Phylogenetic relationships of the Chinese cyprinid genus Rhinogobio Bleeker (Teleostei : Cyprinidae) based on sequences of the mitochondrial DNA control region, with comments on character adaptations

Rhinogobio is a cyprinid genus restricted to the river drainages of China. Sequences of the mitochondrial DNA control region were determined for four Rhinogohio species and one outgroup species, Coreius heterodon, to investigate the phylogenetic relationships within the genus. The control region of the Rhinogobio species ranges from 922 to 930 base pairs and comprises 930 base pairs in Coreius. Our phylogenetic analysis indicates two distinct lineages in the genus Rhinogobio. The first includes only R. ventralis. In the second lineage there are three species, two closely related species R. cylindricus and R. hunanensis, and their sister species R. typus. An analysis of character adaptations suggests an evolutionary trend in this genus towards a relatively lower body and caudal peduncle depth, a shorter dorsal fin, and a more anterior anus. In addition, there is a trend towards shorter barbels and relatively larger eyes. Some or all of these traits may be associated with a habitat shift from fast-flowing turbid rivers to slower-flowing clear river habitats.

Phylogenetic relationships of glyptosternoid fishes (Siluriformes : Sisoridae) inferred from mitochondrial cytochrome b gene sequences

To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi. (C) 2003 Elsevier Inc. All rights reserved.

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces : Cypriniformes) inferred from cytochrome b sequences

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily "Danioninae" did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the "Leuciscinae" in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leuciscinae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.

Characterization and phylogenetic analysis of the chitinase gene from the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus

A putative chitinase gene was identified within the fragment EcoRI-K of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearNPV, also called HaSNPIV) genome. The open reading frame (ORF) contains 1713 nucleotides (nt) and encodes a protein of 570 amino acids (aa) with a predicted molecular weight of 63.6 kDa. Transcription started at about 18 h post infection (p.i.) and the protein was first detected at 20 h p.i. The times of transcription and expression are characteristic of a late baculovirus gene. 5' and 3' RACE indicated that transcription was initiated from the adenine residue located at -246 nt upstream from the ATG start site and the poly (A) tail was added at 267 nt downstream from the stop codon. This is the first report on the molecular characterization of a chitinase from a single nucleocapsid NPV. The phylogeny of baculoviral chitinase genes were extensively examined in comparison with chitinases derived from bacteria, fungi, nematode, actinomycetes, viruses, insects and mammals. Neighbor-joining and most parsimony analyses showed that the baculoviral chitinases were clustered exclusively within gamma-proteobacteria. Our results strongly suggest that baculoviruses acquired their chitinase genes from bacteria. (C) 2004 Elsevier B.V. All rights reserved.

Sequence variations of the S7 ribosomal protein gene in primitive cyprinid fishes: Implication on phylogenetic analysis

Cyprinidae is the largest fish family in the world and contains about 210 genera and 2010 species. Appropriate DNA markers must be selected for the phylogenetic analyses of Cyprinidae. In present study, the 1st intron of the S7 ribosomal protein (r-protein) gene is first used to examine the relationships among cyprinid fishes. The length of the 1st intron obtained by PCR amplification ranges from 655 to 859 by in the 16 cyprinid species investigated, and is 602 by in Myxocyprinus asiaticus. Out of the alignment of 925 nucleotide sites obtained, the parsimony informative sites are 499 and occupy 54% of the total sites. The results indicate that the 1st intron sequences of the S7 r-protein gene in cyprinids are rich in informative sites and vary remarkably in sequence divergence from 2.3% between close species to 66.6% between distant species. The bootstrap values of the interior nodes in the NJ (neighbor-joining) and MP (most-parsimony) trees based on the present S7 r-protein gene data are higher than those based on cytochrome b and the d-loop region respectively. Therefore, the 1st intron sequences of the S7 r-protein gene in cyprinids are sensitive enough for phylogenetic analyses, and the 1st intron is an appropriate genetic marker for the phylogenetic reconstruction of the taxa in different cyprinid subfamilies. However, attempts to discuss whether the present S7 r-protein gene data can be applied to the phylogeny of the taxa at the level of the family or the higher categories in Cypriniformes need further studies.

