Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei : Cyprinidae) in China inferred from cytochrome b sequences

Aim: To test a vicariant speciation hypothesis derived from geological evidence of large-scale changes in drainage patterns in the late Miocene that affected the drainages in the south-eastern Tibetan Plateau. Location: The Tibetan Plateau and adjacent areas. Methods: The cytochrome b DNA sequences of 30 species of the genus Schizothorax from nine different river systems were analysed. These DNA sequences were analysed using parsimony, maximum likelihood and Bayesian methods. The approximately unbiased and Shimodaira-Hasegawa tests were applied to evaluate the statistical significance of the shortest trees relative to alternative hypotheses. Dates of divergences between lineages were estimated using the nonparametric rate smoothing method, and confidence intervals of dates were obtained by parametric bootstrapping. Results: The phylogenetic relationships recovered from molecular data were inconsistent with traditional taxonomy, but apparently reflected geographical associations with rivers. Within the genus Schizothorax, we observed a divergence between the lineages from the Irrawaddy-Lhuit and Tsangpo-Parlung rivers, and tentatively dated this vicariant event back to the late Miocene (7.3-6.8 Ma). We also observed approximately simultaneous geographical splits within drainages of the south-eastern Tibetan Plateau, the Irrawaddy, the Yangtze and the Mekong-Salween rivers in the late Miocene (7.1-6.2 Ma). Main conclusions: Our molecular evidence tentatively highlights the importance of palaeoriver connections and the uplift of the Tibetan Plateau in understanding the evolution of the genus Schizothorax. Molecular estimates of divergence times allowed us to date these vicariant scenarios back to the late Miocene, which agrees with geological suggestions for the separation of these drainages caused by tectonic uplift in south-eastern Tibet. Our results indicated the substantial role of vicariant-based speciation in shaping the current distribution pattern of the genus Schizothorax.

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.

Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning

1140 bp of cytochrome b gene were amplified and sequenced from 14 species of primitive cyprinid fishes in East Asia. Aligned with other ten cytochrome b gene sequences of cyprinid fish from Europe and North America retrieved from Gene bank, we obtained a matrix of 24 DNA sequences. A cladogram was generated by the method of Maximum likelihood for the primitive cyprinid fishes. The result indicated that subfamily Leuciscinae and Danioninae do not form a monophyletic group. In the subfamily Danioninae, Opsariichthys biden and Zacco platypus are very primitive and form a natural group and located at the root. But the genera in subfamily Danioninae are included in different groups and have not direct relationship. Among them, Aphyocypris chinensis and Yaoshanicus arcus form a monophyletic group. Tanichthys albonubes and Gobiocypris rarus have a close relation to Gobioninae. The genus Danio is far from other genera in Danioninae, In our cladogram, the genera in Leuciscinae were divided into two groups that have no direct relationship. The genera in Leuciscinae distributed in Europe, Sibera and North America, including Leuciscus, Rutilus, Phoxinus, N. crysole, Opsopoeodus emilae, form a monophyletic group. And the Leuciscinae in southern China including Ctenopharyngodon idellus, Mylopharyngodon piceus, Squalibarbus and Ochetobius elongatus have a common origination.

