中国科群系统发育与地理分布格局研究进

中国科群鱼类至今已记录8属23种(亚种)，但分布于云南澜沧江、怒江等水系的一些种类及分布于四川西南地区的属和石爬属的一些种的有效性仍存疑问或争议，值得进一步研究。分子生物学证据为解决种级阶元分类地位的争议，或者为系统发育研究提供了微观证据。但形态学之间、形态学与分子生物学之间、分子生物学之间的研究结果均不完全吻合，甚至同一作者不同年代形态学与分子生物学的研究结果也相互矛盾。鱼类的分布格局及不同阶元的分化与青藏高原的3次隆升有着密不可分的关系。鱼类的分化不仅体现在各大水系之间，也体现在同一水系的不同支流或上下游之间。该类群的分化既包括了自然阻障形成导致的分类阶元的隔离分化过程，也包括了同一阶元在同一水系扩散分化的生态适应过程。这两个过程的交织，使得鱼类的分化和分布异常复杂。尽可能收全鱼类现生种类，发现更多的分类学证据，形态特征与分子证据的有机结合，是今后鱼类分类、系统发育和地理分布格局研究的发展方向。     

中国(鱼兆)科(鱼匽)(鱼兆)群系统发育与地理分布格局研究进展

中国鮡科鰋鮡群鱼类至今已记录8属23种(亚种),但分布于云南澜沧江、怒江等水系的一些种类及分布于四川西南地区的属和石爬属的一些种的有效性仍存疑问或争议,值得进一步研究。分子生物学证据为解决种级阶元分类地位的争议,或者为系统发育研究提供了微观证据。但形态学之间、形态学与分子生物学之间、分子生物学之间的研究结果均不完全吻合,甚至同一作者不同年代形态学与分子生物学的研究结果也相互矛盾。鱼类的分布格局及不同阶元的分化与青藏高原的3次隆升有着密不可分的关系。鰋鮡鱼类的分化不仅体现在各大水系之间,也体现在同一水系的不同支流或上下游之间。该类群的分化既包括了自然阻障形成导致的分类阶元的隔离分化过程,也包括了同一阶元在同一水系扩散分化的生态适应过程。这两个过程的交织,使得鰋鮡鱼类的分化和分布异常复杂。尽可能收全鰋鮡鱼类现生种类,发现更多的分类学证据,形态特征与分子证据的有机结合,是今后鰋鮡鱼类分类、系统发育和地理分布格局研究的发展方向。     

基于16S rRNA和Cyt b基因序列的鰶亚科系统发育研究

对鰶亚科4属5种鱼类的线粒体基因组16S rRNA和Cyt b基因片段序列进行序列比较和系统发育关系分析。结果显示:5种鰶亚科鱼类的16S rRNA和Cy tb基因片段同源序列长度分别为525 bp和402 bp,序列联合后的序列总长度为927 bp,其中多态位点178个,简约信息位点123个。选取太平洋鲱Clupea pallasii和大西洋鲱C.harengus为外类群,采用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯法(BI)分别对2个基因片段序列进行了聚类分析,并联合2个基因片段利用邻接法、最大简约法和贝叶斯法进行分析。系统发育分析显示:斑鰶Konosirus punctatus与花鰶Clupanodon thriss亲缘关系最近,分布于美洲大陆的真鰶属Dorosoma鱼类与印度洋、太平洋分布的斑鰶属、花鰶属和海鰶属Nematalosa鱼类亲缘关系较远。     

Phylogeny of the East Asian botiine loaches (Cypriniformes,Botiidae) inferred from mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> 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, andLeptobotia, 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.     

Molecular phylogeny of the stromateoid fishes (Teleostei: Perciformes) inferred from mitochondrial DNA sequences and compared with morphology-based hypotheses

