基于线粒体COI基因分析钩手水母的群体遗传结构

钩手水母(Gonionemus vertens)为大西洋和太平洋广布种, 是我国习见的有毒水母种类之一。本文对采自黄渤海海域4个地理群体的104个钩手水母线粒体COI基因序列进行扩增, 并结合GenBank上其他182个钩手水母同源序列进行序列变异分析。在286个基因序列中共检测出52个多态位点, 定义了14种单倍型。总群体的单倍型多样性和核苷酸多样性分别为0.743 ± 0.012和1.046% ± 0.097%, 与其他几种大型水母相比, 钩手水母总群体的遗传多样性处于较高水平。AMOVA结果显示, 60.17%的分子变异源于群组间, 13.37%的分子变异源于群体内, 26.46%的分子变异源于组内群体间, 群组间、群体内和组内群体间的遗传分化均极显著。F_st值统计检验表明, 中国厦门群体与乐亭、东营、烟台、大连群体间存在显著的遗传分化, 大连与东营、烟台群体间也存在显著的遗传分化。系统分析结果显示, 钩手水母群体间存在2个明显的单倍型谱系分支。不同的钩手水母地理群体间具有复杂的遗传模式, 钩手水母复杂的生活史、扩散能力、地理隔离和海流分布可能是影响钩手水母遗传结构的重要因素。     

基于线粒体COI基因的海蜇不同地理群体遗传特征

对采自辽东湾和韩国江华岛的2个海蜇群体56个个体的线粒体COI基因序列进行扩增,并结合GenBank上其他15个海蜇样品的同源序列对其进行序列变异分析,研究海蜇群体的遗传特征和群体遗传结构状况.在所分析的71个个体中共检测到28个多态位点,定义了32种单倍型.海蜇群体呈现出高的单倍型多样性(0.91±0.06～0.94±0.01)和中等或较低的核苷酸多样性[(0.60±0.34)%～(0.68±0.40)%].与其他几种大型水母相比,海蜇群体的遗传多样性水平较高.系统分析结果显示,海蜇群体间具有2个明显的单倍型谱系分支.比较海蜇不同群体间的遗传分化指数(F_ST)和分子变异分析(AMOVA)发现,在本研究取样范围内不同海蜇群体间存在明显的遗传结构.不同海蜇群体存在复杂的遗传模式,海蜇独特的生活史特征、其分布海域的海流状况及人为因素如增殖放流等可能是造成海蜇这种复杂遗传模式的原因.     

基于线粒体COI基因的中国西南地区木领针蓟马地理种群的遗传分化分析

【目的】木领针蓟马Helionothrips mube近年来成为芋头Colocasia esculenta上的一种常见害虫。本研究旨在探讨其中国西南地区地理种群间的遗传变异。【方法】通过Sanger法测定了21个地理种群132头木领针蓟马的线粒体COI基因序列,利用MEGA, DnaSP, Arlequin和Network等软件对木领针蓟马种群间的遗传多样性、遗传分化、分子变异等进行分析。【结果】获得的木领针蓟马132条线粒体COI序列(643 bp)中共发现34个变异位点、16种单倍型,其中单倍型H1出现频率最高、分布最广。木领针蓟马总群体的遗传多样性较高(Hd=0.712, Pi=0.00413, K=2.655),遗传分化程度极大(Fst=0.3443),基因交流水平不高(Nm=0.96)。分子方差分析(AMOVA)表明,木领针蓟马的遗传分化主要来自种群内部,Mantel检测出种群地理距离与遗传距离呈正相关。总群体中性检验Tajima’s D值显著负值,Fu’s Fs值不显著,错配分布曲线呈多峰。综合种群间遗传距离、单倍型系统发育树及中介网络图结果,表明四川成都(CHD)、云南昌宁(CHN)和贵州遵义(ZY)3个种群的遗传分化程度均高于其他种群。【结论】中国西南地区木领针蓟马总群体的遗传多样性较高,遗传分化明显,种群间的基因交流受到地理距离的影响,总群体在较近的历史时期内没有出现扩张现象。     

