Phylogeny of the East Asian botiine loaches (Cypriniformes, Botiidae) inferred from mitochondrial cytochrome b gene sequences

The Botiinae have traditionally represented a subfamily of the Cobitidae. At present, the classification and phylogenetic relationships of the Botiinae are controversial. To address systematic and phylogenetic questions concerning this group, we sequenced the complete cytochrome b gene from 34 samples, of which 24 represented 13 species of the East Asian botiine fishes, while the other 10 were non-botiine loach species. For the 1140 bp sequences determined, 494 sites were variable ones, of which 424 were parsimony informative. With Myxocyprinus asiaticus as an outgroup, molecular phylogenetic trees were constructed using the neighbor-joining, maximum parsimony, maximum likelihood and Bayesian methods. All molecular phylogenetic trees revealed that botiine fishes form a monophyletic group and are distantly related to other loaches, suggesting that the Botiinae should be placed in their own family. Within the Botiinae, there are three genera; Botia, Parabotia, and Leptobotia, each genus forming a monophyletic group, with the genus Botia as the most ancestral split. Our molecular results are in agreement with morphological analyses of botiines, suggesting that Botia is the ancestral genus, while Leptobotia and Parabotia were resolved as more derived sister groups.

Phylogenetic studies of Chinese labeonine fishes (Teleostei : Cyprinidae) based on the mitochondrial 16S rRNA gene

The mitochondrial 16S ribosomal RNA gene is sequenced from 24 ingroups taxa, including 18 species from Labeoninae grouped in 13 genera. Phylogenetic analyses are subjected to neighbor joining, maximum parsimony, maximum likelihood and Bayesian analyses. Phylogenetic analysis indicates that Labeoninae is basically a monophyletic assemblage and can be divided into 2 major clades: one comprising the genera Cirrhinus, Crossocheilus and Garra; and the other consisting of the genera Labeo, Sinilabeo, Osteochilus, Pseudoorossocheilus, Parasinilabeo. Ptychidio, Semilabeo, Pseudogyricheilus, Rectori and Discogobio. According to our present analysis, the features such as the presence of the adhesive disc on the chin and the pharyngeal teeth in 2 rows used in the traditional taxonomy of Labeoninae provide scarce information for phylogeny of labeonine fishes.

Phylogeny of the cuttlerishes (Mollusca : Cephalopoda) based on mitochondrial COI and 16S rRNA gene sequence data

To clarify cuttlefish phylogeny, mitochondrial cytochrome c oxidase subunit 1 (COI) gene and partial 16S rRNA gene are sequenced for 13 cephalopod species. Phylogenetic trees are constructed, with the neighbor-joining method. Coleoids are divided into two main lineages, Decabrachia and Octobrachia. The monophyly of the order Sepioidea, which includes the families Sepiidae, Sepiolidae and Idiosepiidae, is not supported. From the two families of Sepioidea examined, the Sepiolidae are polyphyletic and are excluded from the order. On the basis of 16S rRNA and amino acid of COI gene sequences data, the two genera (Sepiella and Sepia) from the Sepiidae can be distinguished, but do not have a visible boundary using COI gene sequences. The reason is explained. This suggests that the 16S rDNA of cephalopods is a precious tool to analyze taxonomic relationships at the genus level, and COI gene is fitter at a higher taxonomic level (i.e., family).

Cloning and sequencing of the growth hormone gene of large yellow croaker and its phylogenetic significance

Using conserved primers and the PCR reaction, the growth hormone (GH) gene and the 3'-UTR of the large yellow croaker (Pseudosciaena crocea) were amplified and sequenced. The gene structure was analyzed and compared to the GH genes of 5 other percoid fish downloaded from Genbank. Also the GH gene of the large yellow croaker and the genes from 14 Percoidei and 2 Labroidei species were aligned using Clustal X. A matrix of 564 bp was used to construct the phylogenetic tree using maximum parsimony and neighbor-joining methods. Phylogenetic trees by the two methods are identical in most of the clades with high bootstrap support. The results are also identical to those from morphological data. In general, this analysis does not support the monophyly of the families Centropomidae and Carangidae. But our GH gene tree indicates that the representative species of the families Sparidae and Sciaenidae are a monophyletic group.

