Sequence Difference of Mitochondrial DNA Control Region and Genetic Differentiation of Cervinae in China

[Objective] The study aimed at analyzing Genetic Differentiation of Cervinae. [Method] The complete mitochondrial DNA control region of five species of Cervinae was determined by direct DNA sequencing. Homologous sequences of others Cervinae were gained from GenBank, and then analyzed through biology software. [Result] The lengths of their control region were 921-1 072 bp, the nucleotide content of T, A, C, and G was 32.1%, 30.2%, 22.7% and 15.0% separately. Genetic distance of each species ranged from 0.062-0.106, which belonged to level of inter-genus. The molecular phylogenetic tree indicated that red deer, skia deer and White-lipped Deer had close relationship, and they constituted one branch with sambar deer. Eld＇s deer and elk deer constituted the second branch, and hog deer constituted the third branch alone. [Conclusion] Hog deer and fallow deer should be incorporated in Cervus, divergence time is about 1.55-2.60 million years among Cervinae in China.

A Molecular Phylogeny of Macaca Based on Mitochondrial Control Region Sequences

Nucleotide sequences of segments of the mitochondrial control regions were analyzed to infer the phylogenetic relationships among 7 macaques.High nucleotide diversity in Macaca assamensis and relatively low diversity in M.thibetana were found.Based on the ML tree from control regions,species in our study can roughly be sorted into three species groups except for the phylogenetic position of M.fascicularis,i.e.,silenus group,including M.leonina;sinica group,including M.arctoides,M.assamensis,and M.thibetana;and fascicularis group,including M.mulatta and M.cyclopis.A discrepancy between earlier studies (Fooden & Lanyon,1989;Tosi et al,2003a;Deinard & Smith,2001;Evans et al,1999;Hayasaka et al,1996;Morales & Melnick,1998),our result supported the hypothesis that M.fascicularis diverged earlier than M.leonina.Mitochondrial paraphyly in eastern M.mulatta (with respect to M.cyclopis) and eastern M.assamensis (with respect to M.thibetana) were clearly observed in our study.In accordance with the results of Y chromosome,allozyme,nuclear genes and some morphological data (Delson,1980;Fooden & Lanyon,1989;Fooden,1990;Tosi et al,2000,2003a,b;Deinard & Smith,2001),our study on control region sequences supported M.arctoides to be classified into the sinica group.However,this result disagreed with the previous mtDNA studies (Hayasaka et al,1996;Morales & Melnick,1998;Tosi et al,2003a).

Broader pattern of tandem repeats in the mitochondrial control region of Perciformes

Perciformes,the largest order of vertebrates with 20 suborders,is the most diverse fish order that dominates vertebrate ocean life.The complete mitochondrial control region(CR) of Trichiurus japonicus(Trichiuridae,Scombroidei) and Pampus sp.(Stromateidae,Stromateoidei) were amplified and sequenced.Together with data from GenBank,the tandem repeats in the mitochondrial CR from 48 species,which covered nine suborders of Perciformes,are reported in this study.The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei.The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence.Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks,which was first reported in Perciformes and vertebrates.This might have resulted from interruption of the polymerase activity during the H-strand synthesis.The four broader patterns presented here for the tandem repeats,including those in both the 5' and 3' ends,only in the either 5' or 3' end,and in the central conserved domain of the control region,will be useful for understanding the evolution of species.

Structure of Mitochondrial DNA Control Region of Pholis fangi and Its Phylogenetic Implication

In this study, the entire mitochondrial DNA(mtDNA) control region(CR) of Pholis fangi was amplified via polymerase chain reaction followed by direct sequencing. The length of the mtDNA CR consensus sequence of P. fangi was 853 bp in length. In accordance with the recognition sites as were previously reported in fish species, the mtDNA CR sequence of P. fangi can be divided into 3 domains, i.e., the extended terminal associated sequence(ETAS), the central conserved sequence block(CSB), and the CSB domain. In addition, the following structures were identified in the mtDNA CR sequence of P. fangi: 2 ETASs in the ETAS domain(TAS and cTAS), 6 CSBs in the central CSB domain(CSB-F to CSB-A), and 3 CSBs in the CSB domain(CSB-1 to CSB-3). These demonstrated that the structure of the mtDNA CR of P. fangi was substantially different from those of most other fish species. The mtDNA CR sequence of P. fangi contained one conserved region from 656 bp to 815 bp. Similar to most other fish species, P. fangi has no tandem repeat sequences in its mtDNA CR sequence. Phylogenetic analysis based on the complete mtDNA CR sequences showed that there were no genetic differences within P. fangi populations of the same geographical origin and between P. fangi populations of different geographical origins.

