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.

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.

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.

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.

Robust Stabilizing Regions of Fractional-order PI~λ Controllers for Fractional-order Systems with Time-delays

This study focuses on a graphical approach to determine the robust stabilizing regions of fractional-order PIλ（proportional integration） controllers for fractional-order systems with time-delays. By D-decomposition technique, the existence conditions and calculating method of the real root boundary（RRB） curves, complex root boundary（CRB） curves and infinite root boundary（IRB）lines are investigated for a given stability degree. The robust stabilizing regions in terms of the RRB curves, CRB curves and IRB lines are identified by the proposed criteria in this paper. Finally, two illustrative examples are given to verify the effectiveness of this graphical approach for different stability degrees.

Limited Heredity Diversity of the Critically Endangered Guizhou Golden Monkeys

Guizhou golden monkey(Rhinopithecus brelichi)was a unique,endangered and endemic primate species in Guizhou Province.It was an isolated population caused by habitat loss and fragmentation due to the human disturbance in the recently 30 years in China,only distributed in Fanjingshan National Natural Reserve,Guizhou Province.To know the background with demonic population structure,we sequenced 867 bp of the mitochondrial DNA D-loop from 312 fresh fecal samples,results showed there 11 haplotypes among these samples,h was 0.517,πwas 0.00413.It indicated that this species had the lowest genetic diversity among four golden monkeys in China and need strengthen the conversation concern for this species immediately.

Genetic variation of the small yellow croaker(Larimichthys polyactis)inferred from mitochondrial DNA provides novel insight into the fluctuation of resources

The small yellow croaker(Larimichthys polyactis)belongs to the family Sciaenidae,which is an offshore warm fish species and widely distributed in the western Pacific.In this study,the variation of genetic diversity and genetic differentiation among L.polyactis populations was analyzed by mitochondrial DNA control region.A total of 110 polymorphic sites were checked,which defined 134 haplotypes.High level of haplotype diversity(h=0.993±0.002)was detected in the examined range.Population genetic structure analyse(analysis of molecular variance,Fst)showed there were high gene flow among L.polyactis populations.The result showed that there were relatively high genetic diversity and low genetic differentiation among the Yellow Sea and the East China Sea populations,which can be attributed to diverse habitats,wide distribution range and high mutation rate of control region.Using phylogenetic methods,coalescent analyses(neutrality tests,mismatch distribution analysis,Bayesian skyline analyses)and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence,we inferred that the genetic make-up of extant populations of L.polyactis was shaped by Pleistocene environmental impacts on the historical demography of this species.Besides,relatively constant genetic diversity and larger effective population size were detected in recent L.polyactis population.The result showed that the fishing policy certainly,such as the summer closed fishing,played a role in protecting resources of L.polyactis.This study can offer a wealth of biological novelties which indicates genetic structure of L.polyactis population and provides the foundation for resources protection and policy setting.

Genetic diversity in Japanese populations of the Eurasian Collared Dove

Background:Eurasian Collared Dove(Streptopelia decaocto)is a species distributed in the Eurasian continent and North Africa,and inhabiting mainly in Saitama Prefecture in Japan.Eurasian Collared Dove is one of the most prosper-ous invaders in the world,and Japanese Eurasian Collared Dove has also been introduced from overseas.The Japa-nese population has declined to one-hundredth over 30 years and is being protected.In this study,we analyzed its genetic diversity in order to understand the genetic differences between wild populations of Eurasian Collared Dove and those bred in zoos.Methods:A sequence of about 1.9 kb mtDNA was determined for 20 wild Eurasian Collared Doves living in Saitama,Japan and 20 zoo-bred Eurasian Collared Doves,and population genetic analysis was performed.Results:In the COI gene,778 bp had the same sequence in all the 40 individuals examined,and no mutation sites could be confirmed.In the control region,two base substitution sites were confirmed in 1140 bp long sequence.Three haplotypes were detected in 20 individuals in wild,whereas all 20 zoo-bred individuals possessed the same haplotypes possessed in the wild population.Conclusion:Haplotypes of zoo-bred individuals were also retained among the wild individuals,confirming that no genetic problems could occur if the zoo-bred individuals were released to the wild for the Japanese Eurasian Collared Dove propagation program.