Genetic structure of Chinese sucker population Myxocyprinus asiaticus in the Yangtze River based on mitochondrial DNA marker

The sequencing analysis of the mitochondrial DNA control region (mtCR DNA) was performed to assess the genetic divergence and population structure of the Chinese sucker Myxocyprinus asiaticus (Cypriniformes Catostomidae) using four sample lots from natural populations of the Yangtze River. The mtCR DNA sequences of approximately 920 base pairs were obtained. A total of 223 nucleotide positions were polymorphic, and these defined 39 haplotypes. Of the 39 haplotypes, 37 (90%) were not shared, and among the populations as a whole there was little sharing of haplotypes. The average haplotype diversity (0.958) and the average nucleotide diversity (0.052) indicated a higher level of genetic diversity of Chinese sucker through the river. Analysis of molecular variation (AMOVA) of data revealed significant partitioning of variance (P<0.001) among populations (60.29%), and within populations (39.71%). The topology according to the neighbor joining and maximum parsimony methods showed mosaic composition of the 39 haplotypes, suggesting that the populations wore not completely divergent. The pairwise F statistic values, however, indicated that the population structuring existed to some extent among the geographic populations. There was a positive relationship between the aquatic distance and the genetic distance (Fst) among the populations (P<0.05). Based on our data, it is suggested that genetic drift, gene flow, and stochastic events are the possible factors influencing the population structure and genetic variation.

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 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.

Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes

The mitochondrial DNA control region is amplified and sequenced from 8 genera and 10 species of gobiobotine fishes. The phylogenetic tree of Gobiobotinae and some representative species of other Cyprinid subfamilies obtained by the method of neighborhood joining, maximum likelihood and maximum parsimony with Danio rerio as an outgroup indicates that Gobiobotinae fishes are a monophyletic group which is close to Gobioninae subfamily. Gobiobotinae should be included into subfamily Gobioninae in terms of phylogenetic analysis. The research result supports that Gobiobotinae can be divided into genus Xenophysogobio and Gobiobotia. Xenophysogabio is the most primitive genera in the subfamily.

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.

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 molecule 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 60 the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%-0.30% sequence divergence per million years.

Phylogenetic relationships among six species of Epistylis inferred from 18S-ITS1 sequences

Phylogenetic relationships among six species of Epistylis (i.e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E, galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. 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 macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.

A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda : Penaeidae) based on mitochondrial dna sequences of selected species from the Indo-West Pacific

Phylogenetic relationships within Metapenaeopsis remain largely unknown. The modern revision of the genus suggests that the shape of the petasma, followed by the presence of a stidulating organ, are the most important distinguishing taxonomic features. In the present study, phylogenetic relationships were studied among seven Metapenaeopsis species from the Indo-West Pacific based on partial sequences of mitochondrial 16S rRNA and cytochrome c oxidase I (COI) genes. Mean sequence divergence was 6.4% for 16S and 15.8% for COI. A strikingly large nucleotide distance (10.0% for 16S and 16.9% for COI) was recorded between M. commensalis, the only Indo-West Pacific species with a one-valved petasma, and the other species with a two-valved petasma. Phylogenetic analyses using neighbor-joining, maximum parsimony, and maximum likelihood generated mostly identical tree topologies in which M. commensalis is distantly related to the other species. Two clades were resolved for the remaining species, one with and the other without a stridulating organ, supporting the main groupings of the recent taxonomic revision. Results of the present study also indicate that the deep-water forms represent a relatively recent radiation in Metapenaeopsis.

