长江中上游银[鱼句]线粒体DNA遗传多样性分析

银[鱼句]（Squalidus argentatus）是长江常见小型鱼类,分布广泛于干支流,资源量较大。本研究采用线粒体DNA（mtDNA）细胞色素b基因序列对长江中上游干流江津、荆州、监利、洪湖、黄石江段及支流赤水河、湘江等7个江段共217尾银[鱼句]样品的遗传结构和遗传多样性进行了分析。结果显示,银[鱼句]群体Cyt b基因序列分别检出了81个变异位点和97个单倍型,平均单倍型多样性（Hd）和核苷酸多样性（Pi）分别为0.966和0.008 6。分子方差分析（AMOVA）显示,长江中上游银[鱼句]群体存在显著遗传分化。群体间两两比较分析发现,赤水河群体与其他群体基因交流程度低,遗传分化显著,其他群体间没有显著遗传分化。中性检验结果不支持银 历史上发生过群体扩张。     

基于线粒体COI序列变异的高原鼢鼠种群遗传分化研究

基于线粒体COI基因序列对高原鼢鼠7个地理种群的遗传多样性、遗传分化和基因流进行分析,158条COI基因序列中发现了570个变异位点,界定了54个COI单倍型。总体单倍型多样性指数Hd为0.911,种群单倍型多样性在0.278—0.964之间,高原鼢鼠的种群遗传多样性较高。群体总的遗传分化系数Fst为0.611,群体间的基因流Nm在-0.020—3.700之间,部分地理种群之间的遗传分化程度高,基因流弱。AMOVA分子变异分析显示,高原鼢鼠的遗传变异主要来自种群之间(77.56%),种群内部的遗传变异较低(22.44%)。中性检验(P0.01)与错配分析显示高原鼢鼠种群经历了群体扩张事件。IBD未检测到地理距离与种群间遗传距离的显著性相关关系(R2=0.124,P=0.118)。综合分析认为,高原鼢鼠不同地理种群间遗传分化的原因除地理隔离外,还与迁移扩散方式、进化过程和其他环境因素有关。     

中国近海细鳞鯻线粒体控制区的遗传多样性

通过线粒体控制区序列的分析,研究采自中国南海及东海5个群体102尾细鳞鯻的遗传多样性。发现在962 bp序列中有205个变异位点,其中135个为简约信息位点,共定义102个单倍型。中国近海细鳞鯻总体呈现出较高的遗传多样性特征(Hd=1.000,Pi=0.022),其中博鳌最高(Hd=1.000,Pi=0.028),平潭最低(Hd=1.000,Pi=0.014)。不同地理群体间无明显分化,基因交流频繁(Fst=-0.014—0.041,P0.05);中性检验均为显著负值,推测在16.9万年—5.06万年前,即中-晚更新世出现种群扩张。系统邻接树和单倍型网络图均出现3个显著分化的谱系(谱系间Fst=0.508—0.698,P0.001;净遗传距离Da=0.024—0.031),且各谱系中均有不同地理来源的群体。3个谱系间分歧时间大约在1.07百万年—0.24百万年前,推测可能是更新世冰期边缘海的出现导致群体隔离而产生分化。谱系A(Lineage A)包含85.3%的个体,其总体遗传多样性较高(Hd=1.000,Pi=0.012),其中平潭最高(Hd=1.000,Pi=0.014),合浦最低(Hd=1.000,Pi=0.010);群体间Fst在-0.021—0.068之间,P0.005;AMOVA分析显示只有1.97%的变异来自于种群间,表明群体间也无明显分化;中性检验均为显著负值,推测在25.4万年—7.6万年前出现种群扩张。中国近海细鳞鯻主要受到中-晚更新世海侵和海退的影响而出现种群扩张使得谱系间发生二次接触,最终形成具有显著谱系结构但无地理分化的情况。     

