Phylogenetic position of three Condylostoma species （Protozoa,Ciliophora, Heterotrichea） inferred from the small subunit rRNA gene sequence

The systematically poorly known ciliate genus Condylostoma was erected by Vincent in 1826. About 10 morphotypes have been reported, but any molecular investigations concerning this group so far are lacking. In this work, the small subunit ribosomal RNA （SS rRNA） gene of three marine Condylostoma species was sequenced, by which the phylogenetic trees were constructed by distancematrix, maximum parsimony and Bayesian inference methods. The results show that （1） all the trees have similar topologies with high supports; （2） Condylostoma is mostly related to the genus Condylostentor; and （3） three Condylostoma species as well as Condylostentor auriculatus cluster together and form a sister group with other heterotrichs. This is moderately consistent with the assessment of phylogenetic relationships of Condylostoma-related heterotrichs from the morphological information. The phylogenetic relationship of some other related heterotrichs, Peritromus, Folliculina, Stentor and Blepharisma, has been also discussed.     

Mitochondrial cytochrome b sequence variations and phylogeny of the East Asian bagrid catfishes

The mitochondrial DNA cytochrome b gene was sequenced from 8 bagrid catfishes in China. Aligned with cytochrome b sequences from 9 bagrid catfishes in Japan, Korea and Russia retrieved from GenBank, and selected Silurus meridionalis, Liobagrus anguillicauda, Liobagrus reini and Phenacogrammus interruptus as outgroups, we constructed a matrix of 21 DNA sequences. The Kimura's two-parameter distances were calculated and molecular phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The results show that (i) there exist 3-bp deletions of mitochondrial cytochrome b gene compared with cypriniforms and characiforms; (ii) the molecular phylogenetic tree suggests that bagrid catfishes form a monophyletic group, and the genus Mystus is the earliest divergent in the East Asian bagrid catfishes, as well as the genus Pseudobagrus is a monophyletic group but the genus Pelteobagrus and Leiocassis are complicated; and (iii) the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%～0.30% sequence divergence per million years.     

The first Sinomastodon (Gomphotheriidae, Proboscidea) skull from the Quaternary in China

The first Sinomastodon(Gomphotheriidae,Proboscidea) skull of the Early Pleistocene,collected from the Renzidong Cave deposits in Anhui Province,Eastern China,is described here as S.jiangnanensis sp.nov.As the only brevirostrine trilophodont gomphotheriid known from the Old World,Sinomastodon was mainly indigenous to China from the Early Pliocene to the Pleistocene.Compared with a few single Pleistocene teeth previously found in China,S.jiangnanensis sp.nov.is represented by a relatively complete skull,mandible and dentition,which is the first discovery of a Quaternary Sinomastodon skull from China.With a brevirostrine,elephant-like skull,no lower tusks,and simple bunodont and trilophodont intermediate molars,the new species is morphologically distinct from other gomphotheres and should belong to the genus Sinomastodon.The new species is more progressive than S.hanjiangensis and the Pliocene type species S.intermedius in its skull and mandible morphology,but is evidently more primitive than the Pleistocene S.yangziensis in its molar morphology.The faunal analysis suggests that the emergence of S.jiangnanensis sp.nov.in Jiangnan area and its southward migration may have been related to a cooling event at the beginning of the Quaternary in Eastern China.     

Sequence analysis of cytochrome b gene indicates that East Asian group of cyprinid subfamily Leuciscinae (Teleostei: Cyprinidae) evolved independently

The sequences of mitochondrial cytochrome b gene of cyprinid subfamily Leuciscinae are analyzed. Phylogenetic trees generated with methods of neighbor-joining, maximum likelihood and maximum parsimony with Phenacogrammus as an outgroup indicate that Leuciscinae is not a monophyletic group but includes two discrete subgroups. The East Asian group of the subfamily Leuciscinae, including the genera Ctenopharyngodon, Elopichthys, Luciobrama, Mylopharyngodon, Ochetobius, and Squaliobarbus, is close to Aristichthys and Hypophthalmichthys, and they form a monophyletic group which is distant from the leuciscine genera in Europe, Siberia and North America, such as Phoxinus, Leuciscus, Abramis, Rutilus, Chondrostoma, Alburnus, Opsopoedus, Lythrurus, and Pimephales. Our study suggests that the diversified East Asian group of the subfamily Leuciscinae should have an independent origination.     

