Molecular phylogeny of gobioid fishes (Perciformes: Gobioidei) based on mitochondrial 12S rRNA sequences

The molecular phylogeny of the gobioid fishes, comprising 33 genera and 43 valid species, was examined by use of complete mitochondrial 12S rRNA and tRNA(VAL)genes. Both parsimony and neighbor-joining analyses revealed comparable results and are generally congruent with those of morphological studies. The Odontobutis, which was always placed at the base of the phylogenetic trees, can be treated as a sister group of all other nonrhyacichthyid gobioids. Within eleotrid fishes, the monophyly of the Eleotrinae is strongly supported by molecular data. The Butinae is closer to fishes with five branchiostegal rays and should be treated as a sister group of the latter. The group with five branchiostegal rays, except for sicydiines, can be divided into two groups according to their epural counts. Fish with one epural, the Gobiinae of Pezold plus Microdesmidae, form a monophyletic group which is sister to those with two epurals, the Oxudercinae and Gobionellinae of Pezold. However, Sicydiinae, which have one epural, are closer to the Oxudercinae and Gobionellinae rather than to the Gobiinae. Since progressive reduction in epural number has been observed along this lineage, the sicydiines should be treated as a derived group within the groups with two epurals.     

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

Despite some popularity of hamsters as pets and laboratory animals there is no reliable phylogeny of the subfamily Cricetinae available so far. Contradicting views exist not only about the actual number of species but also concerning the validity of several genera. We used partial DNA sequences of two mitochondrial (cytochrome b, 12S rRNA) and one partial nuclear gene (von Willebrand Factor exon 28) to provide a first gene tree of the Cricetinae based on 15 taxa comprising six genera. According to our data, Palaearctic hamsters fall into three distinct phylogenetic groups: Phodopus, Mesocricetus, and Cricetus-related species which evolved during the late Miocene about 7-12MY ago. Surprisingly, the genus Phodopus, which was previously thought to have appeared during the Pleistocene, forms the oldest clade. The largest number of extant hamster genera is found in a group of Cricetus-related hamsters. The genus Cricetulus itself proved to be not truly monophyletic with Cricetulus migratorius appearing more closely related to Tscherskia, Cricetus, and Allocricetulus. We propose to place the species within a new monotypic genus. Molecular clock calculations are not always in line with the dating of fossil records. DNA based divergence time estimates as well as taxonomic relationships demand a reevaluation of morphological characters previously used to identify fossils and extant hamsters.     

Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA genes

Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features.     

中国沙塘鳢属鱼类线粒体12S rRNA基因序列分析

沙塘鳢属鱼类为东亚特有的小型淡水经济鱼类,中国产沙塘鳢属鱼类分类问题长期存在争议。本文测定了中国产沙塘鳢属鱼类全部种类的线粒体12S rRNA基因部分序列,结合GenBank中下载的2种日本沙塘鳢属鱼类和塘鳢科鱼类同源序列,探讨中国产4种沙塘鳢属鱼类的物种有效性,分析沙塘鳢属鱼类的系统发育关系。作者所使用的同源序列长度为690bp,其中变异位点258个,简约信息位点201个,包括插入/缺失位点34个,转换/颠换平均值为3.0,表明12S rRNA基因是研究沙塘鳢属鱼类系统发育关系的合适分子标记。基于p-distance模型的6种沙塘鳢属鱼类种内遗传距离为0.000—0.024,种间遗传距离为0.058—0.064,支持暗色沙塘鳢和中华沙塘鳢为不同种,中国产沙塘鳢属鱼类包括中华沙塘鳢、河川沙塘鳢、海丰沙塘鳢、鸭绿江沙塘鳢4个种的观点;至于中国还有没有新的沙塘鳢属鱼类,尚有待进一步研究。系统发育分析表明海丰海塘鳢是河川沙塘鳢的姐妹群,暗色沙塘鳢与O.hikimius的亲缘关系最为密切,而同属其余类群之间的系统发育关系则由于自展数据支持率较低而尚不明确。中国产沙塘鳢和日本产沙塘鳢并未单独分群,推测沙塘鳢属鱼类的共同原始祖先可能广泛分布于中国、朝鲜和日本等东亚地区,约在4.9—6.5百万年前的上新世开始分化,系统发育过程比较适合离散假说。     