东海海域口虾蛄种群遗传多样性

为准确掌握中国沿海口虾蛄(Oratosquilla oratoria)种群遗传结构、合理开发利用其资源,采用线粒体DNA(mt DNA)细胞色素氧化酶Ⅰ(COⅠ)序列分析方法检测东海海域(庙子湖岛、南韭山、大陈岛、南麂岛)口虾蛄种群遗传多样性,并与黄渤海群体和南海群体进行比较分析(基因序列来源于Gen Bank)。经PCR扩增与测序获得100条658 bp的东海海域口虾蛄COⅠ基因序列,基于这些序列分析得到的变异位点数、单倍型数、单倍型多样性指数与核苷酸多样性指数分别为60、60、0.963±0.011和0.005 94±0.000 44,分析认为东海海域口虾蛄具有较高的单倍型多样性和较高的核苷酸多样性。单倍型分子系统树、分子方差分析及两两群体间的遗传分化系数(Fst)分析结果表明,东海海域口虾蛄遗传变异主要来自于群体内(Fst=﹣0.007 78,P0.05),各地理群体间遗传分化不显著,Fst值范围为﹣0.016 53~﹣0.009 08(P0.05),它们可能进行了一定程度的基因交流;通过与黄渤海群体及南海群体基因序列比较分析,口虾蛄东海群体、黄渤海群体与南海群体遗传变异主要来自于群体间(Fst=0.849 71,P0.01),且单倍型分子系统树存在2个显著分化的单倍型类群。东海群体与黄渤海群体间存在显著的遗传分化(Fst=0.884 58,P0.01),而与南海群体间不存在显著的遗传分化(Fst=0.020 44,P0.05),这种遗传结构模式可能与历史上的气候变化及所处海域海洋环境条件相关。建议今后对中国沿海口虾蛄资源进行开发利用时,将黄渤海群体看作一个管理单元,东海群体与南海群体看作一个管理单元。     

三个地理种群的董氏须鳅遗传多样性及种群历史动态

研究采用线粒体DNA Cyt b和D-loop基因分析西辽河、松花江和穆棱河3条水系董氏须鳅(Barbatula toni)的遗传多样性和种群结构, 并探讨其种群演变历史。结果表明: 3条水系119个董氏须鳅样本共检测出57个单倍型, 各群体间不存在共享单倍型; 3个董氏须鳅地理群体均呈现出较高的单倍型多样性(0.805—0.926)和较低的核苷酸多样性(0.00095—0.00458); AMOVA分子方差分析、群体间分化指数(F_ST)、系统发育树及单倍型网络图均表明3个地理种群已经出现高度分化, 群体间遗传变异占总变异的79.45%, 遗传分化显著(P<0.01)。中性检验和错配分析表明, 松花江和穆棱河群体历史上发生了群体快速扩张。参考鳅科鱼类Cyt b基因0.68—0.84%/Ma的进化速率, 估算3个地理群体的分歧时间为1.082—0.669 Ma前, 松花江和穆棱河群体扩张时间为0.071—0.047 Ma前, 推测我国董氏须鳅在中更新世期随冰期迁移至不同避难所, 形成各地理群体, 并于晚更新世早期经历了群体扩张事件。     

基于线粒体DNA细胞色素b基因和控制区序列分析西藏雅鲁藏布江黄斑褶鮡种群遗传多样性

采用线粒体DNA（mtDNA）Cyt b基因和D-loop控制区为分子标记,对分布于西藏雅鲁藏布江大峡谷以上里龙段和以下墨脱段2个群体的黄斑褶 （Pseudecheneis sulcata）共60个样本进行遗传多样性研究。获得联合基因有效序列长度为1 893 bp,包括Cyt b基因1 060 bp和D-loop控制区833 bp。结果显示,里龙和墨脱2个群体的单倍型多样性值（Hd）均较高（0.701和0.761）,核苷酸多样性值（π）均较低（0.001 00和0.001 09）;高频率的单倍型Hap1和Hap2为2个群体所共享,推测为祖先单倍型;同时,里龙和墨脱群体分别存在5个和6个特有单倍型,且在2个群体中不共享;分子方差分析（AMOVA）显示遗传变异主要来源于种群内部,群体间呈中度遗传分化水平（Fst = 0.090 44,P < 0.05）;中性检验（Tajima''s D、Fu''s Fs）和核苷酸不配对（SSD、Hir）分析结果揭示,黄斑褶 种群曾经历过种群扩张现象。本研究推测,黄斑褶 2个群体间的基因流动存在障碍,雅鲁藏布大峡谷的海拔落差及水文情势等生态屏障可能是阻碍黄斑褶 迁徙和交流的主要原因。     