Mitochondrial DNA control region diversity and population structure of Pacific herring(Clupea pallasii)in the Yellow Sea and the Sea of Japan

To investigate the genetic variation and population structure of Pacific herring in the Yellow Sea and the genetic differentiation between the Yellow Sea and the Sea of Japan, fragments of 479-bp mitochondrial DNA control region were sequenced for 110 individuals collected from three different periods in the Yellow Sea and one locality in the Sea of Japan. High haplotype diversity and moderate nucleotide diversity were observed in Pacific herring. AMOVA and exact test of population differentiation showed no significant genetic differentiations among the three populations of the Yellow Sea and suggested the populations can be treated as a single panmictic stock in the Yellow Sea. However, a large and significant genetic differentiation （ФST=0.11; P=0.00） was detected between the populations in the Yellow Sea and the Sea of Japan. The high sea water temperature in the Tsushima Strait was thought a barrier to block the gene exchange between populations of the two sea areas. The neutrality tests and mismatch distribution indicated recent population expansion in Pacific herring.

Directional region control of the thermal fractal diffusion of a space body

We present a directional region control （DRC） model of thermal diffusion fractal growth with active heat diffusion in three-dimensional space. This model can be applied to predict the space body heat fractal growth and study its directional region control. When the nonlinear interference term and the inner heat source term are generalized functions, the relationship between the particle aggregation probability and the interference terms can be obtained using the norm theory. We can then predict the aggregation form of particles in different regions. When the nonlinear interference terms in the model are expressed as a trigonometric function and its composite function, our simulations show that the DRC method of thermal fractal diffusion is effective and has reference value for the directional control of actual fractal growth systems.

Comparative Analysis of Mitochondrial Control Region Sequence from Three Flatfish Species(Pleuronectidae)

The 5’-end of the mitochondrial control region sequences of three flatfishes (Pleuronectiformes: Pleuronectidae) were amplified and sequenced. These sequences were compared with those of other three Pleuronectids species retrieved from GenBank. A phylogenetic tree was constructed based on the partial control region sequences. The results of phyloge- netic analysis are consistent with those of conventional systematics. Compared to previous studies, the structure of the 5’-end of mitochondrial control region was analyzed. The terminal associated sequence motif and its complementary motif were i- dentified at the 5’-end of the sequences. A conserved sequence block, named as CM5’d, was identified in the 5’-end of con- trol region sequences in all Pleuronectids. Another central conserved sequence block, named as CSB-F, was detected in the central conserved blocks.

Population Genetic Analysis of Sillago nigrofasciata (Perciformes:Sillaginidae) Along the Coast of China by Sequencing Mitochondrial DNA Control Region

Sillago nigrofasciata, a small to moderate size nearshore species, is newly found along the eastern and southern coasts of China. The present study is carried out in order to analyze the population genetics of the S. nigrofasciata. The control region sequence of mitochondrial DNA revealing 73 haplotypes were obtained from 162 individuals collected at 8 locations along the coast of China. The whole S. nigrofasciata population along the coast of China showed a low nucleotide diversity(0.012) and a high population diversity(haplotype diversity)(0.943), and all the 8 local populations showed low nucleotide diversities(0.014 – 0.001), suggesting the protective measures are effective. The haplotypes of the 8 local populations were widely distributed in haplotype network diagram and neighbor-joining phylogenetic tree, while no branch associating with sampling locations was detected. Recent gene flow analysis showed asymmetric gene exchanges among local populations. The pairwise FST values and unweighted pair-group method with arithmetic mean(UPGMA) tree revealed a certain amount of genetic difference among local populations. Moreover, analysis of molecular variance(AMOVA) reflected genetic differences between hypothetical subdivision groups. Neutral test and mismatch distribution of pairwise nucleotide suggested S. nigrofasciata may have experienced recent population expansion events. The historical geographic events associating with ice age may be the main explanation to the heterogeneity among local populations with short geographic distances, and the homogeneity among local populations with long geographic distances.