基于线粒体COI基因序列探讨泥蚶的遗传分化

采用PCR技术对我国沿海地区7个泥蚶群体的线粒体COI基因部分序列进行了测定和遗传分析。在来自7个群体的38个泥蚶样本均得到660 bp的COI基因片段序列,共103个多态位点,组成17种单倍型;数据分析表明：7个群体形成了二大类群：福建以北(包括福建)的5个群体（江苏盐城、浙江奉化、浙江乐清养殖和自然群体、福建福鼎）形成一个类群,类群内的遗传距离为0.0016;福建以南的类群（广东湛江、海南海口）形成一个类群,遗传距离为0.0006;二个类群之间的遗传距离为0.1529,表现为高度的分化。因此我国沿海泥蚶已分化形成福建以南和以北二大类群,二大类群之间的遗传分化已达到亚种水平。     

利用COI基因序列分析长江与澜沧江水系日本沼虾群体的遗传结构

测定了我国长江水系和澜沧江水系的日本沼虾9个群体,共79个个体的线粒体COI基因序列片段(约450bp),结果发现有89个变异位点,共计有46个单倍型。其中云南昆明(KM)群体具有较丰富的遗传多样性(h=1.000,π=0.028),而重庆(CQ)群体的遗传多样性最小(h=0.700,π=0.008)。AMOVA分析表明,群体间的遗传变异占总遗传变异的9.66%,而90.34%的遗传变异源于群体内。采用邻接法(NJ)构建的分子系统树显示,46个单倍型明显地聚为长江中下游和长江上游与澜沧江两个族群。其结果可以为合理开发和利用日本沼虾自然野生资源,以及建立和保护日本沼虾种质资源库及基因库提供必要的参考。     

罗氏沼虾不同群体线粒体COI基因的序列差异和遗传标记研究

利用PCR方法扩增获得罗氏沼虾（Macrobrachiumrosenbergii）线粒体DNA的COI基因,测定该基因片段序列。分析了罗氏沼虾缅甸原种F1代、江苏养殖群体和广西选育F2代3个群体共17只个体的序列核苷酸位点差异和遗传多态。结果表明,缅甸原种F1代遗传多样性最为丰富,江苏养殖群体和广西选育群体的遗传多样性相对贫乏。在长度为498bp的基因片段中,共检测到10个多态性核苷酸位点（占2.01%）,17只个体具有5种基因型,3群体各自的平均核苷酸位点差异分别为0.88%、0.07%和0。UPGMA分子系统聚类树显示,江苏养殖群体和广西选育群体的遗传关系最近,其单倍型混杂聚成一支,而缅甸原种F1群体相对独立为另外一支。COI基因可以作为区分两分支群体的遗传标记。     

基于线粒体COI基因序列的大豆食心虫中国东北地理种群遗传多样性分析

【目的】大豆食心虫Leguminivora glycinivorella (Matsumura)是一种危害大豆的主要害虫,在中国北方地区危害较重。本研究旨在探讨大豆食心虫在中国东北不同地理种群间的遗传变异。【方法】测定了10个不同地理种群153个个体的线粒体细胞色素氧化酶亚基Ⅰ (mtCOI)基因的657 bp序列,利用DnaSP 5. 0和Arlequin 3. 5. 1. 2等软件对大豆食心虫种群间的遗传多样性、基因流水平和分子变异进行分析。【结果】结果表明：10个地理种群间的COI基因共有36个变异位点和17个单倍型,其中1个单倍型为10个种群所共享。总种群的单倍型多样性指数Hd为0.456,各地理种群单倍型多样度范围在0~0.634之间。总群体的固定系数Fst为0.12545,遗传分化系数Gst为0.06326,总基因流Nm为3.49,且各种群间的基因流均大于1,种群间基因交流的水平较高。【结论】大豆食心虫种群内遗传多样性水平处于中低等水平。总群体和各种群的Tajima’s D检验结果皆不显著,说明中国东北地区大豆食心虫在较近的历史时期内没有出现种群扩张现象。AMOVA分子变异分析结果表明,大豆食心虫的遗传分化主要来自种群内部,而种群间未发生明显的遗传分化。各地理种群的单倍型在系统发育树上和中介网络图上散布在不同的分布群中,缺乏明显的地理分布格局。各种群的遗传距离与地理距离之间没有显著线性相关性,种群间的基因交流并未受到地理距离的影响。     