长江中上游银鮈线粒体DNA遗传多样性分析

银鮈(Squalidus argentatus)是长江常见小型鱼类,分布广泛于干支流,资源量较大。本研究采用线粒体DNA(mt DNA)细胞色素b基因序列对长江中上游干流江津、荆州、监利、洪湖、黄石江段及支流赤水河、湘江等7个江段共217尾银鮈样品的遗传结构和遗传多样性进行了分析。结果显示,银鮈群体Cyt b基因序列分别检出了81个变异位点和97个单倍型,平均单倍型多样性(Hd)和核苷酸多样性(Pi)分别为0.966和0.008 6。分子方差分析(AMOVA)显示,长江中上游银鮈群体存在显著遗传分化。群体间两两比较分析发现,赤水河群体与其他群体基因交流程度低,遗传分化显著,其他群体间没有显著遗传分化。中性检验结果不支持银鮈历史上发生过群体扩张。     

不同生境夏蜡梅群体遗传多样性的RAPD分析

利用RAPD技术对天台大雷山4个不同生境：灌丛、常绿阔叶林、杉木林和竹林中的夏蜡梅群体进行遗传多样性研究。12个随机引物在80个个体中共检测到182个可重复的位点,其中多态位点为49个,总的多态位点百分率为26.92%。4个群体的多态位点百分率在6.04%~11.54%之间,平均为8.93%,其中竹林群体最高,常绿阔叶林群体最低,大小顺序为竹林群体＞灌丛群体＞杉木林群体＞常绿阔叶林群体,Shannon指数和Nei指数估算结果为灌丛群体最高,其次是竹林群体,第三是杉木林群体,最低的是常绿阔叶林群体。AMOVA分子差异分析表明夏蜡梅群体间遗传分化程度高,71.91%的变异存在于群体间,28.09%的变异存在于群体内,群体间的基因分化系数（G_ST）为0.627 4。夏蜡梅群体间的基因流很低,N_m=0. 297 0。聚类分析结果表明杉木林群体和灌丛群体最先聚在一起,再与常绿阔叶林群体相聚,最后与竹林群体聚在一起。可见,夏蜡梅在各生境间有着不同的遗传多样性,且在各生境间发生了明显的遗传分化。     

基于线粒体控制区的序列变异分析中国东南部沿海凤鲚种群遗传结构

为了解中国东南部沿海凤鲚(Coilia mystus)的种群遗传多样性和遗传结构, 本文分析了长江口(CJ)、钱塘江口(QT)、闽江口(MJ)和九龙江口(JL)4个凤鲚地理群体的mtDNA控制区561 bp片段的序列变异。65尾样本共检测到28个单元型。4个群体总的单元型多样性和核苷酸多样性均较高(h = 0.9433 ± 0.0168, π = 0.0317 ± 0.0158), 但单个群体的核苷酸多样性水平却很低, 其中以CJ最高(π = 0.0080 ± 0.0046), MJ最低(π = 0.0015 ± 0.0013)。MJ与JL群体之间以及CJ与QT群体之间的平均K2P遗传距离很小, 分别为0.3%和0.8%; 而CJ、QT分别与MJ、JL群体之间的遗传距离均较大, 达到了6%。采用最大似然法(ML)、最大简约法(MP)和邻接法(NJ)分别构建的单元型间的系统发育树揭示, 4个凤鲚群体构成CJ-QT 和MJ-JL 2个支系, 且具有极高的支持率。单元型的网络分析也显示这两个支系间有高达28步的突变次数。AMOVA分析显示大部分的遗传变异来自这两支系群体间(90.77%), 表明凤鲚群体间存在着显著的地理分化。种群分化指数和基因流分析也表明, 支系间群体有着明显的遗传分化(F_ST > 0.9, N_m < 0.03)。所有分析结果支持所研究的凤鲚标本属于两个不同的地理种群, 且种群的分化至少已达到亚种水平。采用BEAST和TRACER软件得到凤鲚两个亚种的最近共同祖先约在0.34–0.46百万年前, 处于更新世晚期, 推测可能是第四纪晚期的气候旋回和海平面的升降导致了凤鲚的种群分化。     