中国地鼠线粒体DNA 16S rRNA基因序列分析及分子系统发育研究

目的通过克隆分析中国地鼠16S基因的部分序列,对中国地鼠16S基因的结构和功能进行初步探索和揭示。方法从GenBank中已报道的啮齿动物16S基因保守区设计一对引物,进行PCR扩增,测序。用Blastn与GenBank中七种啮齿类动物的16S基因进行序列比较,分析其碱基组成及变异情况,并用邻接法(NJ)、非加权组平均法(UPGMA)构建分子系统树,在分子水平上探讨中国地鼠和其他啮齿类动物的进化关系,对中国地鼠的种属地位进行了进一步验证。结果获得了中国地鼠线粒体16S基因的部分序列,其碱基组成A、T、C、G分别为40.5%、24.5%、18.7%、16.3%,与其他七种啮齿类动物的碱基含量相比,各碱基含量基本相似。NJ进化树表明,中国地鼠、金黄地鼠与欧洲仓鼠先聚为一支,小鼠与大鼠先聚为一支,东方田鼠、台湾田鼠与东欧田鼠先聚为一支。结论中国地鼠和金黄地鼠的亲缘关系最近,与传统的分类地位基本吻合。     

Molecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms

The nasuta subgroup is a cluster of morphologically almost similar forms with a wide range of geographic distribution. During the last three decades nature of inter-relationship among the members has been investigated at different levels of organization. The phylogenetic relationships of the members of the nasuta subgroup of the immigrans species group of Drosophila was made by employing Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeats-PCR (ISSR-PCR) polymorphisms, mitochondrial 12S rRNA, 16S rRNA and Cytochrome C Oxidase subunit I (CoI) gene sequences. The phylogenetic tree generated by RAPD analysis is in nearly complete congruence with the classification based on morphophenotypic characters. The 12S and 16S rRNA genes were highly conserved across the nasuta subgroup and revealed only 3 and 4 variable sites respectively, of which only one site was informative. The CoI gene, on the other hand, revealed 57 variable sites of which 25 sites were informative. All the three species of orbital sheen complex were included in a major cluster in the phylogenetic trees derived from mitochondrial gene sequence data consistent with the morphophenotypic classification. The CoI analysis placed two species of frontal sheen complex, D. n. nasuta and D. n. albomicans in two different clades and this is inconsistent with morphological classification. The molecular clock suggested that divergence between the kohkoa complex and the albomicans complex occurred approximately 2.2 MYA, indicating recent evolution of the nasuta subgroup. The higher transition bias in the mitochondrial genes reported in the present study also suggested recent evolution of the nasuta subgroup.     

The rate of mitochondrial 12S rRNA gene evolution is similar in freshwater turtles and marsupials

Assertions that the ``conventional' rate of mitochondrial DNA (mtDNA) evolution is reduced in poikilotherms in general and turtles in particular were tested for side-necked turtles (Pleurodira: Chelidae). Homologous data sets of mitochondrial 12S rRNA gene sequences were used to compare the average divergence between the Australian and South American species for two Gondwanan groups: the chelid turtles and the marsupials. The mean nucleotide divergences between continental groups for both the turtles and the marsupials are remarkably similar. These data suggest that the rate of evolution of mitochondrial 12S rRNA gene is not substantially slower in turtles than in the homeothermic marsupials. Received: 24 February 1997 / Accepted: 30 June 1997     

Molecular phylogeny of Pneumocystis based on 5.8S rRNA gene and the internal transcribed spacers of rRNA gene sequences

To clarify the phylogenetic relationships and species status of Pneumocystis, the 5.8S rRNA gene and the internal transcribed spacers (ITS, 1 and 2) of Pneumocystis rRNA derived from rat, gerbil and human were amplified, cloned and sequenced. The genetic distance matrix of six Pneumocystis species compared with other fungi like Taphrina and Saccharomyces indicated that the Pneumocystis genus contained multiple species including Pneumocystis from gerbil. The phylogenetic tree also showed that Pneumocystis from human and monkey formed one group and four rodent Pneumocystis formed another group. Among the four members, Pneumocystis wakefieldiae was most closely related to Pneumocystis murina and Pneumocystis carinii, and was least related to gerbil Pneumocystis.     