基于线粒体COI基因的桔小实蝇种群遗传分化研究

【目的】推测桔小实蝇Bactrocera dorsalis在中国的扩散路径和新发生地区的入侵来源。【方法】本研究测序获得来自中国、泰国、日本、老挝、孟加拉国和美国等地31个种群的192头桔小实蝇个体的COI序列（1 496 bp,占COI基因全长97.3%）,并以软件DnaSP 5.0, MEGA 6.0和Arlequin 3.5等完成各种群的遗传多样性、种群间的遗传分化以及单倍型分析。【结果】所测31个桔小实蝇种群总体表现出较高水平的核苷酸多样性（0.00663）和高水平的单倍型多样性（0.98069）。以F-统计法度量种群间遗传分化程度, 结果显示中国桔小实蝇地理种群间遗传分化较弱, 中国种群与泰国、日本、老挝、孟加拉国、美国种群间的遗传分化程度不同, 中国种群与美国种群及日本种群的遗传分化最大。而Mantel检验发现,中国、泰国、日本、老挝、孟加拉国和美国种群间的遗传分化与空间距离有关（R=0.670, P<0.0001）, 中国种群间的遗传分化不是地理隔离所造成的（R=0.038, P=0.534）。中国种群与泰国、日本、老挝、孟加拉国和美国种群间不存在共享单倍型。根据种群系统发育树,可将中国原发生地区种群划分为西南、东南两大分支。中性检验和错配分析结果均表明桔小实蝇曾存在大规模的扩张。【结论】桔小实蝇以东南地区和西南地区为源头向中国内陆扩散,其中广东、福建、广西和贵州种群为中国内陆种群较为有影响力的源头。根据遗传多样性、遗传分化、单倍型分析,推测新发生地区桔小实蝇的来源, 例如安徽合肥桔小实蝇种群主要来源于福建长乐、广东珠海和上海。     

叶螨线粒体COI基因中央区段的PCR扩增

根据二点叶螨线粒体ＣＯＩ基因序列设计１对ＰＣＲ引物,对叶螨科不同种属的线粒体ＣＯＩ基因中央区段进行了ＰＣＲ扩增,结果表明该对引物能成功扩增叶螨科７属９种叶螨的约３４０ｂｐ的同源片段,由于叶螨ＤＮＡ序列资料非常有限,扩大引物的使用范围成为快速获得物特定基因序列的有效途径,研究结果使根据叶螨线粒体ＣＯＩ基因序列信息探索其系统演化成为可能,另外,还对模板ＤＮＡ分离方法进行了优化。     

利用COI基因序列分析长江与澜沧江水系日本沼虾群体的遗传结构

测定了我国长江水系和澜沧江水系的日本沼虾9个群体,共79个个体的线粒体COI基因序列片段（约450 bp）,结果发现有89个变异位点,共计有46个单倍型。其中云南昆明（KM）群体具有较丰富的遗传多样性（h=1.000,π=0.028）,而重庆（CQ）群体的遗传多样性最小（h=0.700,π=0.008）。AMOVA分析表明,群体间的遗传变异占总遗传变异的9.66%,而90.34%的遗传变异源于群体内。采用邻接法（NJ）构建的分子系统树显示,46个单倍型明显地聚为长江中下游和长江上游与澜沧江两个族群。其结果可以为合理开发和利用日本沼虾自然野生资源,以及建立和保护日本沼虾种质资源库及基因库提供必要的参考。     

Phylogeny of the green lacewing Chrysoperla nipponensis species‐complex (Neuroptera: Chrysopidae) in China,based on mitochondrial sequences and AFLP data

Abstract Several studies have indicated that the green lacewing, Chrysoperla nipponensis (Neuroptera: Chrysopidae) may include more than one valid species. We investigated the phylogenetic status of Chrysoperla nipponensis s.l. in China and Japan using mitochondrial sequences and AFLP data. The molecular phylogenetic analyses based on mitochondrial genes showed that the C. nipponensis species‐complex comprises four clades, each having high support values. In addition, the phylogenetic tree based on AFLP data indicates that the species‐complex comprises three groups. These results confirm that C. nipponensis s.l. comprises at least three genetically distinct clades and suggests that two of these clades may be closely related to populations of C. nipponensis in Japan. However, these clades cannot be recognized as species until analysis of their courtship songs has been completed.     