MITOCHONDRIAL DNA POLYMORPHISM IN CONTROL REGION FROM CHINESE YUGU POPULATION

Objective To investigate the mitochondrial DN A sequence polymorphism sites in Chinese YUGU ethnic group and to provide basic da ta used in forensic purpose. Methods Genomic DNA was extracted from the hole blood of 100 unrelated individuals of Chinese YUGU ethnic group by standard chelex-100 method. The sequence polymorphism sites was determined by PCR amplification and direct sequencing. Results 54 polymorphic sites were noted in mtDNA np16091-16418 region, and 46 haplotypes were identifi ed. The genetic diversity was calculated to be 0.9691, and the genetic identity was calculated to be 0.0406. Conclusion There are some particul ar polymorphism sites in Chinese YUGU ethnic group. The results suggest that seq uence polymorphism from np16091-16418 in human mitochondrial DNA can be used as a biological marker for forensic identity.

A DNA-binding protein factor in K562 nuclear extract interacts with positive control region (PCR) in the 5'flanking sequence of human β-globin gene

It has been known that there are at least three regulatory regions (NCR1, NCR2 and PCR) in the 5'-flanking sequence (from -610 bp to +1bp) of human β-globin gene and that the function of PCR is unique to the human erythroleukemia (K562) cells. Here we have detected a DNA-binding protein factor (termed NFEa) in K562 cells, which can bind specifically to the PCR of human β-globin gene. The sequence of the binding site is 5'ACTGATG3' (between -222 bp and -216 bp). The NFEa is erythroid-specific and perhaps specific for K562 cells. It seemed that this factor differed from the erythroid-specific tran-scriptional factor (NFE-1) using competition assay. The presence of the NFEa further supported that the function of the cis-acting element PCR was specific for K562 cells, and helps us to understand the mechanism of the regulation of the expression of human β-globin gene in the human K562 cells.

Sequence polymorphism of human mitochondrial DNA control region in Chinese Dongxiang unrelated individuals

Objective: To investigate the mitochondrial DNA sequence polymorphism in Chinese Dongxiang ethnic group and to provide basic data used in ethnic origin investigation and forensic purpose. Methods: Genomic DNA was extracted from the whole blood of 100 unrelated individuals of Chinese Dongxiang ethnic group by standard Chelex-100 method. The sequence polymorphism was determined by PCR amplification and direct sequencing. Results: Eighty-two polymorphic sites were identified in mtDNA D-loop region 16 091 - 16 418 np, and 88 haplotypes were found. The genetic diversity was calculated to he 0.9969, and the genetic identity was 0.013 2. Conclusion: There are some particular polymorphic sites in Chinese Dongxiang ethnic group, and these sites provide an important basis to investigate the origin of Dongxiang and the relationship between Dongxiang and other ethnic groups. The result also suggested that sequence polymorphism from 16 091 -16 418 np in human mitochondrial DNA control region can be an useful tool for forensic identity.

The Genetic Structure and Diversity of Repomucenus curvicornis Inhabiting Liaoning Coast Based on Mitochondrial COⅠ Gene and Control Region

[Object] This study was conducted to explore the genetic diversity and structure of the wild Repomucenus curvicornis inhabiting Liaoning Coast, China. [Method] The mitochondrial COⅠ gene and control region（CR） were PCR amplified from the wild R. curvicornis populations from the Liaodong Bay（n=22） and the northern Yellow Sea（n=18）, sequenced and analyzed for genetic diversity. [Result] The contents of A, T, C and G of 624 bp COⅠ gene were 24.09%, 31.04%, 25.28%, and 19.59%, and those of 460 bp CR fragment were 32.96%, 32.80%, 14.86% and 19.38%, respectively. The total number of variable sites, average number of nucleotide differences（ k）, haplotype diversity（H） and nucleotide diversity（π） based on COⅠ gene were 38, 4.67,（0.96±0.02） and（0.007 5±0.004 2）, and those based on CR fragment were 26, 3.35,（0.97 ±0.02） and（0.007 3±0.004 3）, respectively. Based on mitochondrial COⅠ gene and CR, the genetic diversity of Liaodong Bay population was lower than that of the northern Yellow Sea population. The AMOVA analysis based on CR fragments revealed almost significant genetic divergence between the Liaodong Bay and the northern Yellow Sea populations, while there was no significant genetic divergence based on COⅠ gene. The results showed that CR and COⅠ gene are effective molecular markers for detecting the genetic diversity of R. curvicornis population, while CR is more reliable than COⅠ gene in detecting the genetic structure. [Conclusion] CR is an appropriate marker for genetic analysis of marine fish population.