从江及周边地区稻田鲤的遗传结构及系统发育关系

为探究贵州从江及邻近的榕江、黎平和锦屏以及广西三江、湖南的通道和靖州等地稻田鲤Cyprinus carpio Linnaeus的遗传结构及系统关系, 研究基于mtDNA Cyt b基因测序技术对6个地理群体进行了分析。447尾稻田鲤中共界定出29种Cyt b基因序列单倍型, 结合NCBI中鲤同源序列的系统发育和序列比对分析表明, 从江及邻近苗侗族地区稻田鲤是一个含欧亚2大谱系、3个鲤亚种和多个母系血统成分的混合群体, 主体类群是华南鲤C. carpio rubrofuscus, 同时混有欧洲鲤C. carpio carpio和远东鲤C. carpio haematopterus, 遭受国内外鲤养殖品种的遗传渗析。遗传多样性分析显示, 欧洲鲤亚种群体为低H_d低π, 遗传多样性贫乏, 远东鲤和华南鲤2个亚种群体呈高H_d低π特点。华南鲤6个稻田群体除锦屏为低H_d低π外, 其余都为高H_d低π, 从江的H_d最高, 黎平的π最高。遗传分化和分子方差(AMOVA)分析显示, 谱系间和亚种间存在显著的遗传分化(P<0.001), 锦屏和三江与其他群体存在中等-高度的分化等级, 其余群体间分化较弱, 群体间变异贡献率为16.69%, 群体内为81.14%。综合分析表明, 从江及邻近地区稻田鲤群体间存在有限的遗传交流, 群体内和群体间有不同的遗传结构。研究丰富了该地区稻田鲤遗传背景资料, 可为湘黔桂交界苗侗族地区稻田鲤的种质资源鉴定与保护提供理论依据。     

Analysis of genetic diversity in common loon Gavia immer using RAPD and mitochondrial RFLP techniques

We used random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLP) of mitochondrial cytochrome b (cyt b ) gene to evaluate the genetic diversity in common loon Gavia immer populations from two regions in the United States: New England (NE) and Michigan (MI). RAPD analysis with 18 primers showed 74% polymorphism in NE and 50% in MI loons (similarity coefficient F = 0.92). Although no population-specific markers were found, the frequencies of some RAPD bands varied between the two populations suggesting geographical differences. RFLP analyses with Bam HI enzyme and a 307-bp mitochondrial cyt b gene showed four haplotypes in the NE loon samples and two in the MI samples. The mtDNA haplotype diversity was 0.74 for NE and 0.51 for MI loons, supporting the RAPD data that NE loons have greater genetic diversity than MI loons.     

Phylogenetic analysis of different breeds of domestic chickens in selected area of Peninsular Malaysia inferred from partial cytochrome b gene information and RAPD markers

The present investigation was carried out in an attempt to study the phylogenetic analysis of different breeds of domestic chickens in Peninsular Malaysia inferred from partial cytochrome b gene information and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis using both neighbor-joining (NJ) and maximum parsimony (MP) methods produced three clusters that encompassed Type-I village chickens, the red jungle fowl subspecies and the Japanese Chunky broilers. The phylogenetic analysis also revealed that majority of the Malaysian commercial chickens were randomly assembled with the Type-II village chickens. In RAPD assay, phylogenetic analysis using neighbor-joining produced six clusters that were completely distinguished based on the locality of chickens. High levels of genetic variations were observed among the village chickens, the commercial broilers, and between the commercial broilers and layer chickens. In this study, it was found that Type-I village chickens could be distinguished from the commercial chickens and Type-II village chickens at the position of the 27th nucleotide of the 351?bp cytochrome b gene. This study also revealed that RAPD markers were unable to differentiate the type of chickens, but it showed the effectiveness of RAPD in evaluating the genetic variation and the genetic relationships between chicken lines and populations.     

