Speciation of two sympatric coastal fish species, Girella punctata and Girella leonina (Perciformes, Kyphosidae)

Girella punctata and Girella leonina are sympatric sister species showing extensive distributional overlap in shallow rocky reefs in the Pacific Ocean south of the Japanese Islands. Differences between the two species in external morphological characters, such as number of pored lateral line scales, colour of opercular flap and shape of caudal fin, are congruent with genetic divergence. Nucleotide identity between the two species in the 3.3 kbp region of partial mitochondrial DNA containing the D-loop region, in 12S and 16S ribosomal RNA (rRNA) and transfer RNA genes is 95%. To estimate divergence time, Bayesian analysis was conducted using a dataset comprising concatenated nucleotide sequences from the two rRNA genes of three girellid and nine other fish species. Using the Elopomorpha – Clupeocephala split (265 million years ago (mya)) as a calibration point, divergence between G. punctata and G. leonina is estimated as having occurred 6.0±1.4 mya. Speciation is suggested to have been caused by geographical isolation associated with formation of the Japanese Islands, which resulted in disjunction of Girella habitat.     

从12S rRNA基因序列研究中国蛙科24种的进化关系

测定了中国蛙科动物24种和蟾蜍科的中华大蟾蜍线粒体12S rRNA基因长约400bp片段的序列。采用邻接法,对其数据的系统发生分析表明24种可分成3个支系：第一个支系包括棘腹蛙、合江棘蛙、棘胸蛙、大头蛙、虎纹蛙、倭蛙、泽陆蛙共７种,其中３种棘蛙组成一个单系;第二个支系由３种湍蛙,即戴云湍蛙、华南湍蛙和武夷湍蛙组成,应属于湍蛙亚科;第三支系包含余下的１４种蛙,其中５种林蛙和４种臭蛙分别组成一个单系;２种侧褶蛙先聚合后,再与弹琴水蛙聚合,２种粗上先聚合在一起,再与由林蛙组成的单系群聚合。第三支系首先与第二支系相聚,然后它们与第一支系形成姐妹群,即由蛙亚科的７个物种组成的第一支系,不与蛙亚科另１４个物种组成的第三支系直接聚合,表明第一支系的物种可能不属于蛙亚科。此外,分子证据提示把陆蛙属、大头蛙属、虎纹蛙属、棘棘属、臭蛙属、粗皮蛙属和侧褶蛙属从原来的蛙属分出有其合理性。、     

中国林蛙的分子系统关系

测定了 6种林蛙和用作外群的 2种侧褶蛙和 1种陆蛙的线粒体 12SrRNA基因序列 393bp。序列两两对位比较表明内外群间的位点替换率是 7 3%到 2 3 1% ,内群中物种间则为 0 0 %到 9 2 %。依据上述DNA序列 ,用距离法和最大简约法的系统发育分析表明 :①研究的 6种林蛙聚为一支 ,构成单系群 ,并有高的BPs值(90 %以上 )支持 ;② 6种林蛙可以分成 2个姐妹群 ,即中国林蛙、黑龙江林蛙和桓仁林蛙为一组 (BPs >94% ) ,峨眉林蛙、昭觉林蛙和镇海林蛙为一组 (BPs >5 0 % ) ;③昭觉林蛙与镇海林蛙有较近的亲缘关系 ;④中国林蛙的榆中种群与牡丹江种群间的遗传分化似乎达到了种级分化水平。     