基于线粒体ND1和16S rRNA基因序列探讨中国蝴蝶12科的系统发育关系(鳞翅目: 双孔次亚目: 蝶类)

对中国12科共32种代表蝶类的ND1基因和16S rRNA 基因进行了序列测定（包括新测30种ND1基因和9种16S rRNA基因）和比较分析, 同时采用邻接法、最大似然法和贝叶斯法构建了12科蝶类的系统发育树, 探讨了其高级分类群的系统发育关系。序列分析的结果显示: 经比对处理后的两个基因总长度为869 bp, 其中保守位点373个, 可变位点496个, 简约信息位点375个; A+T的平均含量为80.2％, 明显高于C+G的平均含量19.8％。分子系统树表明: 蛱蝶科不是单系群; 珍蝶类、斑蝶类和喙蝶类位于蛱蝶科内; 粉蝶科和凤蝶科具有共同祖先。据此建议: 绢蝶科应归入凤蝶科; 蚬蝶科归入灰蝶科; 珍蝶类、斑蝶类和喙蝶类作为蛱蝶科中的亚科, 眼蝶类从蛱蝶科中分离出来独立成科。另外, 环蝶类的系统分类地位还有待于进一步研究。     

Higher-level systematics of rodents (Mammalia,Rodentia): Evidence from the mitochondrial 12S rRNA gene

Phylogenetic relationships among major rodent superfamilies traditionally have been difficult to establish because of the apparent high level of convergence and parallelism seen among morphological characters and/or rapid differentiation of rodent groups in the Paleocene/Eocene. Nucleotide sequence data from the mitochondrial 12S rRNA gene were used to clarify phylogenetic relationships among the major groups of rodents as defined by Brandt (1855) and Tullberg (1899). Based on the approximately 800 bp analyzed for the 12S rRNA gene in 59 mammalian species, including 25 of the 32 extant rodent families, the major rodent groups that could be defined as monophyletic clades were the Hystricognathi, the Muroidea, and the Geomyoidea. In addition, support for superfamilial sister-group relationships was found for Aplodontoidea with Sciuroidea and Dipodoidea with Muroidea.     

Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes

Portions of two mitochondrial genes (12S and 16S ribosomal RNA) were sequenced to determine the phylogenetic relationships among the major clades of snakes. Thirty-six species, representing nearly all extant families, were examined and compared with sequences of a tuatara and three families of lizards. Snakes were found to constitute a monophyletic group (confidence probability [CP] = 96%), with the scolecophidians (blind snakes) as the most basal lineages (CP = 99%). This finding supports the hypothesis that snakes underwent a subterranean period early in their evolution. Caenophidians (advanced snakes), excluding Acrochordus, were found to be monophyletic (CP = 99%). Among the caenophidians, viperids were monophyletic (CP = 98%) and formed the sister group to the elapids plus colubrids (CP = 94%). Within the viperids, two monophyletic groups were identified: true vipers (CP = 98%) and pit vipers plus Azemiops (CP = 99%). The elapids plus Atractaspis formed a monophyletic clade (CP = 99%). Within the paraphyletic Colubridae, the largely Holarctic Colubrinae was found to be a monophyletic assemblage (CP = 98%), and the Xenodontinae was found to be polyphyletic (CP = 91%). Monophyly of the henophidians (primitive snakes) was neither supported nor rejected because of the weak resolution of relationships among those taxa, except for the clustering of Calabaria with a uropeltid, Rhinophis (CP = 94%).      

Molecular phylogeny of musk deer: a genomic view with mitochondrial 16S rRNA and cytochrome b gene

The phylogenetic status of the infra order Pecora is controversial, even though it is supported by paleontological, morphological, and molecular evidence. We analyzed two mitochondrial genes (i.e., 16S rRNA and cytochrome b) to resolve the phylogenetic position of pecoran species, i.e., the Bovidae, Cervidae, and Moschidae endemic to the Indian subcontinent. We used phylogenetic analysis based on different algorithms, including neighbor joining, maximum parsimony, Bayesian inference, maximum likelihood, minimum evolution, median joining network, along with multidimensional scaling, and DNA word analysis. Our results established the basal position of Tragulidae and the monophyly of the infra order Pecora within the Suborder Ruminantia. Our results also demonstrated that Bovidae, Cervidae, and Moschidae are allied with the placement of musk deer as more closely related to bovids than to cervids. Molecular dating based on sequence analysis shows that the radiation of Pecora occurred during the early Oligocene and that the majority of the pecoran families radiated and dispersed rapidly during the Oligocene/Miocene transition.     

Phylogenetic relationships within caniform carnivores based on analyses of the mitochondrial 12S rRNA gene

The complete 12S rRNA gene of 32 carnivore species, including four feliforms and 28 caniforms, was sequenced. The sequences were aligned on the basis of their secondary structures and used in phylogenetic analyses that addressed several evolutionary relationships within the Caniformia. The analyses showed an unresolved polytomy of the basic caniform clades; pinnipeds, mustelids, procyonids, skunks,Ailurus (lesser panda), ursids, and canids. The polytomy indicates a major diversification of caniforms during a relatively short period of time. The lesser panda was distinct from other caniforms, suggesting its inclusion in a monotypic family, Ailuridae. The giant panda and the bears were joined on the same branch. The skunks are traditionally included in the family Mustelidae. The present analysis, however, showed a less close molecular relationship between the skunks and the remaining Mustelidae (sensu stricto) than between Mustelidae (sensu stricto) and Procyonidae, making Mustelidae (sensu lato) paraphyletic. The results suggest that the skunks should be included in a separate family, Mephitidae. Within the Pinnipedia, the grouping of walrus, sea lions, and fur seals was strongly supported. Analyses of a combined set of 12S rRNA and cytochromeb data were generally consistent with the findings based on each gene.     