Use of random amplified polymorphic DNA (RAPD) analysis for the identification of Giardia intestinalis subtypes and phylogenetic tree construction

A comparison of random amplified polymorphic DNA (RAPD) was used to investigate genetic polymorphisms among 25 isolates of Giardia intestinalis and to assess the utility of RAPD for subtype detection and genealogical analysis. Using data obtained for six human and 19 animal-derived isolates in polymerase chain reactions using 13 different primers, phylogenetic trees were constructed and bootstrap values computed by the program FreeTree. Three major clades were distinguished, corresponding to previously defined genetic assemblages A, B, and E. The purported specificity of assemblage E genotypes for artiodactyl hosts was supported. Assemblages A and B showed wide host spectra, including human and animal hosts. No correlation was found between the genotype of analyzed isolates and the presence or absence of the double-stranded RNA Giardiavirus. The results indicate that RAPD data provide reliable genetic information that can be used for both "fingerprinting" and genealogical purposes.     

Phylogenetic Analysis of Different Breeds of Domestic Chickens in Selected Area of Peninsular Malaysia Inferred from Partial Cytochrome b Gene Information and RAPD Markers

The present investigation was carried out in an attempt to study the phylogenetic analysis of different breeds of domestic chickens in Peninsular Malaysia inferred from partial cytochrome b gene information and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis using both neighbor-joining (NJ) and maximum parsimony (MP) methods produced three clusters that encompassed Type-I village chickens, the red jungle fowl subspecies and the Japanese Chunky broilers. The phylogenetic analysis also revealed that majority of the Malaysian commercial chickens were randomly assembled with the Type-II village chickens. In RAPD assay, phylogenetic analysis using neighbor-joining produced six clusters that were completely distinguished based on the locality of chickens. High levels of genetic variations were observed among the village chickens, the commercial broilers, and between the commercial broilers and layer chickens. In this study, it was found that Type-I village chickens could be distinguished from the commercial chickens and Type-II village chickens at the position of the 27th nucleotide of the 351 bp cytochrome b gene. This study also revealed that RAPD markers were unable to differentiate the type of chickens, but it showed the effectiveness of RAPD in evaluating the genetic variation and the genetic relationships between chicken lines and populations.     

Life history variation between species of the relictual genus Borderea (Dioscoreaceae): phylogeography, genetic diversity, and population genetic structure assessed by RAPD markers

The genus Borderea consists of two species, B. pyrenaica and B. chouardii, taxa which have been previously considered as conspecific due to their overall close morphology. These two sole species of the rare genus of Dioscoreaceae are endemic to the Pyrenees (Spain, France). This mountain range likely operated as a refugium for these plants during the last glaciations. B. chouardii is only known from a single population in the Spanish Prepyrenees and has been classified as at risk of extinction in the Red List of Endangered Species (IUCN); B. pyrenaica shows a narrow distribution range in the central Pyrenees and Prepyrenees. We analysed genetic variation, population structure and differentiation in these two taxa using RAPD markers. Our study was conducted on the same seven populations for which very low levels of genetic differentiation were detected previously through allozyme analysis. By contrast, high levels of genetic variability were detected through the RAPD hypervariable markers. Twelve RAPD primers produced 112 distinct bands in the 397 surveyed individuals, totalling 395 different RAPD phenotypes. Only four bands were monomorphic across all samples of Borderea, whereas 21 of the polymorphic bands were species‐specific (20 for B. chouardii, and one for B. pyrenaica). The largest genetic distances were those between the B. chouardii and the B. pyrenaica phenotypes. An analysis of molecular variance showed greater variance between groups (B. chouardii vs. B. pyrenaica, 76.08%) than within groups (3.60%). RAPD band specificity, phenotypic distances, and the partitioning of variance all support the taxonomic separation of the two species. Statistical evaluation of within‐ and among‐population RAPD genetic variability in B. pyrenaica showed that genetic variability was higher within populations (>80%) than among them. No clear pattern of RAPD differentiation could be observed among the six studied populations of this taxon though slight differences in genetic diversity could be observed in the more isolated Prepyrenean populations compared with the more widespread Pyrenean ones. These results suggest a recent postglacial origin of the present B. pyrenaica populations. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80 , 483–498.     