The phylogenetic relationships among 21 species of stromateoid fishes, representing five families and 13 genera, were reconstructed using 3263bp of mitochondrial DNA sequences, including the posterior half of the 16S rRNA and entire COI and Cytb genes. The resultant molecular phylogenies were compared with previous phylogenetic hypotheses inferred from morphological characters. Molecular phylogenetic trees were constructed using the maximum parsimony, maximum likelihood, and Bayesian methods. All three methods resulted in well-resolved trees with most nodes being supported by moderate to high support values. In contrast to previous morphological analyses, which resulted in non-monophyly of Centrolophidae, all three methods utilized for the present molecular analyses supported the monophyly of Centrolophidae, as well as the reciprocal monophyly of the other stromateoid families, previous morphological hypotheses being rejected by the Templeton and Shimodaira-Hasegawa tests. In addition, the three methods indicated a sister-group relationship between Ariommatidae and Nomeidae. The position of Tetragonuridae was, however, incongruent between the MP method and the ML and Bayesian methods, being placed in the most basal position of Stromateoidei in the former, but occupying a sister relationship to Stromateidae in the latter. Comparison of the molecular phylogenies to previous morphological hypotheses suggested that evolutionary changes in morphological characters have not occurred equally among the stromateoid lineages, the evolution of the centrolophids not having been accompanied by appreciable morphological changes, whereas other stromateoids have undergone considerable morphological changes during their evolutionary history. The molecular phylogenies also shed some light on the evolutionary pattern of the pharyngeal sac, two of the four types of sac corresponding to two main lineages of Stromateoidei. Some taxonomic implications were also discussed.     

Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny

The phylogeny of salmonid fishes has been the focus of intensive study for many years, but some of the most important relationships within this group remain unclear. We used 269 Genbank sequences of mitochondrial DNA (from 16 genes) and nuclear DNA (from nine genes) to infer phylogenies for 30 species of salmonids. We used maximum parsimony and maximum likelihood to analyze each gene separately, the mtDNA data combined, the nuclear data combined, and all of the data together. The phylogeny with the best overall resolution and support from bootstrapping and Bayesian analyses was inferred from the combined nuclear DNA data set, for which the different genes reinforced and complemented one another to a considerable degree. Addition of the mitochondrial DNA degraded the phylogenetic signal, apparently as a result of saturation, hybridization, selection, or some combination of these processes. By the nuclear-DNA phylogeny: (1) (Hucho hucho, Brachymystax lenok) form the sister group to (Salmo, Salvelinus, Oncorhynchus, H. perryi); (2) Salmo is the sister-group to (Oncorhynchus, Salvelinus); (3) Salvelinus is the sister-group to Oncorhynchus; and (4) Oncorhynchus masou forms a monophyletic group with O. mykiss and O. clarki, with these three taxa constituting the sister-group to the five other Oncorhynchus species. Species-level relationships within Oncorhynchus and Salvelinus were well supported by bootstrap levels and Bayesian analyses. These findings have important implications for understanding the evolution of behavior, ecology and life-history in Salmonidae.     

基于线粒体COⅠ基因的沙鳅亚科鱼类DNA条形码及其分子系统发育研究

选择线粒体COⅠ基因作为分子标记,进行沙鳅亚科鱼类（Botiinae）DNA条形码及其分子系统发育研究。研究获得了沙鳅亚科7属19种共131个个体的COⅠ基因序列,利用MEGA5.0软件分析了沙鳅亚科鱼类COⅠ基因的序列特征,计算了种内及种间遗传距离。沙鳅亚科鱼类的分子系统发育关系的重建分别采用NJ法和Bayesian法。研究发现,沙鳅亚科COⅠ基因的碱基组成为: A 24.4%、T 29.5%、G 18.0%、C 28.1%。沙鳅亚科鱼类种内平均遗传距离为0.0020.000,种间平均遗传距离为0.1480.008。DNA条形码研究结果显示,所分析的19种沙鳅鱼类各自分别聚成单系分支,表明COⅠ基因在本研究中具有100%的物种鉴别率。同时,系统发育分析支持各属的单系性,并且结果显示沙鳅亚科鱼类聚为两个分支,其中一支由薄鳅属和副沙鳅属构成,另一分支则包括: （沙鳅属、色鳅属）和 中华沙鳅属、（缨须鳅属、安彦鳅属）。因此,COⅠ基因可以作为有效的分子标记对沙鳅亚科进行DNA条形码研究以及分子系统发育研究。       

Phylogenetic relationships and estimation of divergence times among Sisoridae catfishes

Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyzed separately and combined into a single data set to reconstruct phylogenetic relationships among Chinese sisorids. Both Chinese Sisoridae as a whole and the glyptosternoid taxa formed monophyletic groups. The genus Pseudecheneis is likely to be the earliest diverging extant genus among the Chinese Sisoridae. The four Pareuchiloglanis species included in the study formed a monophyletic group. Glaridoglanis was indicated to be earliest diverging glyptosternoid, followed by Glyptosternon maculatum and Exostoma labiatum. Our data supported the conclusion that Oreoglanis and Pseudexostoma both formed a monophyletic group. On the basis of the fossil record and the results of a molecular dating analysis, we estimated that the Sisoridae diverged in the late Miocene about 12.2 Mya. The glyptosternoid clade was indicated to have diverged, also in the late Miocene, about 10.7 Mya, and the more specialized glyptosternoid genera, such as Pareuchiloglanis, originated in the Pleistocene (within 1.9 Mya). The speciation of glyptosternoid fishes is hypothesized to be closely related with the uplift of the Qinghai-Tibet Plateau.     

基于线粒体基因cyt b的鹟亚科部分鸟类系统发育

采用分子系统学方法对鹟亚科(Muscicapinae)6属31种鸟类的cytb基因序列992bp进行系统发生分析。以荒漠伯劳(Lanius isabellinus)和发冠卷尾(Dicrurus hottentottus)为外群,采用贝叶斯法(Bayesian,BI)、最大似然法(Maximum-likelihood,ML)和最大简约法(Maximumparsimony,MP)分别构建鹟亚科的系统发育树。结果支持:寿带属(Terpsiphone)、扇尾鹟属(Rhipidura)与方尾鹟属(Culicicapa)可从鹟亚科中移出,其中寿带属归入王鹟科(Monarchidae),扇尾鹟属与方尾属归入扇尾鹟科(Rhipiduridae);鹟属(Muscicapa)、仙鹟属(Niltava)为单系发生,并聚为姐妹群,亲缘关系较近;姬鹟属(Ficedula)并非单系发生,白眉姬鹟(Ficedulazanthopygia)在3种系统发生树中的位置差别较大,研究结果未能确定其分类地位;铜蓝(Muscicapa thalassina)与白腹蓝(Cyanoptila cyanomelana)亲缘关系较近,前者应从属中移出,后者应从姬属移出,共同归入仙属或列为仙属的姐妹属。上述结论解决了亚科部分有争议属、种间的进化关系,为亚科分类系统提供了DNA水平证据。     

Snakes across the Strait: trans-Torresian phylogeographic relationships in three genera of Australasian snakes (Serpentes: Elapidae: Acanthophis, Oxyuranus, and Pseudechis)

We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis-death adders; Oxyuranus-taipans; Pseudechis-blacksnakes), using parsimony, maximum likelihood, and Bayesian analysis of sequences of the mitochondrial cytochrome b and ND4 genes. In Acanthophis and Pseudechis, we find evidence of multiple trans-Torresian sister-group relationships. Analyses of the timing of cladogenic events suggest crossings of the Torres Strait on several occasions between the late Miocene and the Pleistocene. These results support a hypothesis of repeated land connections between Australia and New Guinea in the late Cenozoic. Additionally, our results reveal undocumented genetic diversity in Acanthophis and Pseudechis, supporting the existence of more species than previously believed, and provide a phylogenetic framework for a reinterpretation of the systematics of these genera. In contrast, our Oxyuranus scutellatus samples from Queensland and two localities in New Guinea share a single haplotype, suggesting very recent (late Pleistocene) genetic exchange between New Guinean and Australian populations.     

独龙江流域鱼类分布特征及其体长与体重的关系(英文)

鱼类主要分布于青藏高原周边,是一群适合于急流生活的科鱼类。在独龙江流域7个点共采集271号鱼类标本(隶属属、属和异齿属),结合各采集点数据绘制大鳍异齿、藏和扁头的分布直方图,结果显示,藏(E. labiatum)在流速较快的独龙江下游各采集点的种群数量较上游高,更适应急流生境。同时研究了这3种鱼类的体长与体重的关系,参数b(W=aLb)的范围在2.8201和3.0131之间,均为异速生长;藏的生长类型最接近等速生长。     