Comparative mitochondrial genome analysis of Cynoglossidae(Teleost:Pleuronectiformes)and phylogenetic implications

Generally,a teleostean group(e.g.,family or genus)owns one type or a set of similar mitochondrial gene arrangement.It is interesting,however,that four different types of gene arrangement have been found in the mitochondrial genome(mitogenome)of Cynoglossidae species.So far,the possible mechanisms of mitogenomic gene rearrangement and its potential implications have aroused widespread attention and caused lots of controversy.Here,a total of 21 Cynoglossidae mitogenomes and a newly sequenced mitogenome of Cynoglossus puncticpes(Pleuronectiformes:Cynoglossidae)were compared.The length ranges from 16417 bp to 18369 bp,which is mainly caused by the length heteroplasmy of control region(CR).Further analysis reveals that the difference of tandem repeats acts as a determining factor resulting in the length heterogeneity.Like most gene rearrangements of Cynoglossinae mitogenomes,tRNA-Gln gene encoded by the L-strand has translocated to the H-strand(Q inversion),accompanied by the translocation of CR in C.puncticpes mitogenome.The typical IQM order(tRNA-Ile-Gln-Met)changed to QIM order.Tandem duplication/random loss and mitochondrial recombination were accepted as the most possible models to account for the rearrangements in C.puncticpes mitogenome.Phylogenetic trees showed a strong correlation between the gap spacer in the rearranged QIM area and phylogeny,which provides a fresh idea for phylogenetic studies in future.

A Stackelberg game model with tax for regional air pollution control

The command-and-control regulation is likely inefficient and costly.This study investigates a regional pollution control scheme with tax(RPCST)under which the central government sets the tax rate under a given pollutant reduction quota and local governments determine their pollution removal rates based on the central government’s policy.First,a one-leader-multi-follower(OLMF)Stackelberg game model is formulated,in which the central government is the leader and the local governments are the followers.Then,a procedure based on bilevel programming and relaxation method is applied to solve the OLMF model.Finally,a case study analyzing the SO2 reduction of the Yangtze River Delta in China is conducted to demonstrate the effectiveness of the RPCST.The results show that RPCST works better than the current command-andcontrol scheme.Our analysis provides a guideline for governments to design optimal tax schemes to effectively solve the regional air pollution crisis.

Genetic diversity and matrilineal structure in Chinese tree shrews inhabiting Kunming,China

Due to their special phylogenetic position in the Euarchontoglires and close affinity to primates,tree shrews have been proposed as an alternative experimental animal to primates in biomedical research.However,the population genetic structure of tree shrews has largely remained unknown and this has hindered the development of tree shrew breeding and selection.Here we sampled 80 Chinese tree shrews（Tupaia belangeri chinensis） in Kunming,China,and analyzed partial mtDNA control region sequence variation.Based on our samples and two published sequences from northern tree shrews（T.belangeri）,we identified 29 substitutions in the mtDNA control region fragment（～ 604 bp） across 82 individuals and defined 13 haplotypes.Seventeen samples were selected for sequencing of the cytochrome b（Cyt b;1134 bp） gene based on control region sequence variation and were analyzed in combination with 34 published sequences to solidify the phylogenetic pattern obtained from control region data.Overall,tree shrews from Kunming have high genetic diversity and present a remarkable long genetic distance to the two reported northern tree shrews outside China.Our results provide some caution when using tree shrews to establish animal models because of this apparent genetic difference.In addition,the high genetic diversity of Chinese tree shrews inhabiting Kunming suggests that systematic genetic investigations should be conducted before establishing an inbred strain for medical and biological research.

