DNA Sequence Analysis of Familial Relationships Among Dasyuromorphian Marsupials

Although modern morphological and molecular analyses support the monophyly of the Australasian marsupial order Dasyuromorphia, there is much less certainty about relationships among its constituent families (Dasyuridae, Myrmecobiidae, and Thylacinidae). While most authors regard Dasyuridae as monophyletic, a few have suggested that thylacines, numbats, or both have their closest relatives among dasyurids. Recent morphocladistic studies have identified several basicranial characters as putative synapomorphies of dasyurids, but no features that clearly implicate thylacinids, myrmecobiids, or both, as the sister group of Dasyuridae. Only two previous DNA studies have included both thylacine and numbat sequences along with dasyurids, and neither provided strong resolution of interfamilial relationships. In this study, we report a more thorough analytical treatment of complete cytochrome b, 12S rRNA, and protamine P1 gene sequences from dasyuromorphians than has heretofore been attempted. Our results concur with previous morphological studies in showing that Dasyuridae is monophyletic and with immunological findings that thylacinids and dasyurids are sister groups, apart from myrmecobiids. However, the level of support for nodes is highly dependent on the method of phylogenetic analysis employed. Our results also suggest that partitioning of sequence data sets to account for substitutional heterogeneity within and among genes does not necessarily lead to a major reduction in the precision of estimated phylogenies.     

An Analysis of Marsupial Interordinal Relationships Based on 12S rRNA, tRNA Valine, 16S rRNA, and Cytochrome b Sequences

The basal split among living marsupials is traditionally placed between the cohorts Ameridelphiaand Australidelphia. Ameridelphia includes all American forms excepting the South AmericanDramicuipx gliroidex (Order Microbiotheria). Australidelphia includes all Australasian taxaplus Dromiciops glinmles. DNA data support Eometatheria Dromiciaps + Diprotodontia +Dasyuromorphia + Notoryctemorphia) but do not resolve the position of bandicoots, whetherwith other australidelphians or with ameridelphians. Also, the most robust molecular trees (DNAhybridization, multigene studies) exhibit minimal branch subdivision and raise the possibility ofartit'actual associations owing to long branch attraction. We analyzed data sets that consistedof complete sequences tor four niitochondrial genes (cytochrome b, 12S rRNA, tRNA valine,16S rRNA). One data set included 14 marsupial taxa. A second data set included 14 marsupialsas well as outgroup sequences (one monolreme; 20 placentals). Phylogenetic analyses includedparsimony, minimum evolution, maximum likelihood, and quartet puzzling. When phylogeneticanalyses were restricted to just the marsupial sequences, there was 75 to 96% boostrap supportfor the separation of Ameridelphia versus Australidelphia. This suggests that either one orboth of these groups are monophyletic. Also, there was 71 to 98% bootstrap support for theseparation of Eometatheria versus Ameridelphia + Peramelina. Nonmonophyly of several a prioriclades was accepted by at least some statistical tests including the following: Diprotodontia+ Peramelina, Notoryctemorphia + Peramelina, Diprotodonlia + Notoryctemorphia, and themonophyly of Australasian marsupials. With the inclusion of outgroup sequences, there wasreduced bootstrap support for associations among marsupial orders and statistical tests failed toreject all interordinal associations that were tested.     

Systematic Position of the African Dormouse Graphiurus (Rodentia, Gliridae) Assessed from Cytochrome b and 12S rRNA Mitochondrial Genes

Gliridae is a small family of rodents including three subfamilies: the Eurasian Glirinae (with three genera) and Leithiinae (with four genera) and the African Graphiurinae (with a single genus). Phylogenetic relationships among these eight genera are not fully resolved based on morphological characters. Moreover, the genus Graphiurus is characterized by numerous peculiar features (morphological characters and geographical distribution), raising the question of its relationships to the family Gliridae. The phylogenetic position of Graphiurus and the intra-Gliridae relationships are here addressed by a molecular analysis of 12S RNA and cytochrome b mitochondrial gene sequences for six glirid genera. Phylogenetic analyses are performed with three construction methods (neighbor-joining, maximum parsimony and maximum likelihood) and tests of alternative topologies with respect to the most likely. Our analyses reveal that Graphiurus is clearly a member of the Gliridae, refuting the hypothesis that the family could be paraphyletic. Among Gliridae, phylogenetic relationships are poorly resolved: the Leithiinae could be monophyletic, there is no support for the subfamily Glirinae, and the closest relative of Graphiurus is not identified. The inclusion of Graphiurus among Gliridae allows us to postulate that its hystricomorphous condition has been achieved convergently with other hystricomorphous rodents.     