鲴亚科分子系统学研究

为探讨鲴亚科(Xenocyprinae)鱼类系统发育关系,研究基于2种线粒体基因和5种核基因序列对鲴亚科各物种的系统发育关系和分化时间进行评估。结果显示:不同方法和数据类型获得了基本一致的拓扑结构。3个属的单系性都得到了很好地支撑;但是,它们之间的进化关系却随着分子标记的不同而改变。这一结果可能是由于早期的基因流或谱系的随机分选所致。此外,银鲴(Xenocypris argentea)、云南鲴(Xenocypris yunnanensis)和黄尾鲴(Xenocypris davidi)之间呈现出嵌套型的谱系关系,暗示它们之间存在基因交流的可能性。基于化石地层年代校正的分子钟估算结果显示,鲴亚科主要类群的分化发生在中新世晚期,约15—12百万年前(Millions of years ago, Ma),这与东亚季风强盛时期的时间相吻合。     

Phylogeny and host-specificity of European seed beetles (Coleoptera, Bruchidae), new insights from molecular and ecological data

We used partial sequences of three mitochondrial genes (12S rRNA, cytochrome b, and cytochrome c oxidase subunit I) to reconstruct the phylogeny of European seed beetles (Bruchidae) belonging to the genera Bruchus Linnaeus and Bruchidius Schilsky. Adult beetles examined in this study were obtained from larvae bred from seeds directly collected in the field. Parsimony, maximum likelihood, and Bayesian inference were used to infer phylogenetic relationships among species. Both genera, Bruchidius and Bruchus, formed monophyletic groups in all analyses. Our results were partially in discrepancy with existing taxonomic groups (Borowiec, 1987). Critical analysis of relationships among taxa, and exhaustive review of host-plants data highlight the very high level of specialization of these seed beetles. Phylogenetically related insects were associated with host-plants belonging to the same botanical tribes.     

独龙江流域鰋鮡鱼类分布特征及其体长与体重的关系

鰋鮡鱼类主要分布于青藏高原周边,是一群适合于急流生活的鮡科鱼类。在独龙江流域7个点共采集271号鰋鮡鱼类标本（隶属鮡属、鰋属和异齿鰋属）,结合各采集点数据绘制大鳍异齿鰋、藏鰋和扁头鮡的分布直方图,结果显示,藏鰋（E．labiatum）在流速较快的独龙江下游各采集点的种群数量较上游高,更适应急流生境。同时研究了这3种鰋鮡鱼类的体长与体重的关系,参数b（W=aL^b）的范围在2．8201和3．0131之间,均为异速生长;藏鰋的生长类型最接近等速生长.     

独龙江流域(鱼匽)(鱼兆)鱼类分布特征及其体长与体重的关系

(鱼匽)(鱼兆)鱼类主要分布于青藏高原周边, 是一群适合于急流生活的(鱼兆)科鱼类. 在独龙江流域7个点共采集271号(鱼匽)(鱼兆)鱼类标本(隶属(鱼兆)属、(鱼匽)属和异齿(鱼匽)属), 结合各采集点数据绘制大鳍异齿(鱼匽)、藏(鱼匽)和扁头(鱼兆)的分布直方图, 结果显示, 藏(鱼匽)(E. labiatum)在流速较快的独龙江下游各采集点的种群数量较上游高, 更适应急流生境. 同时研究了这3种(鱼匽)(鱼兆)鱼类的体长与体重的关系, 参数b(W=aLb)的范围在2.8201和3.0131之间, 均为异速生长;藏(鱼匽)的生长类型最接近等速生长.     

Molecular phylogeny of pontobdelline leeches and their place in the descent of fish leeches (Hirudinea, Piscicolidae)

Phylogenetic relationships of all genera of the fish leech subfamily Pontobdellinae were investigated using mitochondrial (12S rDNA, COI, tRNA-Leu, ND1) and nuclear (28S rDNA) DNA sequences under maximum likelihood, Bayesian inference and parsimony. All methods resulted in trees that corroborated the monophyly of the family Piscicolidae, but recovered their subfamily Pontobdellinae as non-monophyletic. Based on the basal position of the giant Antarctic Megaliobdella szidati , it is hypothesized that the putative ancestor of fish leeches was a free-ranging, large bodied, muscular leech. The next branch contains parasites of cartilaginous fishes, Pontobdella muricata and Pontobdella macrothela . Two remaining genera of the subfamily (the Arctic Oxytonostoma and the Antarctic Moorebdellina ) showed weak affinities to other piscicolid taxa. The obtained phylogenetic hypothesis suggests a possible transition from an ancestral free-ranging life style and temporary parasitism, to parasitism on cartilaginous fishes, followed by parasitism on bony fishes.     