Advances in phylogenetic studies of Nematoda

Nematoda is a metazoan group with extremely high diversity only next to Insecta. Caenorhabditis elegans is now a favorable experimental model animal in modern developmental biology, genetics and genomics; studies. However, the phylogeny of Nematoda and the phylogenetic position of the phylum within animal kingdom have long been in debate. Recent molecular phylogenetic studies gave great challenges to the traditional nematode classification. The new phylogenies not only placed the Nematoda in the Ecdysozoan and divided the phylum into five clades, but also provided new insights into animal molecular identification and phylogenetic biodiversity studies. The present paper reviews major progress and remaining problems in the current molecular phylogenetic studies of Nematoda, and prospects the developmental tendencies of this field.

Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) with emphasis on the genus Epistylis, inferred from small subunit rRNA gene sequences

The peritrichs have been recognized as a higher taxon of ciliates since 1968. However, the phylogenetic relationships among them are still unsettled, and their placement within the class Oligohymenophorea has only been supported by the analysis of the small subunit rRNA gene sequence of Opisthonecta henneguyi. DNA was isolated directly from field-sampled species for PCR, and was used to resolve relationships within the genus Epistylis and to confirm the stability of the placement of peritrichs. Small subunit rRNA gene sequences of Epistylis plicatilis, Epistylis urceolata, Epistylis chysemydis, Epistylis hentscheli, Epistylis wenrichi, and Vorticella campanula were sequenced and analyzed using both distance-matrix and maximum-parsimony methods. In phylogenetic trees, the monophyly of both the genus Epistylis and the subclass Peritrichia was strongly supported, while V. campanula clustered with Vorticella microstoma. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the peristomial area, especially the. peristomial lip, might be the important phylogenetic character within the genus Epistylis.

Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins

SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25 informative SINEs inserted into unique genomic loci during evolution of odontocetes to construct a cladogram. and determine a total of 2.8 kb per taxon of the flanking sequences of these SINE loci to estimate divergence times among lineages. We demonstrate that: (i) Odontocetes are monophyletic; (ii) Ganges River dolphins, beaked whales, and ocean dolphins diverged (in this order) after sperm whales; (iii) three other river dolphin taxa, namely the Amazon, La Plata, and Yangtze river dolphins, form a monophyletic group with Yangtze River dolphins being the most basal; and (iv) the rapid radiation of extant cetacean lineages occurred some 28-33 million years B.P., in strong accord with the fossil record. The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution.

Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning

1140 bp of cytochrome b gene were amplified and sequenced from 14 species of primitive cyprinid fishes in East Asia. Aligned with other ten cytochrome b gene sequences of cyprinid fish from Europe and North America retrieved from Gene bank, we obtained a matrix of 24 DNA sequences. A cladogram was generated by the method of Maximum likelihood for the primitive cyprinid fishes. The result indicated that subfamily Leuciscinae and Danioninae do not form a monophyletic group. In the subfamily Danioninae, Opsariichthys biden and Zacco platypus are very primitive and form a natural group and located at the root. But the genera in subfamily Danioninae are included in different groups and have not direct relationship. Among them, Aphyocypris chinensis and Yaoshanicus arcus form a monophyletic group. Tanichthys albonubes and Gobiocypris rarus have a close relation to Gobioninae. The genus Danio is far from other genera in Danioninae, In our cladogram, the genera in Leuciscinae were divided into two groups that have no direct relationship. The genera in Leuciscinae distributed in Europe, Sibera and North America, including Leuciscus, Rutilus, Phoxinus, N. crysole, Opsopoeodus emilae, form a monophyletic group. And the Leuciscinae in southern China including Ctenopharyngodon idellus, Mylopharyngodon piceus, Squalibarbus and Ochetobius elongatus have a common origination.