Nucleotide sequence variation in the mitochondrial 12S rRNA gene and the phylogeny of African mole-rats (Rodentia: Bathyergidae).

Mitochondrial DNA (mtDNA) sequence variation was examined in eight taxa of the African rodent family Bathyergidae, as well as in two taxa representative of the Old-World hystricognathid rodent families Petromyidae and Thryonomyidae. A total of 812 bp, constituting domains I-III of the 12S ribosomal rRNA gene, were compared for each taxon. The high levels of intrafamilial mtDNA sequence divergence observed (average 16.8, range 3.5-23.2) support an ancient origin for the five genera, 20-38 Mya. These data do not support the current subfamilial groupings of the Bathyergidae. The eastern African naked mole-rat, Heterocephalus glaber, is the most basal representative of the family, with the silvery mole-rat, Heliophobius, being the next most basal. South African forms [dune, common, and cape mole-rats (Bathyergus, Cryptomys, and Georychus, respectively)] group together. The independent origin of the common mole-rat, relative to the naked mole-rat, suggests that complex social systems evolved in parallel along different bathyergid lineages. The 12S rRNA gene is not evolving at a higher rate within the rodent lineages, relative to that seen for artiodactyls and primates. Bathyergid rodents appear to fall at an extreme end of the spectrum of mammalian variation, with respect to both transition/transversion ratios and divergence, showing much lower transition/transversion ratios than those previously reported for intrafamilial comparisons.     

Molecular phylogeny of the crab genus Brachynotus (Brachyura: Varunidae) based on the 16S rRNA gene

The crab genus Brachynotus de Haan, 1833 is restricted to the intertidal and shallow subtidal of the Mediterranean and northeastern Atlantic. It is presently recognized to consist of four species, of which three (B. foresti, B. gemmellari and B. sexdentatus) are endemic to the Mediterranean. The fourth species, B. atlanticus, is found along the Atlantic coasts of northern Africa and southern Europe, but also extends into the western Mediterranean. This high level of endemism suggests that speciation within Brachynotus is strongly correlated with the geography and geology of the Mediterranean Sea. A molecular phylogeny based on the mitochondrial large subunit (16S) rRNA gene indicates that the four species of Brachynotus form a monophyletic group within Atlantic Varunidae. The DNA sequence data also show that the genus Brachynotus can be subdivided into two species groups, one comprising B. atlanticus and B. foresti, and the other one B. gemmellari and B. sexdentatus. While B. atlanticus and B. foresti are clearly genetically distinct, B. gemmellari and B. sexdentatus are identical in the studied region of the 16S rRNA gene, suggesting a recent separation or continuing gene flow.     

尖塘鳢属鱼类线粒体12SrRNA基因序列分析

利用PCR技术扩增和测序了线纹尖塘鳢、云斑尖塘鳢和海丰沙塘鳢线粒体12SrRNA基因,结合从GenBank中下载的部分同源序列,共分析了5种鱼类的系统发育关系。在Kimura2-parameter模型构建的邻接树中,原产泰国的云斑尖塘鳢与原产澳州线纹尖塘鳢均为单系类群,二者为亲缘关系最为密切的姐妹群,海丰沙塘鳢与其它群体的亲缘关系较远,支持将尖塘鳢属从塘鳢属中分出的传统分类处理。尖塘鳢属内云斑尖塘鳢和线纹尖塘鳢鱼类种内DNA序列无差异,而种间差异明显,表明线粒体12SrRNA基因可作为塘鳢科鱼类种类鉴定的良好分子标记。     

Molecular systematics of the order anaspidea based on mitochondrial DNA sequence (12S, 16S, and COI)

Fragments from three mitochondrial genes (12S, 16S, and COI) were sequenced to reconstruct a molecular phylogeny of the opisthobranch order Anaspidea. The molecular phylogeny supports the placement of the genus Akera, a taxon previously regarded by some authors as a cephalaspidean, within the Anaspidea. Incongruence between the molecular data and the classifications based on morphology suggests that some of the taxonomic characters (i.e., shell, parapodia fusion) traditionally used for the classification of sea hares must be reevaluated, since they may be homoplastic. The ancestral nature of Notarchus based on the molecular evidence suggests that homoplasy may be an explanation for the morphological resemblance of this species to the more derived sea hares with highly fused parapodia and concentrated nerve ganglia. Finally, examples are given of how comparative studies of the evolution of learning mechanisms in the anaspidean clade will benefit from the phylogenetic hypothesis presented in this paper.     