镧系氨基酸配合物在生理pH条件下的结构特性及其对DNA的特异性识别

DNA是重要的生物大分子，也是主要的抗癌药物靶分子。小分子与DNA之间的相互作用是以DNA为靶分子的各种物质生物效应的基础，它们之间的特异性结合导致了癌变、突变及细胞的死亡。能够与DNA特异性结合的小分子很多都是临床上广泛应用的抗癌药物。因此，小分子与DNA之间的相互作用不论是对阐述抗癌、抗病毒药物的作用，还是对致癌机理的研究，尤其对抗癌药物的体内筛选都有重要意义。近十年来，开发新型的抗癌药物小分子，使它们具有对DNA序列特异性的识别能力己成为国内外研究的热点。斓系配合物由于具有广泛的光学、磁学和电学等特性使得有可能成为新的DNA特异性识别分子。然而，斓系离子在中性条件下极其容易水解的特性又极大的阻碍了斓系配合物对于DNA的识别性研究。本文在中性条件下合成了铜系氨基酸配合物，并成功的获得了这些配合物的晶体结构，利用这些有确定结构的I系氨基酸配合物与特定的DNA序列相作用，通过多种生物物理方法研究了它们对DNA序列特异性识别。主要的结果如下：1．在近中性条件下，合成了Eu-Val（［Eus_8（L-HVal）_(16)（H_2O）_(32)］Cl_(24)·12.5H_2O），Eu-Asp（［Eu_4（μ3-OH）_4（L-Asp）_2（L-HAsp）_3（H_2O）_7］Cl·11.5H_2O）和Tb-Cys（「Th_2（DL-Cys）_4（H_2O）_8]Cl_2）三种铜系氨基酸配合物，这些配合物的结构由于合成条件（温度，反离子及合成比例）上的差异与已报到的类似配合物的结构具有明显的不同。三种配合物的结构各具特色，从而在与DNA作用时将表现出各自特有的识别性能。2．Eu-Val配合物在与单链DNA作用时，配合物能键合到DNA碱基所在的疏水区，在与富含dC和dT碱基的序列相结合时，发生显著的能量传递，从而极大的增强了配合物中Eu的发射光谱。配合物结合DNA的化学计量比随序列中dC含量的降低而降低。配合物同样能够与处于DNA疏水区的富含dA和dG序列相结合，这种结合不能够产生能量传递，但使得DNA的紫外-可见光谱出现明显的减色和红移现象。此外，这一配合物还能够诱导单链DNApoly（dA）及p01y（rA）产生自身的二级结构，形成双链结构。这为进一步认识斓系离子的生物学效应奠定了基础，斓系氨基酸配合物可以诱导单链poly（dA）及poly（rA）形成自身结构尚无文献报道。3．Eu一AsP配合物能够选择性的稳定非B一构象的Poly（dA）Poly（dT），而使B一构象的印oly（dAdT）］2和［Poly（dGdC）］2变得不稳定。如在1：2比例时，该配合物可使Poly（dA）Polv（dT）的融化温度提高4℃，而使印oly（dAdT）｝2的融化温度降低6℃，［Poly（dGdC）］2则出现了两个转变温度。进一步的圆二色实验结果充分表明Eu一Asp配合物对于富含Poly（dA）Poly（dT）和［Poly（dAdT）］2的双链DNA没有构象上的改变，而对于［Poly（dGdC）］2的双链DNA则产生了显著的构象上的改变，很有可能正是这一改变使得［Poly（dGdC）］2变得极其的不稳定。配合物对［Poly（dGdC）］2的这种不稳定影响随着配合物浓度的逐步升高而越来越明显。变温实验结果清楚的表明，在37℃时，Eu-AsP使[Poly（dGdC）JZ发生了构象转化，并且这种转化是可逆的。4．Tb-Cys配合物与单链（除了poly（dA））和双链DNA都能发生能量传递，从而使得配合物的荧光显著增强。不同的DNA表现出不同的增强效果，表明TbCys配合物对DNA的序列存在选择性，单链要强于双链，富含Poly（dAdG）的序列增强效果最好。单链和双链能量传递的差异表明了配合物能够区分DNA的单链和双链，配合物在与单链作用时结合更强。TbCys配合物在与DNA作用时存在不同的结合位点，而且单链和双链的结合位点明显不同。TbCys配合物能够引起富含dC和dT的单链DNA发生减色效应，而能够引起富含poly（dA）、poly（dAdG）的单链DNA和富含poly（dA）poly（dT）、[Poly（dAdT）］2和［poly（dGdC）］2的双链DNA发生明显的红移。此外，这一配合物同样能够影响双链DNA的稳定性，使得富含poly（dA）Poly（dT）序列变得稳定，而使得富含印oly（dAdT）］2和富含印oly（dGdC）］2的序列变得不稳定。这些结果都表明了配合物对DNA存在选择性。比较不同配合物的差别后能够发现DNA对于不同的配合物同样具有选II择性，这种选择性能够用来区分配合物。一这些钢系氨基酸配合物由于选择了天然的氨基酸作为配体，从而大大的降低了对人体的毒性，进一步表现出的对不同的DNA序列的选择型则使其有望成为新型的抗癌诊疗试剂。

Global transposable characteristics in the complete DNA sequence of the yeast

Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. On the basis of the correlation distance of nucleotide strings, 16 chromosome sequences of the yeast, which are divided into 5 groups, display 4 kinds of the fundamental transposable characteristics: a short increasing period, a long increasing quasi-period, a long major value and hardly relevant.

Studies on alkaloids binding to GC-rich human survivin promoter DNA using positive and negative ion electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding of 13 alkaloids to two GC-rich DNA duplexes which are critical sequences in human survivin promoter. Negative ion ESI-MS was first applied to screen the binding of the alkaloids to the duplexes. Six alkaloids (including berberine, jatrorrhizine, palmatine, reserpine, berbamine, and tetrandrine) show complexation with the target DNA sequences. Relative binding affinities were estimated from the negative ion ESI data, and the alkaloids show a binding preference to the duplex with higher GC content. Positive ion ESI mass spectra of the complexes were also recorded and compared with those obtained in negative ion mode.