Regional averaged controllability for hyperbolic parameter dependent systems

The purpose of this paper is to extend the notion of regional controllability for hyperbolic parameter dependent systems.The key idea is the characterization of the averaged regional control with minimal energy.This control steers the state average(with respect to such a parameter)towards the desired state only on a given part of the system evolution domain.In this paper,we give the precis definition and the properties of this new concept.Then,we use an approach based on an extension of the Hilbert uniqueness method devoted to the calculation of the control in two different cases:zone control and pointwise control.

A genetic diversity comparison between captive individuals and wild individuals of Elliot’s Pheasant (Syrmaticus ellioti) using mitochondrial DNA

Maintaining genetic diversity is a major issue in conservation biology. In this study, we demonstrate the differences of genetic diversity levels between wild and captive individuals of Elliot’s Pheasant Syrmaticus ellioti. Wild individuals showed a higher genetic diversity level than that of the captive individuals. Nucleotide diversity and haplotype diversity of wild individuals were 0.00628 and 0.993, while those of captive individuals were 0.00150 and 0.584 respectively. Only 3 haplotypes of mtDNA control region sequence were identified among 36 captive individuals, while 16 unique haplotypes were identified among the 17 wild individuals in this study. One captive haplotype was shared by a wild individual from Anhui Province. It is concluded that a low number of founders was the likely reason for the lower level genetic diversity of the captive group. Careful genetic man- agement is suggested for captive populations, particularly of such an endangered species, to maintain genetic variability levels.

The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

The complete mitochondrial genome （16,837 bp） from the Keeled box turtle （Pyxidea mouhotii） was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule： a large number of （ATTATATC） n direct tandem repeats followed by （TA） n microsatellite at the 3＇ end of the control region （D-loop）, which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood （ML） and Bayesian （BI） analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1） Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea-Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group （containing Pyxidea） may have originated from two ancestors; 2） the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.

A preliminary investigation on genetic diversity of Sousa chinensis in the Pearl River Estuary and Xiamen of Chinese waters

In this study, the mitochondrial DNA （mtDNA） control region and the mitochondrial cytochrome b gene of stranded Indo-Pacific humpback dolphin （Sousa chinensis） samples from the Pearl River Estuary and Xiamen waters were sequenced and analyzed. The result of mtDNA control region revealed 34 variable sites and four unique haplotypes （named as A, B, C and D） identified among the total samples from these two water areas, and the most common haplotype （A） was shared by 75% of the dolphins sampled from the two water areas. The haplotypic diversity （h） was 0.455 and the nucleodde diversity （π） was 0.0088. The phylogenetic analysis showed that the haplotype A, C, and D were closely related, but the haplotype B （unique for XM01 from Xiamen） was far from the other three. By scanning cytochrome b fragments, two haplotypes （A and B） were identified in these two water areas, and the most common haplotype （A） was shared by 91.67% individuals, while XM01 from Xiamen as the only exception. The data suggest that there is a possibility of gene exchange between the two populations in the Pearl River Estuary and Xiamen waters, and there possibly exists a unique maternal lineage in Xiamen waters.

Population genetic structure of the mantis shrimp Oratosquilla oratoria(Crustacea:Squillidae)in the Yellow Sea and East China Sea

The mantis shrimp O ratosquilla oratoria is an ecologically and economically important species in the Western Pacific. In present study, the population genetic structure of O ratosquilla oratoria from the Yellow Sea and East China Sea was examined with mitochondrial DNA control region sequences. In total, 394 samples were collected from 18 locations and 102 haplotypes were obtained. For the Yellow Sea, the overall nucleotide diversity and haplotype diversity were 0.006 9 and 0.946 8, respectively; while across all the East China Sea locations, the overall nucleotide diversity and haplotype diversity were 0.027 94 and 0.979 0, respectively. The results of AMOVA and pairwise F_(ST)(0.145 2, P <0.001) revealed moderate differentiation between the Yellow Sea and East China Sea populations of O. oratoria. However, neither the neighbor-joining tree nor haplotype network showed clades with geographic pattern, which indicated considerable gene flow was existed between the Yellow Sea and East China Sea, and supporting the high larval dispersal ability in this species. Mismatch distribution analysis and neutrality tests suggested that O. oratoria has undergone population expansion event, and the Pleistocene glacial cycles might have an impact on the historical demography of O. oratoria. The genetic information obtained in this study can provide useful information for sustainable improvements for capture fisheries management strategies.