田山国家级自然保护区木腐真菌物种多样性及分布

木腐真菌是微生物的一个重要类群, 主要以倒木为生长基质, 通过产生各种水解酶将倒木的纤维素、木质素和半纤维素分解为小分子物质, 对促进森林生态系统中的营养物质循环发挥着重要的生态功能。于2016年8月在浙江古田山国家级自然保护区开展的木腐真菌野外调查, 利用形态学和DNA序列分析对采集的标本进行了物种鉴定, 并分析了木腐真菌的物种组成和地理成分。在采集的158份标本中鉴定木腐真菌45属92种, 其中白腐真菌78种, 褐腐真菌14种。古田山的木腐真菌物种区系组成中, 热带-亚热带成分比例最高。在158份木腐真菌标本中, 97份标本采自直径大于10 cm的倒木或树桩上, 分属于76个种, 是木腐真菌生长的主要基质大小类型; 48份标本采自直径为2-10 cm的枝干上, 分属38个种; 13份标本采自直径小于2 cm的枝干上, 分属12种。不同腐烂等级倒木上生长的真菌数量和种类差异明显, 其中一级腐烂倒木上采集到9份标本(7种), 二级腐烂倒木上采集到86份标本(45种), 三级腐烂倒木上49份标本(29种), 四级腐烂倒木上14份标本(14种)。结果表明, 林分中倒木直径大小和腐烂程度是影响木腐真菌生长与分布的重要因子。     

中国北部湾光裸方格星虫可培养微生物的分离鉴定及其活性代谢物产生菌筛选

【目的】本研究从北部湾海域光裸方格星虫(Sipunculus nudus)肠道中分离鉴定可培养微生物,并对筛选菌株的代谢物活性进行研究,为后续开发和利用光裸方格星虫肠道微生物代谢产物提供理论支持。【方法】通过微生物培养、菌株分离纯化和16S rRNA基因序列分析,分析鉴定湛江、北海、防城港三地光裸方格星虫肠道可培养微生物;采用透明圈法、可见分光光度法、平板打孔法等对产胞外活性代谢物的菌株进行筛选和活性分析。【结果】中国北部湾不同海域光裸方格星虫肠道可培养微生物包括弧菌属(Vibrio)、希瓦氏菌属(Shewanella)、假交替单胞菌属(Pseudoalteromonas)、发光杆菌属(Photobacterium)和芽孢杆菌属(Bacillus)等12个细菌属。弧菌属(Vibrio)是3个地区样本共有的优势菌群。具有产胞外水解蛋白酶、壳聚糖酶、多糖以及抑菌活性等能力的菌株主要来自假交替单胞菌属(Pseudoalteromonas)、发光杆菌属(Photobacterium)和芽孢杆菌属(Bacillus)。【结论】中国北部湾不同海域光裸方格星虫肠道可培养微生物在属的种类上存在显著性差异,且光裸方格星虫肠道菌株具有产生多种胞外活性代谢物的能力,是一种良好的海洋活性代谢物来源。     

Age and growth rate determinations of an intertidal bivalve, Phacosoma japonicum, using internal shell increments

A venerid bivalve Phacosoma japonicum (Reeve) occurring commonly in the Japanese coastal area preserves periodic growth lines in the shell cross-section. Long-term shell growth patterns of this species have been traced for many individuals on the intertidal flat of the Seto Inland Sea, west Japan. Sclerochronological analysis of these individuals and specimens collected monthly shows that several growth cessation marks within their shells are formed during the winter of each year prior to spawning. Hence the marks were used for age and growth rate determinations. As large individuals showed little shell growth for more than two years after the formation of 7 or 8 annual increments, this species probably has a lifespan of more than ten years. Shell growth patterns of this species based on annual increments can be accurately approximated by a von Bertalanffy curve. The number of microgrowth increments formed during a year tends to decrease with age, although it varies markedly among specimens of the same age. Furthermore, even in summer during rapid shell growth, the microgrowth increments do not represent daily and/or sub-daily tidal rhythms in many specimens. The results of this study and those by several authors strongly suggest that the annual increments are the key for age and growth rate determinations of both living and fossil bivalve species.     

Systematic studies in Tylosema (Leguminosae)

A contribution to the knowledge of Tylosema (Schweinf.) Torre & Hillc. is presented. The main objectives of this revision were: (1) to elucidate the taxonomic position of the specimens collected in south Angola, (2) to provide a review of species boundaries in the genus, especially between T. fassoglense (Schweinf.) Torre & Hillc. and T. esculentum (Burch.) A.Schreib. and (3) to evaluate the contribution of pollen morphology for delimitation of the species in this genus. Numerical analyses were performed based on morphometric data taken from herbarium specimens. Principal component analysis and cluster analysis divided specimens of Tylosema into four major groups, corresponding to three recognized species and a new taxon. A new micromorphometric character (swollen base of hairs) was found that further contributes to the distinction of T. humifusum (Pic.Serm. & Roti Mich.) Brenan from other species. A new species, T. angolense P. Silveira & S. Castro sp. nov. , is described and illustrated. A taxonomic key and distribution map of studied taxa is also provided. The analyses of pollen morphology allowed for the distinction of the taxonomic groups.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 99–115.