Phylogenetic position of Schnabelia, a genus endemic to China： Evidence from sequences of cpDNA matK gene and nrDNA ITS regions

The chloroplast gene matK and the internal transcribed spacers (ITS) of the nuclear ribosomal DNA from Schnabelia, a genus endemic to China, and 6 genera of Verbenaceae and 13 genera of Lamiaceae were sequenced. The phylogenetic signal and validity outgroups were measured and evaluated by means of the relatively apparent synapomorphy analysis (RASA). Independent and combined phylogenetic analyses for the matK and ITS sequences were performed using the maximum parsimony (MP), neighbor-joining (NJ) and maximum likelihood (ML) methods, indicating that Schnabelia oligophylla and Caryopteris terniflora form a sister-group relationship. The Caryopteris complex is not shown to be a monophyly because Trichostema, C. paniculata and C. forrestii are paraphyletic to the clade containing the remaining members of the complex. A monophyly of Ajugoideae proposed by Cantino et al., including 8 genera in this study, is strongly supported and the closest relatives of Schnabelia are in the Ajugoideae (Lamiaceae), especially near Caryopteris terniflora. The polygenetic analyses also showed that the genera of Lamiaceae and Verbenaceae sampled in this tudy are phylogenetically mixed and the genus Avicennia is distant to other genera of Verbenaceae. RASA and combined analysis can be used as effective approaches to determining the relationships among phylogenetically complex groups.     

Mitochondrial 16S rRNA sequence variations and phylogeny of the Chinese sisorid catfishes

Partial sequences of mitochondrial 16S rRNA gene were obtained by PCR amplification for comparisons among nine species of glyptosternoid fishes and six species of non-glyptosternoids representing 10 sisorid genera. There are compositional biases in the A-rich unpaired regions and G-rich paired regions. A-G transitions are primarily responsible for the Ts/Tv bias in unpaired regions. The overall substitution rate in unpaired regions is almost two times higher than that in the paired regions. Saturation plots at comparable levels of sequence divergence demonstrate no saturation effects. Phylogenetic analyses using both maximum likelihood and Bayesian methods support the monophyly of Sisoridae. Chinese sisorid catfishes are composed of two majorlineages, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by “glyptosternoids Pseudecheneis“. The glyptosternoids may not be a monophyletic group. A previous hypothesis referring to Pseudecheneis as the sister group of monophyletic glyptosternoids, based on morphological evidence, is not supported by the molecular data. Pseudecheneis is shown to be a sister taxon of Glaridoglanis. Pareuchiloglanis might be paraphyletic with Pseudexostoma and Euchiloglanis. Our results also support the hypothesis that Pareuchiloglanis anteanalis might be considered as the synonyms of Pareuchiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.     

Inclusion of the Eastern Asia endemic genus Sorolepidium in Polystichum （Dryopteridaceae）： Evidence from the chloroplast rbcL gene and morphological characteristics

The taxonomic status of the Eastern Asia endemic Sorolepidium is controversial. Some authors accept it as member of the large diverse genus Polystichum, whereas others suggest that it is an independent genus separated from the later by the exindusiate sorus and the absence of aristate teeth at the pinnae margins. Here we infer phylogenetic relationship of Sorolepidium using DNA sequences of the chloro-plast rbcL gene. Phylogenies were inferred using maximum-parsimony, maximum-likelihood, and Bayesian inference methods. Molecular data establish that Sorolepidium is deeply nested within the large genus Polystichum and has a close relationship with P. duthiei and P. lachenense in the model-based analyses. The Kimura 2-parameter distances of the rbcL sequences between S. glaciale and P. duthiei and P. lachenense were 0.1 and 0.2%, respectively. Furthermore, S. glaciale differed from P. duthiei by a single nucleotide in their rbcL sequences. Close relationships between S. glaciale and P. duthiei and P. lachenense are also supported by the shared spore ornamentation with echinate fenes-trate folds.     