COI-based DNA barcoding of Arcoida species (Bivalvia: Pteriomorphia) along the coast of China

DNA barcoding is a promising tool for the rapid and unambiguous identification of species. Some arcoid species are particularly difficult to distinguish with traditional morphological identification owing to phenotypic variation and the existence of closely related taxa. Here, we apply DNA barcoding based on mitochondrial cytochrome c oxidase I gene (COI) to arcoid species collected from the coast along China. Combining morphology with molecular data indicates the 133 specimens of Arcoida could be assigned to 24 species. Because of the deep genetic divergence within Tegillarca granosa, there was an overlap between genetic variation within species and variation between species. Nevertheless, NJ and Bayesian trees showed that all species fell into reciprocally monophyletic clades with high bootstrap values. Our results evidence that the COI marker can efficiently identify species, correct mistakes caused by morphological identification and reveal genetic differentiation among populations within species. This study provides a clear example of the usefulness of barcoding for arcoid identification. Furthermore, it also lays a foundation for other biological and ecological studies of Arcoida.     

Genetic population structure of the net-winged midge, Elporia barnardi (Diptera: Blephariceridae) in streams of the south-western Cape, South Africa: implications for dispersal

SUMMARY 1. The net‐winged midges (Diptera: Blephariceridae), with highly specific habitat requirements and specialised morphological adaptations, exhibit high habitat fidelity and a limited potential for dispersal. Given the longitudinal and hierarchical nature of lotic systems, along with the geological structure of catchment units, we hypothesise that populations of net‐winged midge should exhibit a high degree of population sub‐structuring. 2. Sequence variation in the cytochrome c oxidase subunit I (COI) region of the mitochondrial DNA (mtDNA) was examined to determine patterns of genetic variation and infer historical and contemporary processes important in the genetic structuring of populations of Elporia barnardi. The DNA variation was examined at sites within streams, between streams in the same range, and between mountain ranges in the south‐western Cape of South Africa. 3. Twenty‐five haplotypes, 641 bp in length, were identified from the 93 individuals sampled. A neighbour‐joining tree revealed two highly divergent clades (～5%) corresponding to populations from the two mountain ranges. A number of monophyletic groups were identified within each clade, associated with individual catchment units. 4. The distribution of genetic variation was examined using analysis of molecular variance (amova ). This showed most of the variation to be distributed among the two ranges (～80%), with a small percentage (～15%) distributed among streams within each range. Similarly, variation among streams on Table Mountain was primarily distributed among catchment units (86%). A Mantel's test revealed a significant relationship between genetic differentiation and geographical distance, suggesting isolation by distance (P < 0.001). 5. Levels of sequence divergence between the two major clades, representing the two mountain ranges, are comparable with those of some intra‐generic species comparisons. Vicariant events, such as the isolation of the Peninsula mountain chain and Table Mountain, may have been important in the evolution of what is now a highly endemic fauna. 6. The monophyletic nature of the catchment units suggests that dispersal is confined to the stream environment and that mountain ridges provide effective physical barriers to dispersal of E. barnardi.     

Use of a mitochondrial COI sequence to identify species of the subtribe Aphidina (Hemiptera, Aphididae)

Aphids of the subtribe Aphidina are found mainly in the North Temperate Zone. The relative lack of diagnostic morphological characteristics has hindered the identification of species in this group. However, DNA-based taxonomic methods can clarify species relationships within this group. Sequence variation in a partial segment of the mitochondrial COI gene was highly effective for identifying species within Aphidina. Thirty-six species of Aphidina were identified in a neighbor-joining tree. Mean intraspecific sequence divergence in Aphidina was 0.52%, with a range of 0.00% to 2.95%, and the divergences of most species were less than 1%. Mean interspecific divergence within previously recognized genera or morphologically similar species groups was 6.80%, with a range of 0.68% to 11.40%, with variation mainly in the range of 3.50% to 8.00%. Possible reasons for anomalous levels of mean nucleotide divergence within or between some taxa are discussed.     