Phylogeny of hagfish based on the mitochondrial 16S rRNA gene

The phylogenetic relationships among the species belonging to the family Myxinidae are still debatable. The mitochondrial DNA sequences from the large ribosomal RNA gene may be of great value for systematic and phylogenetic studies within families. Partial sequences of the 16S rRNA gene were obtained for comparisons among the following hagfish species, Paramyxine nelsoni, Paramyxine sheni, Paramyxine taiwanae, Paramyxine yangi, Paramyxine cheni, Eptatretus burgeri, Eptatretus stouii, Eptatretus cirrhatus, Myxine glutinosa, Myxine formosana, Myxine circifrons, Myxine sp1, and Myxine sp2. The boundary of four Paramyxine species (P. sheni, P. taiwanae, P. nelsoni, and P. yangi) from 16S rRNA sequences is ambiguous, however, they are valid based on our unpublished isozyme data as well as the gill aperture arrangement pattern. Both NJ and MP trees constructed from the present molecular data indicate that the genus Paramyxine is diphyletic and Eptatretus paraphyletic. The complexity of Eptatretus and Paramyxine in the clade would not be solved until the farther departed P. cheni is included to form a new clade under the genus Eptatretus. The other clade of Myxininae contains but single genus Myxine.     

Molecular phylogeny based on the 16S rRNA gene of elite rhizobial strains used in Brazilian commercial inoculants

Nitrogen is often a limiting nutrient, therefore the sustainability of food crops, forages and green manure legumes is mainly associated with their ability to establish symbiotic associations with stem and root-nodulating N2-fixing rhizobia. The selection, identification and maintenance of elite strains for each host are critical. Decades of research in Brazil resulted in a list of strains officially recommended for several legumes, but their genetic diversity is poorly known. This study aimed at gaining a better understanding of phylogenetic relationships of 68 rhizobial strains recommended for 64 legumes, based on the sequencing of the 16S rRNA genes. The strains were isolated from a wide range of legumes, including all three subfamilies and 17 tribes. Nine main phylogenetic branches were defined, seven of them related to the rhizobial species: Bradyrhizobium japonicum, B. elkanii, Rhizobium tropici, R. leguminosarum, Sinorhizobium meliloti/S. fredii, Mesorhizobium ciceri/M. loti, and Azorhizobium caulinodans. However, some strains differed by up to 35 nucleotides from the type strains, which suggests that they may represent new species. Two other clusters included bacteria showing similarity with the genera Methylobacterium and Burkholderia, and amplification with primers for nifH and/or nodC regions was achieved with these strains. Host specificity of several strains was very low, as they were capable of nodulating legumes of different tribes and subfamilies. Furthermore, host specificity was not related to 16S rRNA, therefore evolution of ribosomal and symbiotic genes may have been diverse. Finally, the great diversity observed in this study emphasizes that tropics are an important reservoir of N2-fixation genes.     

Molecular systematics of sciurognathi (rodentia): the mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae)

Nucleotide sequence data from the mitochondrial 12S rRNA and cytochrome b genes were used to analyze phylogenetic relationships among sciurognath rodents. Our sample taxa included representatives of 11 sciurognath and 3 hystricognath families with two marsupial species, Didelphis virginiana and Macropus robustus, as outgroups. The dataset was analyzed using both maximum-parsimony (weighted and unweighted) and likelihood methods. Three suprafamilial groupings are strongly supported: Geomyidae + Heteromyidae (Geomyoidea), Sciuridae + Aplodontidae (Sciuroidea), and Pedetidae + Anomaluridae (Anomaluroidea). Although moderately supported, two sister group relationships were identified between Gliridae and Sciuroidea and between Castor and Geomyoidea. In contrast to previous nuclear DNA evidence, the evolutionary affinities between Ctenodactylidae and Hystricognathi (Ctenohystrica) and between Muridae and Dipodidae (Myodonta) are not supported by the mitochondrial data. Molecular divergence dates based on the combined data were estimated for suprafamilial groupings and are discussed in the light of current morphological and paleontological interpretations of rodent phylogeny.