中国松鼠科 Sciuridae (Non-flying squirrels) 动物的分类和分布及系统发育研究

松鼠科隶属于哺乳纲、啮齿目，是一类世界广布性动物，全世界共计36 属 234 种。本文通过形态分析及分子生物学方法，研究了我国松鼠科动物的分类及 系统发育关系，内容包括以下两个方面： 一、中国松鼠科动物的分类 本研究查看了中科院昆明动物研究所、中科院动物研究所、云南大学、四川 省林业科学研究院、四川大学、陕西师范大学、陕西动物研究所、西北大学、上 海自然历史博物馆、广东昆虫所馆藏该科各类群标本。同时，结合相关文献，对 各类群的外形特征进行了详细的描述和系统分类整理，我国共计10 属34 种。测 取可量性状数据共计20800 个（完整头骨共计1300 号），而且还运用多变量及单 变量分析方法进行数据分析，对部分类群的种下分类结果进行分析：1.探讨了分 布于中国境内的明纹花鼠（Tamiops mcclellandii）3 亚种的有效性。2.研究了 隐纹花鼠（Tamiops swinhoei）在中国的分化并描记了分布于四川马尔康地区的 隐纹花鼠为一新亚种（Tamiops swinhoei markamensis）。3.描记了分布于云南 省东北部昭通地区的赤腹松鼠为一新亚种：昭通亚种（Callosciurus erythraeus zhaotongensis）。4. 提出了分布于云南省无量山区的泊氏长吻松鼠为一新亚种： 无量山亚种（Dremomys pernyi wuliangshanensis）。 二、中国松鼠科动物的系统发育研究 2004－2005 年相继到滇西北高黎贡山、香格里拉，滇西南临沧地区，滇东 南马关、麻栗坡、富宁，滇东北昭通地区进行标本采集，基本收集到我国南方松 鼠科属、种样品进行分子生物学研究。 1.中国松鼠科动物各属的系统发育关系 在分析线粒体细胞色数b 基因（1040bp）序列的基础上，运用贝叶斯法 （Bayesian phylogenetic reconstruction approaches）、最简约法（Maximum parsimony method）、邻接法（Neighbor Joining method）构建中国松鼠科动物 所有属间系统发育树。结果表明：所分析的10 属分别聚集为3 群，巨松鼠属Ratufa单独成为一群，丽松鼠属Callosciurus、长吻松鼠属Dremomys、花松鼠属 Tamiops 以及线松鼠属Menetes 成为一群，松鼠属Sciurus、岩松鼠属 Sciurotamias、花鼠属Tamias、旱獭属Marmota 以及黄鼠属Spermophilus 成 为一群。在此基础上我们进一步探讨了中国松鼠科动物的分化与环境变化的关 系。 2.长吻松鼠属的系统发育关系 在分析线粒体细胞色数b 基因（378bp）序列的基础上，我们重建了长吻松 鼠属内5 个类群间的系统发育关系，结合对5 类群外部形态特征的详细比较，我 们探讨并论证了红腿长吻松鼠、橙喉长吻松鼠作为种的地位的有效性，同时论证 了该属内泊氏长吻松鼠最早分化，其次为橙腹长吻松鼠，第三是红腿长吻松鼠， 红颊长吻松鼠和橙喉长吻松鼠是最后分化的类群。