Molecular systematics of Xenocyprinae (Teleostei : Cyprinidae): Taxonomy, biogeography, and coevolution of a special group restricted in east Asia

We surveyed mitochondrial DNA (mtDNA) sequence variation in the subfamily Xenocyprinae from China and used these data to estimate intraspecific, interspecific, and intergeneric phylogeny and assess biogeographic scenarios underlying the geographic structure of lineages. We sequenced 1140 bp of cytochrome b from 30 individuals of Xenocyprinae and one putative outgroup (Myxocypris asiaticus) and also sequenced 297 bp of ND4L, 1380 bp of ND4, 68 bp of tRNA(His), and 69 bp of tRNA(Ser) from 17 individuals of Xenocyprinae and the outgroup (M. asiaticus). We detected high levels of nucleotide variation among populations, species, and genera. The phylogenetic analysis suggested that Distoechodon hupeinensis might be transferred to the genus Xenocypris, the taxonomic status of the genus Plagiognathops might be preserved, and species of Xenocypris and Plagiognathops form a monophyletic group that is sister to the genus Distoechodon and Pseudobrama. The introgressive hybridization might occur among the populations of X. argentea and X. davidi, causing the two species to not be separated by mtDNA patterns according to their species identification, and the process and direction of hybridization are discussed. The spatial distributions of mtDNA lineages among populations of Xenocypris were compatible with the major geographic region, which indicated that the relationship between Hubei + Hunan and Fujian is closer than that between Hubei + Hunan and Sichuan, From a perspective of parasite investigation, our data suggested that the fauna of Hexamita in Xenocyprinae could be used to infer the phylogeny of their hosts. (C) 2001 Academic Press.

Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

The four species of "river dolphins" are associated with six separate great river systems on three subcontinents and have been grouped for more than a century into a single taxon based on their similar appearance. However, several morphologists recently questioned the monophyly of that group. By using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, we demonstrate with statistical significance that extant river dolphins are not monophyletic and suggest that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae.

Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

猕猴属的分子系统学与遗传多样性研究

用六个线粒体基因片段序列数据，对称猴属的分子系统发育关系进行了分析。8种称猴：台湾猴，北平顶猴，藏酋猴，熊猴，红面猴，J厦河猴，狮尾猴和食蟹猴共40个样本用于本研究。结合从GenBank里下载的雯猴的相应序列，用拂拂作为外群构建了系统发育树。由于六个目的片段均为线粒体基因片段，缺乏重组且作为单一位点遗传，因此我们将六个数据集合并为一个数据集进行分析。我们获得了比前人置信度更高的线粒体系统树。除了红面猴，我们的结果支持Delson（1980）的分组。与前人研究结果一致，红面猴与食蟹猴组成员关系较近（尤其是食蟹猴）。恒河猴（相对于台湾猴），熊猴（相对于藏酋猴）和北平顶猴（相对于狮尾猴）都形成了并系。通过线粒体控制区序列和20个微卫星位点对14个恒河猴地理群体的群体结构进行了研究。微卫星数据和线粒体控制区数据均显示恒河猴有较高的遗传多样度。线粒体数据表明各地区的恒河猴群体间的差异显著大于微卫星数据显示的结果。也就是说，基于微卫星数据所得到的群体间基因流远大于基于线粒体数据所得到的群体间基因流。两种分子标记所得到的结果差异应归因为雌性恒河猴的归家冲动和雄性恒河猴的扩散。线粒体数据显示所有恒河猴群体近期没有发生过快速扩张。微卫星数据显示大部分恒河猴群体近期没有经历过瓶颈效应。恒河猴是分布较广的非人灵长类动物，但它的地理差异研究一直颇有争论且不足以划分其亚种。我们对采自包括印度、越南、缅甸和18个中国地区在内的21个地区共35个恒河猴样品的四个线粒体基因片段（COI，Cofl，COlll和12srRNA）进行了研究。食蟹猴、红面猴、台湾猴和史猴的相应序列作为外群。大约长为100bp的序列用于构建最大似然树和贝叶斯树。与前人结果一致（彭燕章等，1993；蒋学龙等，1995；Groves，2001），西部恒河猴（印度）．相当于M.m.mulatta。根据王应祥（2003）的分类，我们的东部恒河猴可分为四组：M．最早分离出来且一个来自缅甸的恒河猴位于该组基部；M.m.brachyurus和M.m．littoralis组成一个大枝，这个大枝与M.m，lasiotus构成姐妹群。