单核苷酸多态性技术在鸡遗传变异中的研究及应用

单核苷酸多态性(SNP)是继限制性片段长度多态性、微卫星标记之后的第三代分子标记,通常呈双等位基因多态。本文从SNP的特点、SNP的发现与检测、SNP数据库、SNP的频率及其与表型的关系等方面简述了SNP在鸡遗传变异中的研究及应用进展。     

Mitochondrial DNA variation in River Usk brown trout, Salmo trutta

Mitochondrial DNA (mtDNA) polymorphism in the essentially non-anadromous River Usk brown trout Salmo trutta population was investigated by restriction analysis. Following mtDNA extraction and purification on caesium chloride density gradients, monomorphic restriction profiles were obtained with Hae III , Hind III , Sau 3AI and Xbal . However, the restriction endonucleases Ava II and HinfIl proved informative. The distribution of four composite genotypes found within the Usk system was heterogeneous, and a fifth genotype appeared exclusively in an outgroup sample from the adjacent River Wye drainage. The source of the observed genetic variation is discussed in relation to estimated divergence times for Usk mtDNA genotypes and the stocking history of the catchment.     

GENETIC AND MORPHOLOGICAL DIVERGENCE AMONG MORPHOTYPES OF THE ISOPOD EXCIROLANA ON THE TWO SIDES OF THE ISTHMUS OF PANAMA

Excirolana braziliensis is a dioecious marine isopod that lives in the high intertidal zone of sandy beaches on both sides of Central and South America. It possesses no larval stage and has only limited means of adult dispersal. Indirect estimates of gene flow have indicated that populations from each beach exchange less than one propagule per generation. Multivariate morphometrics have discovered three morphs of this species in Panama, two of them closely related and found on opposite sides of Central America (“C morph” in the Caribbean and “C′ morph” in the eastern Pacific), the third found predominantly in the eastern Pacific (“P morph”). Though the P and C′ morphs are seldom found on the same beach, they have overlapping latitudinal ranges in the eastern Pacific. A related species, Excirolana chamensis, has been described from the Pacific coast of Panama. Each beach contains populations that remain morphologically and genetically stable, but a single drastic change in both isozymes and morphology has been documented. We studied isozymes and multivariate morphology of 10 populations of E. braziliensis and of one population of E. chamensis. Our objective was to assess the degree of genetic and morphological variation, the correlation of divergence on these two levels of integration, the phylogenetic relationships between morphs, and the possible contributions of low vagility, low gene flow, and occasional extinction and recolonization to the genetic structuring of populations. Genetic distance between the P morph, on one hand, and the other two morphotypes of E. braziliensis, on the other, was as high as the distance between E. braziliensis and E. chamensis. Several lines of evidence agree that E. chamensis and the P morph had diverged from other morphs of E. braziliensis before the rise of the Panama Isthmus separated the C and C′ forms, and that the P morph constitutes a different species. A high degree of genetic differentiation also exists between populations of the same morph. On the isozyme level, every population can be differentiated from every other on the basis of at least one diagnostically different locus, regardless of geographical distance or morphological affiliation. Morphological and genetic distances between populations are highly correlated. However, despite the high degree of local variation, evolution of E. braziliensis as a whole has not been particularly rapid; divergence between the C and C′ morphs isolated for 3 million yr by the Isthmus of Panama is not high by the standard of within-morph differentiation or by comparison with other organisms similarly separated. Alleles that are common in one population may be absent from another of the same morph, yet they appear in a different morph in a separate ocean. The high degree of local differentiation, the exclusive occupation of a beach by one genotype with rare arrival of foreign individuals that cannot interbreed freely with the residents, the genetic stability of populations with infrequent complete replacement by another genetic population, and the sharing by morphs of polymorphisms that are not shared by local populations, all suggest a mode of evolution concentrated in rare episodes of extinction and recolonization, possibly coupled with exceptional events of gene flow that help preserve ancestral variability in both oceans.