鰋鮡鱼类(Glyptosternoid fishes)的系统进化和动物地理学研究

鰋鮡鱼类共包括9 属43 种（亚种），隶属于鲇形目（Siluriformes）鮡科 （Sisoridae）鰋鮡亚科（Glyptosternae）中鰋鮡族（Tribe Glyptosternini）的鰋鮡 亚族（Subtribe Glyptosternina）。鰋鮡鱼类形态上的共同特征为：无胸吸着器，胸、 腹鳍水平展开，第一根鳍条完全分节或在外缘生出许多软骨细条，被外表皮所裹， 在腹面看到的是许多与分节或软骨细条大致对应的横纹皱褶。鰋鮡鱼类集中分布 于青藏高原周边的水系中，部分属种向西分布到了中亚地区的阿姆河上游，是适 应山区急流环境的一群鱼类。近年来一系列的研究表明，鰋鮡鱼类为一单系类群， 它的起源和演化与青藏高原的隆升有着直接的关系。鰋鮡鱼类的系统发育研究， 可以为青藏高原隆升的年代、幅度和形式提供间接的证据，其系统发育树的拓扑 结构也直接反映了东喜马拉雅地区诸水系的形成与演变。 本研究对鰋鮡鱼类9 属进行了系统整理。1. 发现并描述了异齿鰋属 （Oreoglanis）两新种，分别为分布于景东无量山（澜沧江水系）的景东异齿鰋 （O. jingdongensis）和分布于怒江水系南景河和南滚河的无斑异齿鰋（O. immaculatus）。认为分布于中国的异齿鰋属鱼类均属于尖须异齿鰋种组（O. siamensis species group）。指出区分异齿鰋属两个种组：尖须异齿鰋种组和细尾 异齿鰋种组（O. delacouri species group）的特征是下唇中部是否具有中央缺刻， 尾型的差别（新月型尾或凹型尾）不能用来区分两个种组，给出了异齿鰋属的检 索表，并绘制了异齿鰋属鱼类分布图。2. 对鮡属（Pareuchiloglanis）鱼类进行了 系统整理，通过外部形态度量性状的比较，认为分布于澜沧江水系的，曾经被鉴 定为扁头鮡（P. kamengensis）的标本，应属于大鳍鮡（P. macropterus），扁头鮡 和大鳍鮡之间的最明显的差别在于腹鳍前长的不同。前者的腹鳍前长为体长的 53.2-64.9%，后者的腹鳍前长均不达体长的50%。3. 通过比较金沙江水系分布的 5 种鮡属鱼类，中华鮡（P. sinensis）、前臀鮡（P. anteanalis）、壮体鮡（P. robusta）、 四川鮡（P. sichuanensis）和天全鮡（P. tianquanensis），认为天全鮡和四川鮡之 间分布水系重叠，外部形态亦无差别，天全鮡很可能为四川鮡的同物异名。给出 了鮡属鱼类的系统检索表，并绘制了鮡属鱼类分布图。利用分子系统学的原理和方法对鰋鮡鱼类进行系统发育研究。测定了6 属 15 种鰋鮡鱼类和鮡科中非鰋鮡鱼类4 属7 种共28 个体的线粒体Cyt b 基因部分 片段和全序列（1138 bp），结合从GenBank 下载的相关类群相同的基因序列，以 魾属（Bagarius）的巨魾（B. yarrelli），纹胸鮡属（Glyptothorax）的穴形纹胸鮡 （G. cavia）、亮背纹胸鮡（G. dorsalis）、扎那纹胸鮡（G. zainaensis），福建纹胸 鮡（G. fukiensis fukiensis）、海南纹胸鮡（G. fukiensis hainanensis），黑鮡属（Gagata） 的长丝黑鮡（G. dolichonema）以及褶鮡属（Pseudecheneis）的黄斑褶鮡（P. sulcatus） 和无斑褶鮡（P. immaculatus）作为外类群，采用贝叶斯法（Bayesian）、最简约 法（maximum pasimony, MP）和邻接法（neighbour-joining, NJ）构建系统发育树。 结果显示： 1. 鰋鮡鱼类为一单系类群，并且与褶鮡属互为姐妹群关系； 2. 原鮡属、鰋属和凿齿鮡属是鰋鮡鱼类的三个基部类群； 3. 异齿鰋属构成为一个单系群，大鳍异齿鰋最早从该属的基部分化出来； 4. 石爬鮡属构成一个单系，并与分布于金沙江水系的中华鮡＋前臀鮡构成姐妹 群，黄石爬鮡和青石爬鮡的单倍型相互交错；显示两个物种的分类是不合适的， 而是同一水系不同支流种群之间梯度变异的例子，依据本次研究所得出的三个分 支图，结合青石爬鮡自西至东分布于金沙江、雅砻江、大渡河、青衣江、岷江等 的分布格局以及形态特征的分布，显示形态特征的分布变化有以下趋势：自西至 东，腹鳍位置逐渐前移；颌须渐趋缩短；胸鳍趋向发达、伸达腹鳍起点。这些变 化趋势是同一水系不同支流种群之间梯度变异的极好例子； 5. 分布于澜沧江以西（包括澜沧江）水系的鮡属鱼类（扁头鮡、细尾鮡、短鳍 鮡）与分布于怒江和伊洛瓦底江水系的拟鰋属鱼类构成为一支，并且二者共同与 分布于元江上游（红河水系）的大孔鮡构成为单系。其中，短体拟鰋和拟鰋互为 姐妹种；而扁头鮡和短鳍鮡也互为姐妹种；细尾鮡的系统地位则尚不能确定； 6. 无论在MP 树、贝叶斯树还是NJ 树中，石爬鮡属、鮡属、拟鰋属和异齿鰋属 构成一个单系，并且支持率达到了100％。 7. 鰋属位于鰋鮡鱼类的基部，是较早就从鰋鮡鱼类祖先中演化出来的一个类群， 鰋类的口吸盘是一个趋同性状，是在急流环境条件下形成的一种适应性性状，在 鰋类各属中不是同源特征； 8. 鮡属鱼类不是一个单系类群，分布于金沙江流域的鮡属鱼类与同流域分布的石爬鮡属鱼类聚成一支；澜沧江及其以西水系分布的鮡属鱼类与同流域分布的拟 鰋属鱼类聚成一支，之后这两支又同异齿鰋属共同构成为一个大支。 结合鰋鮡鱼类的系统发育分支图对其动物地理学进行研究。鰋鮡鱼类是由类 似纹胸鮡属（Glyptothorax）鱼类的祖先演化而来，鰋属（Exostoma）和凿齿鮡 属（Glaridoglanis）是较早就从从类似原鮡的祖先中演化出来，鮡属、石爬鮡属、 拟鰋属和异齿鰋属这一大支由类似原鮡的祖先演化而来。在青藏高原强烈隆起等 重大地理隔离事件发生之前，类似于现生的原鮡属鱼类已经广布喜马拉雅山脉东 西两侧。在青藏高原强烈隆起等重大地理隔离事件发生后，鰋鮡鱼类在相同的地 理隔离下独自演化为现在的分布格局。