白腹鼠属（Niviventer）分子系统发育关系和小家鼠（Mus musculus）分子系统地理学研究

本工作用线粒体细胞色素b基因全序列探讨了白腹鼠属（Niviventer）分子系统发育关系，利用线粒体控制区全序列研究小家鼠（Mus musculus）在中国的分子系统地理学。 在白腹鼠属的分子系统发育研究中，本研究首次对来自青藏高原东南部和台湾的9种（安氏白腹鼠、川西白腹鼠、社鼠、刺毛鼠、梵鼠、灰腹鼠、褐尾鼠、台湾白腹鼠和台湾社鼠）32个个体的细胞色素b全序列进行了测定和分析。用最大简约法、最大似然法和贝叶斯法三种构树方法构出的进化树一致表明，9种分为3个线粒体DNA系：系A包括社鼠、台湾社鼠、台湾白腹鼠、刺毛鼠、梵鼠和灰腹鼠6种；系B包括安氏白腹鼠和川西白腹鼠2种；系C仅包括褐尾鼠一种。应用DNA分类的分析方法表明台湾社鼠不应是社鼠的亚种，而应是一个独立的种。此外，以来自更新世中晚期（1.2-0.13百万年）的社鼠化石为依据推算该属的分歧时间。结果表明该属的起源于1.64百万年前，系A和系B分化发生在1.46百万年以前，该属的其余物种分化时间为1.29-0.67百万年前。这些分化时间和青藏高原的最后一次隆起、昆黄运动以及第四纪大冰期时间相一致，提示地理隔离和冰期作用可能对该属的形成演化起到重要的作用。 在小家鼠的分子系统地理学研究中，通过测定来自中国12个采集地的184只小家鼠的控制区全序列，并结合了Genbank里的单倍型，首次研究小家鼠在中国的分子系统地理格局、种群历史和生物地理过程。184个样品定义了66个单倍型，单倍型多样性为0.95，核苷酸多样性为0.012。用66个单倍型及Genbank里来自周边国家的62个小家鼠单倍型进行分子系统发育分析，邻接法和贝叶斯法构得的分子系统发育树基本一致。结果表明小家鼠在中国分为两个线粒体DNA系（南方系和北方系）。分子变异等级分析结果表明主要的分子变异发生在两个线粒体DNA系之间（84.03%）。根据研究结果推断长江是两个线粒体DNA系之间基因交流受限的主要地理障碍。单倍型进化网络关系表明两个线粒体DNA是异域扩散。两个系的单倍型歧点分布图呈钟型分布，说明经历了快速的种群扩散。经推算小家鼠在中国北方系的种群扩散时间为16 600（22 000－11 000）年前，而南方系的种群扩散时间早于北方系，扩散时间为20 000（40 000－6 700）年前。依据单倍型和核苷酸的多样性、单倍型进化网络关系以及单倍型歧点分布图综合推断小家鼠在中国的两个系在末冰期时经历了快速的种群扩张导致今天的地理分布格局。根据系统发育树的结果推断，北方系种群的大体扩散方向是从北往南，而南方系是从南往北迁移。小家鼠以长江为界分为南方系和北方系的系统地理模式、扩散方向和种群的扩散时间与人以长江为界分为南方人和北方人、扩散方向、扩散时间（60 000－16 000）基本一致，这可能暗示人类活动对小家鼠的迁移产生的重要影响。