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。     

从12S rRNA基因序列探讨中国10种壁虎的系统关系

对肌肉样品采用SDS／蛋白酶K裂解,酚－氯仿抽提和乙醇沉淀提取总DNA,用线粒体12SrDNA通用引物扩增,用银染测序和ABI Prism 310型遗传分析仪测定了Gekko japonicus,G.swinhonis,G.hokouensis,G.gecko,Cyrtopodion elongatus,C.russowi,Teratoscincus roborowskii,Hemidactylus bowringii.,H.frenatus和Gehyra mutilata 10种壁虎的线粒体12SrRNA基因片段的序列,对位排列后的序列长421bp,含201个变异位点,属间核苷酸变异范围为0．228－0．282,属内是0．005－0．263。重建的分子系统树将10种壁虎聚为三支：第1支是大壁虎和截趾虎,第2支由壁虎属其余的3个种构成一个单系;第三支由基余3个属的5个种组成,研究结果表明：截趾虎与壁虎属4物种亲缘关系较近;吐鲁番沙虎和弯脚虎属2物种,晰虎属2物种之间的亲缘关系较近,支持Russell(1976)关于弯脚虎属与晰虎属间进化关系的研究结果而不支持Kluge(1987)将沙虎属另立亚科的系统发生假说;铅山壁虎与无蹼壁虎最先聚为姐妹群,再与多疣壁相聚组成一个单系。     

Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequences

Mitochondrial DNA (12S rRNA, 16S rRNA) sequences were analysed within Tarentola mauritanica and other selected species of Tarentola. Several highly genetically distinct lineages occur in North Africa, revealing phylogroups in southern and central Morocco, northern Morocco, Algeria, Tunisia, and Libya. A single haplotype characterizes populations across Spain, Portugal, Italy, Menorca, Crete, and Tunisia raising the possibility of an anthropogenic introduction followed by rapid population expansion throughout southern Europe. T. mauritanica is paraphyletic with respect to T. angustimentalis, a Canary islands endemic. The high genetic diversity observed across North Africa suggests T. mauritanica may represent a species complex.     

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.     

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.     

Molecular Support for the Placement of Saiga and Procapra in Antilopinae (Artiodactyla, Bovidae)

The evolutionary history of the bovid subfamily Antilopinae is unclear. Traditionally, this subfamily is subdivided into two tribes: Neotragini (dwarf antelopes) and Antilopini (gazelles and their relatives). Here, we report new sequences for the 12S and 16S rRNA genes in the enigmatic antilopine taxa Procapra gutturosa and Saiga tatarica and analyze the phylogenetic relationships of these taxa relative to other antilopines. Our study demonstrates the close affinity of the saiga antelope to Gazella despite the conventional systematic allocation of Saiga to the Caprinae subfamily. The second member of the Saigini tribe, Pantholops hodgsoni (Tibetan gazelle), falls within Caprinae. In all of our analyses, Procapra gutturosa occupied a basal position in the Antilopinae clade or was a sister-group to the dwarf antelope Madoqua. This suggests early separation of Procapra from other antelopes.     

Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources

During studies on the bacteriology of appendicitis in children, we often isolated from inflamed and non-inflamed tissue samples, an unusual bile-resistant pigment-producing strictly anaerobic gram-negative rod. Phenotypically this organism resembles members of Bacteroides fragilis group of species, as it is resistant to bile and exhibits a special-potency-disk pattern (resistance to vancomycin, kanamycin and colistin) typical for the B. fragilis group. However, the production of brown pigment on media containing haemolysed blood and a cellular fatty acid composition dominated by iso-C15:0, suggests that the organism most closely resembles species of the genus Porphyromonas. However, the unidentified organism differs from porphyromonads by being bile-resistant and by not producing butyrate as a metabolic end-product. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism represents a distinct sub-line, associated with but distinct from, the miss-classified species Bacteroides putredinis. The clustering of the unidentified bacterium with Bacteroides putredinis was statistically significant, but they displayed > 4% sequence divergence with each other. Chromosomal DNA-DNA pairing studies further confirmed the separateness of the unidentified bacterium and Bacteroides putredinis. Based on phenotypic and phylogenetic considerations, it is proposed that Bacteroides putredinis and the unidentified bacterium from human sources be classified in a new genus Alistipes, as Alistipes putredinis comb. nov. and Alistipes finegoldii sp. nov., respectively. The type strain of Alistipes finegoldii is CCUG 46020(T) (= AHN243(T)).     