Phylogenetic relationships of host insects of Cordyceps sinensis inferred from mitochondrial Cytochrome b sequences

This study used the sequence of the mitochondrial Cytochrome b(Cytb)to estimate phylogenetic relationships among host Hepialidae insects of Cordyceps sinensis.Genome DNA of host insect was extracted from the dead larva head part of 18 cordyceps populations and 2 species of Hepialus,and the Cytb fragment of host insect was amplified with PCR technique.The nucleotide sequence alignments and their homologous sequences of 24 species host Hepialidae insects of Cordyceps sinensis were obtained from GenBank and were used to construct phylogenetic trees based on neighbor-joining method.The results showed that genus Bipectilus diverged earlier than genus Hepialus and Hepialiscus.Hepialus host insects of Cordyceps sinensis have multitudinous species with different morphological characteristics and geographical distributions.The interspecific genetic differentiations are obvious in Hepialus.Thus,the genus Hepialus might be considered as polyphyletic origin.Cytb sequences have abundant variations among the host insects of Cordyceps sinensis on spe- cific and generic level.The divergence rate of Cytb sequences among the species in Hepialus ranged from 0.23% to 9.24%,except that Hepialus pratensis and Hepialus jinshaensis have the same sequence.Cytb sequence can be used for species identification of host insects of Cordyceps sinensis,but further confirmation in more host insect species is needed.To obtain the Cytb sequence of host insect by ampli- fying DNA extracted from the head part of dead larva in cordyceps turns out to be an effective and accurate approach,which will be useful for studies on phylogeny and genetic structure of host insects of cordyceps populations,especially for analyzing relationships between C. sinensis and its host insects.     

Investisations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 （Tetraodontiformes,Tetraodontidae）

The phylogenetic relationships within the genus Takifugu Abe, 1949 （Tetraodontiformes, Tetraodontidae） remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsi- mony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that （1） the genus Takifugu is a monophyletic assemblage; （2） the genus is divided into 6 subgroups based on the moecular data; and （3） there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.     

Reappraisal of phylogenetic status and genetic diversity analysis of Asian population of Lentinula edodes

Phylogenetic relationship within the Lentinula genus is constructed based on the sequenced ITS fragments of the 60 Chinese wild L. edodes isolates and the sequence data of 48 isolates of different species from other districts downloaded from the GenBank. The 108 isolates of Lentinula genus are divided into two branches and seven groups, one branch and two groups in the New World, and the other branch and five groups in the Old World, and the isolates clustering of different groups corresponds obviously with the classification of the morphological species. Asian isolates are partitioned in group Ⅰ and Ⅴ, two of the five groups of the Old World, by which the germplasm resources status represented is of great importance shown by the phylogenetic analysis. Group Ⅴ which fills up the blank of geographic distribution has become one of the mainstream groups with an increased isolate number, while group Ⅰ has a tendency to dissimilate into two subgroups (Ia and Ib) with a huge isolate quantity and a coverage of most tested districts, suggesting that China (or Asia) is an important genetic diversity center of the natural population of Lentinula genus. Genetic analysis of Asian isolates based on groups Ia, Ib and group Ⅴ indicates that the diversity of the east coastal-land, northwestern highland and southwestern China and Himalayas districts is the most plentiful, which is the three priorities in diversity protection of Asian Lentinula population.     

A Cambrian micro-lobopodian and the evolution of arthropod locomotion and reproduction

The evolutionary success of arthropods, the most abundant and diverse animal group, is mainly based on their segmented body and jointed appendages, features that had evolved most likely already before the Cambrian. The first arthropod-like animals, the lobopodians from the Early Cambrian, were unsclerotized and worm-like, and they had unjointed tubular legs. Here we describe the first three-dimensionally preserved Cambrian lobopodian. The material presented of Orstenotubulus evamuellerae gen. et sp. nov. is the smallest and youngest of a lobopodian known. O. evamuellerae shows strikingly detailed similarities to Recent tardigrades and/or onychophorans in its cellular-structured cuticle and the telescopic spines. It also shows similarities to other, longer known lobopodians, but which are ten times as large as the new form. These similarities include the finely annulated body and legs, which is characteristic also for Recent onychophorans, and paired humps continuing into spines situated dorsally to the leg insertions, a feature lacking in the extant forms. The morphology of O. evamuellerae not only elucidates our knowledge about lobopodians, but also aids in a clearer picture of the early evolution of arthropods. An example is the single ventral gonopore between a limb pair of O. evamuellerae, which indicates that a single gonopore, as developed in onychophorans, tardigrades, pentastomids, myriapods and insects, might represent the plesiomorphic state for Arthropoda, while the paired state in chelicerates and crustaceans was convergently achieved. Concerning life habits, the lateral orientation of the limbs and their anchoring spines of the new lobopodian imply that early arthropods were crawlers rather than walkers.     