Phylogeny of Snub-Nosed Monkeys Inferred from Mitochondrial DNA,Cytochrome B,and 12S rRNA Sequences

Snub-nosed monkeys (Rhinopithecus spp.) are confined to isolated mountainous regions in China and North Vietnam. Their systematic classification and phylogenetic relationship has been controversial. The structures of mitochondrial DNA cytochrome b and 12S rRNA show that the 4 species of Rhinopithecus are quite different from other colobines. It is reasonable to regard them as an independent genus, as determined by external features, morphometric characters and behavior. However, whether or not there should be a subdivision between the Vietnamese and Chinese species at the subgeneric level remains to be clarified; more evidence from a large range of Asian colobine species is needed. The Guizhou species, Rhinopithecus brelichi, is a valid species, which is more closely related to Pygathrix than the other species ( R. roxellana, R. bieti and R. avunculus) are. Results also indicate that 3 species—Rhinopithecus roxellana, R. bieti and R. avunculus—might have diverged from R. brelichi, but the phylogenetic relationship of R. avunculus is not clear.     

麂属(Muntiacus)动物线粒体12S rRNA、细胞色素b基因和多药耐药基因序列分析及其分子进化关系

对麂属（Muntiacus)中的3种动物：赤麂（M.muntjak)(2n=6♀,7♂）,小麂（M.reevesi)(2n=46),黑麂（M.cri.nifrons)(2n=8♀,9♂）线粒体DNA 12S rRNA和细胞色素b基因784bp左右的片段和核基因－多药耐药基因（multidrug resistance,MDR1)的728bp左右的片段进行了序列分析,并根据序列信息建立了分子系统树,同时探讨了这3种动物的起源,分类地位及进化关系。     

根据12S rRNA和Cyt b基因部分序列鉴定药用猴骨样品

利用线粒体12S rRNA基因和cyt b基因部分序列,通过DNA序列比对的方法,对毫州市药品监督管理局送检的三件猴骨样品（BZ01、BZ02和BZ03）进行了分子鉴定。结果表明,BZ01号样品为藏酋猴（Macaca thibetana）,BZ02和BZ03号样品为猕猴（Macaca mulatta）,通过本文的研究,作者还提出,在利用DNA序列比对法进行近缘物种的鉴定时,不同种群间的DNA序列变异,可能对结果造成一定的影响。     

Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Site-Directed Mutagenesis of Cytochrome b5 for Studies of Its Interaction with Cytochrome P450

We have shown earlier that microsomal cytochrome b ₅ can form a specific complex with mitochondrial cytochrome P450 (cytochrome P450scc). The formation of the complex between these two heme proteins was proved spectrophotometrically, by affinity chromatography on immobilized cytochrome b ₅, and by measuring the cholesterol side-chain cleavage activity of cytochrome P450scc in a reconstituted system in the presence of cytochrome b ₅. To further study the mechanism of interaction of these heme proteins and evaluate the role of negatively charged amino acid residues Glu42, Glu48, and Asp65 of cytochrome b ₅, which are located at the site responsible for interaction with electron transfer partners, we used sitedirected mutagenesis to replace residues Glu42 and Glu48 with lysine and residue Asp65 with alanine. The resulting mutant forms of cytochrome b ₅ were expressed in E. coli, and full-length and truncated forms (shortened from the C-terminal sequence due to cleavage of 40 amino acid residues) of these cytochrome b ₅ mutants were purified. Addition of the truncated forms of cytochrome b ₅ (which do not contain the hydrophobic C-terminal sequence responsible for interaction with the membrane) to the reconstituted system containing cytochrome P450scc caused practically no stimulation of catalytic activity, indicating an important role of the hydrophobic fragment of cytochrome b ₅ in its interaction with cytochrome P450scc. However, full-length cytochrome b ₅ and the full-length Glu48Lys and Asp65Ala mutant forms of cytochrome b ₅ stimulated the cholesterol side-chain cleavage reaction catalyzed by cytochrome P450scc by 100%, suggesting that residues Glu48 and Asp65 of cytochrome b ₅ are not directly involved in its interaction with cytochrome P450scc. The replacement of Glu42 for lysine, however, made the Glu42Lys mutant form of cytochrome b ₅ about 40% less effective in stimulation of the cholesterol side-chain cleavage activity of cytochrome P450scc, indicating that residue Glu42 of cytochrome b ₅ is involved in electrostatic interactions with cytochrome P450scc. Residues Glu42 and Glu48 of cytochrome b ₅ appear to participate in electrostatic interaction with microsomal type cytochrome P450.     