Chaotic motions of the L-mode to H-mode transition model in tokamak

The chaotic dynamics of the transport equation for the L-mode to H-mode near the plasma in a tokamak is studied in detail with the Melnikov method. The transport equations represent a system with external and parametric excitation. The critical curves separating the chaotic regions and nonchaotic regions are presented for the system with periodically external excitation and linear parametric excitation, or cubic parametric excitation, respectively. The results obtained here show that there exist uncontrollable regions in which chaos always take place via heteroclinic bifurcation for the system with linear or cubic parametric excitation. Especially, there exists a controllable frequency, excited at which chaos does not occur via homoclinic bifurcation no matter how large the excitation amplitude is for the system with cubic parametric excitation. Some complicated dynamical behaviors are obtained for this class of systems.

Genetic Diversity and Structure in Japanese Populations of the Osprey (<i>Pandion haliaetus</i>), Based on mtDNA

Osprey is a type of bird of prey that lives almost all over the world. In Japan, it is designated as a near-threatened species because it has less than 1000 individuals. In recent years, it inhabits more inland than in coastal areas. In this study, we conducted a population genetic analysis focusing on what kind of genetic structure Japanese Osprey retains and whether there are differences between coastal and inland populations. We also performed genetic diversity assessments. We sequenced about 2.3 kb of mtDNA for 27 individuals in Japan, and phylogenetic analysis, network analysis, neutrality test and mismatch distribution analysis were performed. Eighteen haplotypes were detected in 27 individuals, indicating that genetic diversity was sufficiently high. Both unique and common haplotypes were detected between inland and coastal populations, suggesting gene flow between the two populations. Phylogenetic analysis results show no genetic differentiation in the Japanese Osprey population. From the results of network analysis, neutrality test and mismatch distribution analysis, it was inferred that the Japanese Osprey had a population expansion in the past. This study indicated that the dispersion of Japanese Osprey was random and there were no restrictions on the breeding area. The information presented here can be used towards implementing future conservation actions.

Mitochondrial genotyping of cultured Piaractus brachypomus revealed low diversity and mutations in regions involved in metabolisms and proliferation

In Amazonia,small-oriented family businesses or communities cultivate freshwater organisms as a source of income.Although effective management is fundamental for optimizing cultivated stocks,Amazonian aquaculture belittles the importance of genetic diversity,relying primarily on phenotypical characteristics during breeders’selection.To provide a“proof of concept”built on the premise that implementing modern technologies is crucial to optimizing fish stocks in rural Amazonian fish farms,we conducted a pilot study assessing genetic diversity on cultivated Piaractus brachypomus from Caquet´a,Colombia.We used mitochondrial control region(CR)sequences to evaluate heterogeneity.Our data revealed low genetic diversity and suggested that most sampled individuals probably originated from a single maternal lineage.Haplotype diversification resulted from discrete point mutations not associated with geographical location.Polymorphisms accumulate in non-conserved CR regions,yet the most divergent haplotypes display mutations in conserved CR sequences with roles in mitochondrial metabolisms and proliferation.Overall,our results indicate a need in the local industry to design breeding strategies to enhance diversity to avoid deleterious effects caused by inbreeding and domestication.

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.

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.

Regional constrained control problem for a class of semilinear distributed systems

The aim of this paper is to investigate a regional constrained optimal control problem for a class of semi[inear distributed systems, which are linear in the control but nonlinear in the state. For a quadratic cost functional and a closed convex set of admissible controls, the existence of an optimal control is proven, and then this is characterized for three cases of constraints. A useful algorithm is developed, and the approach is illustrated through simulations for a heat equation.