Hierarchical recognition on the taxonomy of <Emphasis Type="Italic">Nitzschia closterium</Emphasis> f. minutissima

Nitzschia closterium f. minutissima, a marine eukaryotic unicellular diatom, originally classified as Bacillariophyta/Bacillariophyceae/Bacillariales/Bacillariaceae/Nitzschia, is one of the most important feed sources in mariculture. In this study, its morphological features were examined under DIC Microscopy （differential interference contrast microscope）; its pigments and fatty acids composition were analyzed by using High Performance Liquid Chromatography （HPLC） and gas chromatography （GC）; the complete Actin cDNA, part 18S rDNA, complete ITS1 and ITS2 sequences, part 28S rDNA sequences, and a putatively encoding A5 fatty acid desaturase gene were cloned respectively and further functioned in transgenic yeast. The sequence alignments were separately conducted using the related sequences from Nitzschia closterium f. minutissima, Cylindrotheca closterium （Bacillariophyta/Baci- Ilariales/Bacillariaceae/Cylindrotheca） and Phaeodactylum tricornutum （Naviculales） with ClustalX 1.83. No distinct difference was discovered between N. closterium f. minutissima and P. tricornutum in both biochemical and molecular level. Their identity was more than 99.6% among 18S rDNA, 5.8S rDNA and actin-gene sequences, and is up to 98.6% even among ITS1 and ITS2 sequences. Their △5 desaturase similarity was 99.4%. However, the lower similarity was disclosured between N. closterium f. minutissima and Cylindrotheca closterium, which shared less than 40% identity in the ITS1 and ITS2 sequences. So, N. closterium f. minutissima should not be placed in Bacillariales, Bacillariaceae, Nitzschia, but in Naviculales, Phaeodactylaceae, Phaeodactylum, and it was actually a strain of P. tricornutum.     

Analysis of diversity of CO I gene and system generation of nine species of chitons

Cytochrome c oxidase subunit Ⅰ(COⅠ) genes from 9 chiton species in China’s coast area were sequenced. A phylogeny tree about these gene sequences were reconstructed together with other 4 COⅠgene sequences of chitons from Genbank. The affinity genetic relationship and the taxonomic status of molecular evolution for these 13 chiton species were analyzed. The results show that Liolophura japonica and Onithochiton hirasei belong to Chitonidae, Acanthochiton rubrolineatus and Acanthochiton dissimilis belong to Acanthochitonidae, and Placiphorella japonica and Mopalia retifera belong to the same family Mopliidae. However, Lepidozona coreanica, Ischnochiton comptus, and Ischnochiton hakodadensis are not supposed to be referred to Ischnochi-tonidae according to the genetic distance analysis (L. coreanica, I. comptus, and I. hakodadensis are usually classed as Ischnochitonidae according to their morphological character). Furthermore, I. hakodadensis could not been classed as Ischnochiton, and it is more likely to be treated as a close relative of Lepidozona.     

Phylogenetic position of Ephedra rhytidosperma, a species endemic to China： Evidence from chloroplast and ribosomal DNA sequences

The chloroplast genes matK and rbcL, ribosomal gene 18S and ITS regions of nuclear ribosomal DNA from Ephedra rhytidosperma, a species endemic to China, were sequenced and its phylogenetic position was investigated. Independent and combined phylogenetic analyses for the DNA sequences from 16 taxa representing 15 species of the genus Ephedra were performed using the maximum parsimony （MP）, neighbor-joining （N J）, minimum evolution （ME） and maximum likelihood （ML） methods. The results indicate that E. rhytidosperma is closely related to E. equisetina. The divergence time between them is estimated to be 10.85±2.44 Ma based on the results of the relative-rate tests and the evolutionary rate of rbcL gene.     

Southern rice black-streaked dwarf virus:A new proposed Fijivirus species in the family Reoviridae