用mtDNA 12S rRNA序列变异检验鲤形目鱼类系统发育关系

通过对鲤形目鱼类5个科的代表类群的完整线粒体12S rRNA进行测序和分析,以检验目前的形态学假说。经序列比对后,有1000个位点,其中467个位点在茎区,533个在环区;有395个位点为变化位点,其中267个为系统发育信息位点。采用邻接法和最大简约法进行了系统发育分析,其结果支持鲤科鱼类成为一个单系群,非鲤科的鲤形目鱼类成为另一个单系群的观点,这与Siebert提出的假说相一致。鲤科鱼类包含3个主要的分支,即鱼丹系、鲤系和雅罗鱼系;但在非鲤科鲤形目鱼类中,其关系不能得到很好的解决,其中鳅科是复系,平鳍鳅科、条鳅亚科和花鳅亚科可能有较近的亲缘关系。     

几种腹蛇12S rRNA和Cyt b基因片段序列的初步研究

首次对我国几种腹属蛇类的１２Ｓ ｒＲＮＡ和Ｃｙｔ ｂ基因的部分序列进行了测定。１２Ｓ ｒＲＮＡ基因片段序列结果揭示：中介蝮有较大的种下分化。本文为蝮属蛇类的分子系统学研究提供了一些资料。     

Phylogenetic Relationships and the Radiation of Sigmodontine Rodents in South America: Evidence from Cytochrome b

Phylogenetic relationships among South American sigmodontine rodents were examined based on the complete sequence for the mitochondrial cytochrome b gene [1140 base pairs (bp)] for 66 species and between 759 and 1140 bp for an additional 19 species. Thirty-eight South American genera were represented, coming from eight of nine tribes. Outgroups included the North American murid rodents Peromyscus, Reithrodontomys, Scotinomys, and Neotoma, the Old World murine rodents Mus and Rattus, and the geomyoid genera Thomomys, Geomys, Dipodomys, and Perognathus as the most distant outgroup. The South American sigmodontines were supported as a monophyletic lineage. Within this radiation several clear-cut suprageneric groupings were identified. Many of the currently recognized tribal groupings of genera were found fairly consistently, although not always with high levels of bootstrap support. The various tribes could not be linked hierarchically with any confidence. In addition, several genera stand out as unique entities, without any apparent close relatives. The overall pattern suggests a rapid radiation of the sigmodontines in South America, followed by differentiation at the tribal and generic levels.     

The Phylogenetic Relationships of the Gobioninae (Teleostei: Cyprinidae) Inferred from Mitochondrial Cytochrome b Gene Sequences

The Gobioninae are a group of morphologically and ecologically diverse Eurasian freshwater cyprinid fishes. The intergeneric relationships of this group are unresolved and the possible monophyly of this subfamily remains to be established. We used complete mitochondrial cytochrome b gene sequences from most genera within the gobionine group, in addition to a selection of cyprinid outgroups, to investigate the possible monophyly of this group and resolve the interrelationships within the group. Our results support the monophyly of the Gobioninae and identify four monophyletic groups within the subfamily; the Hemibarbus group, the Sarcocheilichthys group, the Gobio group, and the Pseudogobio group. The morphologically aberrant genera Gobiobotia, Xenophysogobio and Gobiocypris are included in the Gobioninae, with the latter a sister group of Gnathopogon.     