Novel insights into the spatial genetic patterns of the finless porpoise from East to Southeast Asia

Several cetacean species are endemically distributed throughout the Indo-Pacific.Due to disproportionate sampling and research efforts across the Indo-Pacific region,the spatial genetic structure of these species remains poorly understood.This has led to poor phylogeographic knowledge and ambiguous taxonomic classification of many Indo-Pacific cetacean species.Of these,the finless porpoise(genus Neophocaena)is a small cetacean obligatory to the inshore waters from East Asia to the Persian Gulf of the Indian Ocean.To date,two species are generally recognized:the narrow-ridged finless porpoise inhabiting temperate and subtropical waters,and wideridged finless porpoises inhabiting subtropical and tropical waters.Early research efforts focused on the temperate waters off the northern China.However,recent studies have proposed that the primary divergence within the genus may lie between the Indian Ocean and Pacific region,which remains to be tested with more samples from tropical and subtropical regions.Here,we examined the genetic relationship among the finless porpoises from the Gulf of Thailand to the Taiwan Strait using both mitochondrial and autosomal markers.Bayesian assignment analysis suggested a minimum of four genetic populations within the study areas,corresponding to the narrowridged finless porpoise from the Taiwan Strait(TWSn),and the three wide-ridged finless porpoise populations from the Taiwan Strait(TWSw),Pearl River Delta region(PRDw),and the Gulf of Thailand(Thaiw),respectively.The minimum spanning network of the mtDNA control region found shared haplotypes among finless porpoises in Chinese waters,but those from the Gulf of Thailand formed a unique matriline lineage.Consistently,the genetic differentiation or divergence within the South China Sea(Thaiw vs.PRDw)appears to be higher than that of most finless porpoise populations examined to date,and meets the threshold values of species or sub-species level proposed for the cetacean species.The Mantel test detected a strong correlation between the geographic and genetic matrices within the South China Sea(r>0.99,p<0.001),indicating that the divergence associated with isolation-by-distance(IBD)has been accumulating in recent history.Our results imply that the formation and maintenance of the spatial genetic pattern of the finless porpoise is more complex than previously thought.However,this cannot be addressed by the current taxonomic classification of the genus.

The complete mitochondrial genome of Cervaphis quercus （Insecta： Hemiptera： Aphididae： Greenideinae）

The mitochondrial genome of Cervaphis quercus has been sequenced and annotated. The entire genome of 15 272 bp encodes two ribosomal RNA genes （rrnL and rrnS）, 22 transfer RNA （tRNA） genes, 13 protein-coding genes and a control region. The genome has the same gene order as that found in the inferred ancestral insect. Nucleotide composition is highly A＋T biased. All protein-coding genes use standard mitochondrial initiation codons. Secondary structure models of the two ribosomal RNA genes ofC. quercus are similar to those proposed for other insects. All tRNAs have the classic clover-leaf structure, except for the dihydrouridine （DHU） arm of trnS （AGN）, which forms a simpleloop. The presence of structural elements in the control region is also discussed, with an emphasis on the possible regulation of replication and/or transcription. Comparison withmitochondrial genomes of other aphid species shows their gene arrangements are conserved; however, the variety of repeat regions in species from a different aphid subfamily,Aphidinae, suggests that they resulted from independent evolutionary events.

Taxonomic status of Chinese blue sheep(Pseudois nayaur):new evidence of a distinct subspecies

The blue sheep is an endemic species to the Qinghai-Tibet Plateau and surrounding regions.It has been regarded as having 2 subspecies:Pseudois nayaur nayaur and P.n.szechuanensis.However,such a classification remains controversial.Herein,we analyze 10 microsatellite loci and part of the mitochondrial control region for clarification in such taxonomic debates.We use samples from 168 individuals from 6 geographic populations covering almost all the distribution areas of the species in China to carry out comparisons.Phylogenetic trees derived from both the microsatellite and mitochondrial markers combined with the discriminant analysis of principal components(DAPC)and the STRUCTURE analysis reveal that the individuals in the Helan Mountains are well grouped with a distinct evolutionary lineage and are significantly different from the other populations of P.n.szechuanensis according to Fst values,implying that this isolated population should be categorized as a valid subspecies;namely,Pseudois nayaur alashanicus.The isolation-by-distance(IBD)analysis shows a significant positive relationship between genetic and geographical distances among the populations.