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。     

Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA

Following taxonomic revisions in recent years, the originally large family Grapsidae MacLeay, 1838 has become a relatively small and morphologically homogeneous family in terms of adult and larval morphology. Most available molecular studies including more than one genus of the family have also suggested monophyly of the corresponding taxa. However, no single phylogenetic study has ever included all constituent genera of the Grapsidae. In the current study, a molecular phylogeny based on sequences of the mitochondrial 16S rRNA gene from all eight grapsid genera and 34 species is presented and suggests that up to four genera are not monophyletic. This is mainly due to the polyphyletic nature of the genus Pachygrapsus which can be found in six different lineages of the phylogeny, suggesting that the genus currently does not represent a single evolutionary lineage and is in need of taxonomic revision. Amphi-atlantic and trans-isthmian species pairs or populations in four genera are compared and reveal relatively constant and pronounced divergences across the Panama Isthmus as opposed to moderate divergences across the Atlantic Ocean, thereby suggesting occurrence of gene flow across the Atlantic Ocean during the past three million years.     

16SrRNA及rpoC1基因用于螺旋藻、节旋藻系统发育的比较

【目的】利用16S rRNA和rpoC1基因分子标记研究螺旋藻、节旋藻的系统发育关系,并对其区分能力进行比较。【方法】以84株螺旋藻、节旋藻为研究对象,对其进行16S rRNA、rpoC1基因序列的扩增、测序及分析,并对构建的系统发育树进行对比。【结果】rpoC1基因序列保守位点所占比例49.7%、平均G+C百分含量47.7%和序列相似度76%–100%明显低于16S rRNA基因序列的79.4%、55.6%和91%–100%,其变异程度高于16S rRNA基因;基于16S rRNA、rpoC1基因构建的系统发育NJ树拓扑结构基本一致,84株实验藻株分为2个属3个类群,其中仅F-351、F-904-2、F-1070和TJBC14-1藻株为螺旋藻,其余均为节旋藻;虽然2个基因都不能区分形态种和地理种,但rpoC1基因NJ树的置信度(100%)高于16S rRNA基因(99%),属内分群效果也明显优于16S rRNA基因。【结论】支持了螺旋藻、节旋藻为两个不同属的结论,且在属内分类时rpoC1基因比16S rRNA基因具有更高的区分度。     

Corylomyces: a new genus of Sordariales from plant debris in France

The new genus Corylomyces, isolated from the surface of a hazelnut (Corylus avellana) in the French Pyrenees, is described, illustrated and compared with morphologically similar taxa. It is characterised by tomentose, ostiolate ascomata possessing long necks composed of erect to sinuose hairs, and one- or two-celled, opaque, lunate to reniform ascospores. Analyses of the SSU and LSU fragments rDNA gene sequences support its placement in the Lasiosphaeriaceae (Sordariales).     

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.     

Phylogenetic relationships among four species and a sub-species of Mullidae (Actinopterygii; Perciformes) based on mitochondrial cytochrome B, 12S rRNA and cytochrome oxidase II genes

DNA sequence comparisons of three mitochondrial DNA genes were used to reveal phylogenetic relationships among four species and a sub-species of Mullidae family. This is the first report using mitochondrial DNA sequence data to infer intraspecific relationship among different populations of Mullus barbatus and Mullus surmuletus; phylogenetic relationships between M. barbatus and its sub-species; M. barbatus ponticus. Cytochrome b, 12S ribosomal RNA, and cytochrome oxidase II regions of 242 individuals belonging to species M. barbatus, M. surmuletus, Upeneus moluccensis, Upeneus pori and sub-species M. barbatus ponticus were sequenced and phylogenetic trees were constructed using four different algorithms. The phylogenetic trees constructed support the existing taxonomical data of two mullid genera (Mullus, Upeneus). Molecular data shows no significant difference between same species of different geographical populations. The results suggest that the molecular difference is not large enough between M. barbatus and M. barbatus ponticus to consider them as sub-species.