Comparison for DNA primary sequence

In this article, two schemes are suggested based on three exons of beta-globin gene belonging to 10 species for comparison of DNA primary sequences. At first, the positions of four nucleic acid bases were extracted, and then based on the information, as the numerical characterization of DNA sequences, the sequence invariants were derived. Sequences comparisons of 10 species selected in this work by using these invariants were performed. The results, especially with scheme 2, are quite satisfactory.

A novel invariant and sequence comparison for DNA

We consider numerical characterization of DNA primary sequence based on the positions of bases (a, t, c, g) and the pairs of bases X, Y in DNA (X, Y=a, t, c, g). This leads to a representation of DNA by a numerical sequence. Then, we extract a novel invariant (molecular connectivity index) from the derived numerical sequences. The suitable invariant can offer a characterization of DNA primary sequence. Finally, we provide an illustration of its utility by making a comparison between ten DNA sequences belonging to beta-globin gene in different species. The evolutionary relationships of ten species we have revealed in this contribution accord with phylogenetic tree properly.

Self-similarity limits of genomic signatures

It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display genomic signature in chaos game representation is obtained by eliminating effects of the finite sequence. The optimal string length is further shown as a self-similarity limit in computing information dimension. By using the method, self-similarity limits of bacteria complete genomic signatures are further determined.

Sox and Zfx genes in giant panda

By using PCR cloning techniques, the DNA sequences of the HMG box regions of six Sox genes (pSox) and the zinc finger domains of two Zfx genes (pZfx) in the giant panda were identified. The giant panda Sox genes fell into two subfamilies, SOX-S1 and SOX-S2. The pSox and pZfx genes of the giant panda were highly homologous to the corresponding genes in mammals and revealed close substitution rates to those in the primates.

Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

Genetic divergence of orangutan subspecies (Pongo pygmaeus)

Microsatellites and mitochondrial DNA sequences were studied for the two subspecies of orangutans (Pongo pygmaeus), which are located in Borneo (P. p, pygmaeus) and Sumatra (P. p. abelii), respectively. Both subspecies possess marked genetic diversity. Ge

What are the closest relatives of the hot-spring snakes (Colubridae, Thermophis), the relict species endemic to the Tibetan Plateau?

We conducted phylogenetic analyses to identify the closest related living relatives of the Xizang and Sichuan hot-spring snakes (T baileyi and T. zhaoermii) endemic to the Tibetan Plateau, using mitochondrial DNA sequences (cyt b, ND4) from eight specimen

The complete mitochondrial genomes of two species from Sinocyclocheilus (Cypriniformes: Cyprinidae) and a phylogenetic analysis within Cyprininae

We determined the complete mitochondrial DNA sequences for two species of surface- and cave-dwelling-cyprinid fishes, Sinocyclocheilus grahami and S. altishoulderus. Sequence comparison of 13 protein-coding genes shows that the mutation pattern of each single gene is quite similar to those of other vertebrate animal species. Analysis of the ratios of Ka/Ks at these loci between Sinocyclocheilus and two other cyprinid species (Cyprinus carpio and Procypris rabaudi) show that Ka/Ks ratios are differed, consistent with purifying selection and variation in functional constraint among genes. Bayesian analysis and maximum likelihood analysis of the concatenated mitochondrial protein sequences for 14 cyprinid taxa support the monophyly of the family Cyprininae, and further confirm the monophyly of the genus Sinocyclocheilus. The two Sinocyclocheilus species fall within the Cyprinion-Onychostoma lineage, including Cyprinus, Carassius, and Procypris, rather than among the Barbinae, as previously suggested on morphological grounds.

Mitochondrial control region sequence variation within the argali wild sheep (Ovis ammon): evolution and conservation relevance

The phylogenetic relationship of several subspecies of Ovis ammon were analyzed by comparing DNA sequences within the entire mitochondrial D-loop region. Five putative subspecies of ammon (dalai-lamae, darwini, hodgsoni, sairensis and adamerzi) were sampled from four provinces in China [Xinjiang, Qinghai, Gansu and Xizang (Tibet)] and two (servertzovi and nigrimontana) from Uzbekistan. The argalis sampled represent most of the currently recognized putative Subspecies of argali. Analysis of mtDNA sequences revealed high variability within ammon (7.7%), ranging from 2.4 to 11.5%. MaxiMUM-Parsimony tree indicated that nigrimontana from Uzbekistan diverged First, followed by severtzovi from Uzbekistan. The dispersal of argalis into China gave rise to three clades, suggesting that the argali originated in Western Asia and then dispersed throughout the central Asian highlands on a southeastward course. Among the Chinese argalis, mtDNA analysis places dalailamae genetically closer to hodgsoni than to darwini. Severtzovi and.. nigrimontana are two separate subspecies and genetically distinct from the Chinese argali.