基于12S,16S和28S rRNA基因序列的中国小毛瓢虫属系统发育分析

【目的】小毛瓢虫属Scymnus Kugelann昆虫主要捕食蚜虫、蚧虫等害虫,是一类经济上重要的天敌昆虫。目前针对小毛瓢虫属的系统发育研究尚属空白,亚属之间的系统演化关系尚不明确,为了建立合理的分类系统,亟需对小毛瓢虫属的亲缘关系进行研究和探讨。【方法】以华南农业大学馆藏的小毛瓢虫属5亚属共44种为研究对象,采用PCR技术对12S, 16S和28S rRNA基因的部分序列进行扩增;运用MEGA 7.0分析了小毛瓢虫属内12S, 16S和28S rRNA基因的碱基组成,基于K2P模型计算了小毛瓢虫属44种的种间遗传距离;采用最大似然法(maximum-likelihood, ML)和贝叶斯推断法(Bayesian-inference, BI)构建该属的系统发育树。【结果】扩增获得小毛瓢虫属44种的12S rRNA基因序列平均长度为356 bp, 16S rRNA基因序列平均长度为351 bp, 28S rRNA基因序列平均长度为315 bp;序列分析表明,12S rRNA基因的A, T, G和C平均含量分别为38.8%, 43.5%, 11.9%和5.8%, 16S rRNA基因的A, T, G和C平均含量分别为37.6%, 40.3%, 14.4%和7.7%, 28S rRNA基因的A, T, G和C平均含量分别为26.7%, 18.3%, 31.4%和23.5%;基于联合序列分析的种间遗传距离为0.004～0.276,平均遗传距离为0.115。系统发育分析结果表明,小毛瓢虫属为单系起源,而小毛瓢虫亚属Scymnus(Scymnus) Kugelann、毛瓢虫亚属Scymnus(Neopullus) Sasaji、小瓢虫亚属Scymnus(Pullus) Mulsant和拟小瓢虫亚属Scymnus(Parapullus) Yang均为并系起源。【结论】基于12S, 16S和28S rRNA基因序列的小毛瓢虫属系统发育分析显示传统的形态学分类体系与基于分子数据分析的结果部分不一致,这表明应该对该属内各亚属的鉴别特征进行全面检视,筛选并确立各亚属的形态指标,同时也表明该属内的亚属分类单元需重新厘定。     

从12S rRNA基因部分序列探讨络新妇亚科升格为科级阶元的有效性

络新妇亚科曾归入园蛛科,后改为属于肖蛸科,目前又升格为科级阶元。为对络新妇亚科的分类地位作进一步研究,测定了9种蜘蛛线粒体12SrRNA基因的部分序列;另外还从GenBank检索到17种蜘蛛的12SrRNA基因的的相应序列。基于12SrRNA基因序列进行的分子系统发生分析结果表明络新妇亚科即不属于园蛛科、也不属于肖蛸科,而是与肖蛸科或园蛛科均无直接关联的独立支系,这个结果证实了将络新妇亚科升格为科级阶元的有效性。     

Molecular Relationships of the Extinct Pig-Footed Bandicoot Chaeropus ecaudatus (Marsupialia: Perameloidea) Using 12S rRNA Sequences

The pig-footed bandicoot, Chaeropus ecaudatus, is presumed to be extinct as no specimens have been collected or seen since early this century. Usually classified as a specialized member of the family Peramelidae, there is nevertheless still some doubt as to its taxonomic affinities, because this animal is highly specialized and shows several uniquely derived characters. We report here the first attempt to determine the molecular relationships of this animal using mitochondrial 12S rRNA sequences derived from spirit-preserved museum specimens. Phylogenetic analysis shows that the sequence derived from the Chaeropus sample is clearly that of a bandicoot. Within the bandicoot clade, the pig-footed bandicoot is quite distinct from all other taxa. Divergence-time estimates from the 12S rRNA sequences suggest that Chaeropus diverged from the other bandicoot genera in the late Oligocene or early Miocene and that bandicoots diverged from other Australian families in the late Paleocene–early Eocene.     