For the past several years, a novel dwarf disease has been observed on rice (Oryza sativa) in some regions of Guangdong Province and Hainan Province, southern China. Infected plants showed stunting, dark leaf and small enations on stem and leaf back. Typical Fijivirus viroplasma containing crystalline arrayed spherical virons approximately 70―75 nm in diameter and tubular structures were detected in ultrathin sections by an electron microscope in parenchyma phloem cells of the infected plants. The virus was transmitted to rice seedlings by white-backed planthoppers, Sogatella furcifera (Hemiptera: Delphacidae), collected in the diseased fields. Analysis of dsRNA extracts from infected plants revealed ten linear segments, which were similar to the electrophoretic profile of Rice black-streaked dwarf virus (RBSDV). RT-PCR with a single primer which matched to a linker sequence ligated to both 3′ ends of the viral genomic dsRNAs resulted in amplification of genome segments 9 (S9) and 10 (S10) cDNA products. The complete nucleotide sequences of S9 and S10 were obtained from clones of the RT-PCR amplicon exhibited characteristic properties of Fijivirus including low GC content (34.5% and 35.6%), genus conserved 5′ and 3′ termini sequences and similar genome organization. Blast searches indicated that the sequences of S9 and S10 shared 68.8%―74.9% and 67.1%―77.4% nucleotide identities with those of viruses in the Fijivirus group 2, respectively. These values were similar to those among other viruses in the Fijivirus group 2 and considerably lower than those among RBSDV isolates. Phylogenetic trees based on S9 and S10 nucleotide sequences and their putative amino acid sequences showed that this virus represented a separate branch among other Fijiviruses. The virus was also detected by a nested RT-PCR assay in corn (Zea mays), barnyard grass (Echinochloa crusgalli), Juncellus serotinus and flaccidgrass (Pennisetum flaccidum) in and/or adjacent to the infected rice fields. It is proposed that this virus be considered as a new species, Southern rice black-streaked dwarf virus, in the group 2 of the genus Fijivirus in the family Reoviridae.     

Genetic background of phenotypic variation

A noteworthy feature of the living world is its bewildering variability. A key issue in several biological disciplines is the achievement of an understanding of the hereditary basis of this variability. Two opposing, but not necessarily irreconcilable conceptions attempt to explain the underlying mechanism. The gene function paradigm postulates that phenotypic variance is generated by the polymorphism in the coding sequences of genes. However, comparisons of a great number of homologous gene and protein sequences have revealed that they predominantly remained functionally conserved even across distantly related phylogenic taxa. Alternatively, the gene regulation paradigm assumes that differences in the cis-regulatory region of genes do account for phenotype variation within species. An extension of this latter concept is that phenotypic variability is generated by the polymorphism in the overall gene expression profiles of gene networks. In other words, the activity of a particular gene is a system property determined both by the cis-regulatory sequences of the given genes and by the other genes of a gene network, whose expressions vary among individuals, too. Novel proponents of gene function paradigm claim that functional genetic variance within the coding sequences of regulatory genes is critical for the generation of morphological polymorphism. Note, however, that these developmental genes play direct regulatory roles in the control of gene expression.     

An input signal used in process identification-chaos sequence

The sequences which consist of any segment of a chaos sequence are called as C-sequences. These sequences could be used as a kind of input signals to replace M-sequences in the process identification. This substitution is theoretically proved to be feasible. Inverse C-sequences are created in a way similar to inverse M-sequences to solve the problem that C-sequences have nonideal balance property, that is, the numbers of ‘0’ and ‘1’ are unequal. Besides its good pseudo-random property, the sequences have other advantages such as easy to generate, varieties of the segment and adjustable cycle time.     

Phylogeny of SARS-CoV as inferred from complete genome comparison

SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV,the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phyiogenetic tree was constructed. Our results show that all SARS-CoV isolates were clustered into a clique and previously identified coronaviruses formed the other clique. Meanwhile, the three groups of coronaviruses depart from each other clearly in our tree that is consistent with the results of prevenient papers. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. The topology map also shows that the 12 SARS-CoV isolates may be divided into two groups determined by the association with the SARS-CoV from the Hotel M in Hong Kong that may give some information about the infectious relationship of the SARS.     

A new Euprox from the Late Miocene of Yuanmou,Yunnan Province,China,with interpretation of its paleoenvironment

The Yuanmou Basin of Yunnan Province is a hotspot for the research of early homind evolution and its environmental background.During the implementation of the Program“Research of the Origin and Evolution of Early Man and Its Environmental Baqckground” from 1998 to 2001,a huge quantity of hominoid and mammal fossils were collected.The present report systematically describes an Euprox robustus sp.nov.identified during the recent laboratory work on the collected material.Euprox is a group of earliest cervids with true antlers.The new species is the third one of the genus discovered in China.Judged by its morphologic characteristics,the new species feed on juicy and tender leaves of dicotyledon.It implies that the vegetation of its epoch in the Yuanmou Basin is a kind of southern subtropical evergreen forest and the climate is humid and temperate with evident seasonality.The latter is mostly influenced by the monsoon and secondly by the latitude.