Molecular systematics of Blepharida beetles (Chrysomelidae: Alticinae) and relatives

I investigated the phylogenetic relationships within the New World Blepharida and among related genera, using sequences of the Internal Transcriber Spacer 2 (ITS2) of nuclear ribosomal DNA and sequences of the COI and COII genes of the mitochondrial genome. Cladistic analyses were performed using parsimony, maximum likelihood, and Bayesian methods. These methods generated almost identical topologies using the combined data sets. The analyses suggest that Blepharida rhois, the type species, should be separated from the New World Blepharida and that the New World Blepharida might be congeneric with closely related Notozona. Also, according to this phylogeny, all of the New World Blepharida species that feed on Bursera (Burseraceae) form a single monophyletic clade, with the Afrotropical species forming its sister clade. The analyses also identified four main groups of species within the New World Blepharida.     

Molecular phylogeny of the subfamily Schizothoracinae (Teleostei: Cypriniformes: Cyprinidae) inferred from complete mitochondrial genomes

The schizothoracine fishes, members of the Teleost order Cypriniformes, are one of the most diverse group of cyprinids in the Qinghai–Tibetan Plateau and surrounding regions. However, taxonomy and phylogeny of these species remain unclear. In this study, we determined the complete mitochondrial genome of Schizopygopsis malacanthus. We also used the newly obtained sequence, together with 31 published schizothoracine mitochondrial genomes that represent eight schizothoracine genera and six outgroup taxa to reconstruct the phylogenetic relationships of the subfamily Schizothoracinae by different partitioned maximum likelihood and partitioned Bayesian inference at nucleotide and amino acid levels. The schizothoracine fishes sampled form a strongly supported monophyletic group that is the sister taxon to Barbus barbus. A sister group relationship between the primitive schizothoracine group and the specialized schizothoracine group + the highly specialized schizothoracine group was supported. Moreover, members of the specialized schizothoracine group and the genera Schizothorax, Schizopygopsis, and Gymnocypris were found to be paraphyletic.     

Evolution of a Neotropical marine fish lineage (Subfamily Chaenopsinae, Suborder Blennioidei) based on phylogenetic analysis of combined molecular and morphological data

Phylogenetic relationships within tube blennies (Chaenopsinae) were reconstructed using Bayesian, maximum parsimony and likelihood analyses of multiple molecular markers (mitochondrial DNA: COI; nuclear DNA: TMO-4C4, RAG1, Rhodopsin, and Histone H3) and 148 morphological characters. This total-evidence based topology is well-resolved and congruent across analytical methods with strong support for the monophyly of the Chaenopsinae, all included genera and several internal nodes. A rapid radiation in the early evolution of chaenopsins is inferred from the relatively poor support values for relationships among basal lineages and their divergence into different habitats (rocky reefs, coral reefs and the reef/sand interface). Rates of molecular evolution in chaenopsins, as inferred by divergence among four putative transisthmian geminate species pairs, are rapid compared to other fishes. Conflicts among genetic markers and morphology are especially evident within the genus Coralliozetus, with different species relationships supported by morphology, TMO-4C4, and RAG1 plus Rhodopsin. This study hypothesizes a novel sistergroup relationship between Ekemblemaria and Hemiemblemaria, consistent with morphological, molecular and habitat use data. Our total evidence phylogenetic hypothesis indicates that previously hypothesized morphological characters supporting a close relationship between Hemiemblemaria and Chaenopsis plus Lucayablennius resulted from convergent evolution in these relatively free-swimming blennies.     

基于28S rDNA D1-D2基因片段与16S rDNA部分序列联合分析的叶肢介系统发育研究

叶肢介(Conchostraca)的系统发育问题一直是甲壳动物研究中颇具争议的一个课题.本研究测定了我国2种叶肢介(Eocyzicus mongolianus,Eoc yzicus orientalis)的28S rDNA D1-D2区基因序列和16S rDNA E-G区序列,并与GenBank中的20种叶肢介序列一起...