用12S rRNA基因序列研究斑腿蝗科二属六种的进化关系

采用DNA测序技术测定了中国斑腿蝗科昆虫6种和斑翅蝗科的红胫小车蝗线粒体12S rRNA基因长约345 bp片段的序列。在获得的345 bp的序列中,A+T约占71.8%,其中135个核苷酸位点存在变异 (约占39.1%)。PAUP4.0b数据分析软件构建该6种蝗虫的MP和NJ分子系统树显示,稻蝗属和蔗蝗属各为独立的一支。在稻蝗属一支中,中华稻蝗与山稻蝗关系很近,而与小稻蝗关系较远,这与形态学结果相吻合;在蔗蝗属一支中,异歧蔗蝗与斑角蔗蝗亲缘关系较近,而与等歧蔗蝗关系较远,这与形态学研究结果并不吻合,有待进一步的研究。     

Phylogenetic Relationships Within the Genus Potorous (Marsupialia: Potoroidae) Based on Allozyme Electrophoresis and Sequence Analysis of the Cytochrome b Gene

Controversy over the taxonomic designations within the genus Potorous has highlighted problems associated with using only morphological data. The recent rediscovery of Gilbert's Potoroo has allowed us to reexamine the relationship of this species to other extant potoroos. Phylogenetic relationships and estimated divergence times are presented, based on electrophoretic and cytochrome b sequence data. There was considerable concordance between the data sets. We conclude that Gilbert's Potoroo is a separate species and should be referred to by its original name, Potorous gilbertii (Gould 1841). Estimates for potoroid divergences are in line with those of Flannery (1989).     

基于12S和16S rRNA序列的湍蛙属部分物种的系统发育关系

测定了湍蛙属 6个种共 10个种群 ,以及 4个外群种的线粒体 12S和 16SrRNA基因片段 ,比对后有94 0bp序列 ,发现 35 2个变异位点、 186个简约性位点。运用NJ法、MP法、ML法构建了系统关系树 ,各系统树一致表明内群为一单系群 ,分为两组 :第一组中 ,四川湍蛙两种群先聚合 ,再和棕点湍蛙聚为一支 ;第二组中 ,香港湍蛙和戴云湍蛙聚为一支 ,而香港大屿山离岛湍蛙种群首先与华南湍蛙相聚 ,再与武夷湍蛙构成姐妹支。研究结果表明 :香港地区增加 1种湍蛙分布 ;戴云湍蛙是一有效种 ;四川湍蛙的石棉和洪雅种群间遗传差异达到或超过其他种间的分歧水平。     

Molecular phylogeny of the higher taxa of Odonata (Insecta) inferred from COI, 16S rRNA, 28S rRNA,and EF1‐α sequences

In this study, we sequenced both two mitochondrial genes (COI and 16S rRNA) and nuclear genes (28S rRNA and elongation factor‐1α) from 71 species of Odonata that represent 7 superfamilies in 3 suborders. Phylogenetic testing for each two concatenated gene sequences based on function (ribosomal vs protein‐coding genes) and origin (mitochondrial vs nuclear genes) proved limited resolution. Thus, four concatenated sequences were utilized to test the previous phylogenetic hypotheses of higher taxa of Odonata via Bayesian inference (BI) and maximum likelihood (ML) algorithms, along with the data partition by the BI method. As a result, three slightly different topologies were obtained, but the BI tree without partition was slightly better supported by the topological test. This topology supported the suborders Anisoptera and Zygoptera each being a monophyly, and the close relationship of Anisozygoptera to Anisoptera. All the families represented by multiple taxa in both Anisoptera and Zygoptera were consistently revealed to each be a monophyly with the highest nodal support. Unlike consistent and robust familial relationships in Zygoptera those of Anisoptera were partially unresolved, presenting the following relationships: ((((Libellulidae + Corduliidae) + Macromiidae) + Gomphidae + Aeshnidae) + Anisozygoptera) + (((Coenagrionidae + Platycnemdidae) + Calopterygidae) + Lestidae). The subfamily Sympetrinae, represented by three genera in the anisopteran family Libellulidae, was not monophyletic, dividing Crocothemis and Deielia in one group together with other subfamilies and Sympetrum in another independent group.     

Cytochrome bc 1 and b 6 f complexes of photosynthetic membranes

All photosynthetic membranes contain a cytochrome bc ₁ or b ₆ f complex that catalyzes the oxidation of quinols and the reduction of a high-potential electron carrier, such as cytochrome c ₂ or plastocyanin. The cytochrome complex also functions in the translocation of protons across the membrane and as a consequence, establishes the proton motive force that is used for the synthesis of ATP. The structure and function of the cytochrome complexes are first reviewed in this chapter. Amino acid sequence information for almost all of the protein subunits of these complexes is now available, and these allow for a detailed consideration of functional domains in the protein subunits and for a further discussion of the evolution of the cytochrome complex in photosynthetic organisms.