Serologic and genetic analysis of group B streptococci isolated from adult patients

Serologic and genetic typing with RAPD (Random Amplified Polymorphic DNA) method was used for epidemiologic analysis of GBS. 125 strains isolated from various clinical samples from adult patients were tested. In serologic typing seven serotypes have been found. Serotypes III and R were the most often encountered, containing 37,6% and 20,8% of samples. There was no dependence between serologic type and disease process. Optimalisation of RAPD reaction parameters was based on the standard strains of GBS. In the group of strains tested with the use of RAPD method, eleven genetic profiles were found, with prevalence of profile B (25,8%). Five other profiles occured with similar frequency (8,8% - 12,8%). Among streptococci isolated from patients with the infection of genitourinary tract, great differentiation in the genetic profiles of the strains has been found. Each serologic type contained various genetic profiles. Genetic variety showed by RAPD method indicates the raised ability of this technique to find differences among isolates of GBS.     

烟粉虱B型和Q型群体遗传结构的RAPD分析

近20年来,烟粉虱B型传入世界各地并暴发成灾,成为一种重要的农业入侵害虫; 烟粉虱Q型则是近几年引起人们高度重视的一种新的入侵生物型,目前已传入许多国家并造成一定危害。本文利用RAPD分子标记对烟粉虱B型和Q型不同地理种群的遗传结构进行了分析。结果表明：（1）引物H16对烟粉虱B型不同种群扩增的特异带,能有效区分烟粉虱B型和Q型、浙江非B/Q型种群;（2）烟粉虱Q型种群各项遗传多样性指数均比烟粉虱B型的要高;（3）我国烟粉虱Q型来自伊比利亚半岛的可能性比来自中东地区的可能性要大。另外,聚类分析结果提示,RAPD分子标记能有效地区分烟粉虱不同生物型,但可能不适用于生物型之间亲缘关系分析。     

RAPD analysis of genetic diversity and population structure of Elymus sibiricus (Poaceae) native to the southeastern Qinghai-Tibet Plateau, China

Genetic diversity of Elymus sibiricus (Poaceae) was examined in eight populations from the southeast Qinghai-Tibet Plateau. We detected 291 RAPD polymorphic loci in 93 samples. The percentage of polymorphic bands (PPB) was 79%. Genetic diversity (H(E)) was 0.264, effective number of alleles (N(E)) was 1.444, Shannon's information index (H(O)) was 0.398, and expected Bayesian heterozygosity (H(B)) was 0.371. At the population level, PPB = 51%, N(E) = 1.306, H(E) = 0.176, I = 0.263, and H(B) = 0.247. A high level of genetic differentiation was detected based on Nei's genetic diversity analysis (G(ST) = 32.0%), Shannon's index analysis (33.7%), and the Bayesian method (θ(B) = 33.5%). The partitioning of molecular variance by AMOVA demonstrated significant genetic differentiation within populations (60%) and among populations (40%). The average number of individuals exchanged between populations per generation (N(m)) was 1.06. The populations were found to share high levels of genetic identity. No significant correlation was found between geographic distance and pairwise genetic distance (r = 0.7539, P = 0.9996). Correlation analysis revealed a significant correlation (r = 0.762) between RAPD H(E) found in this study and ISSR H(E) values from a previous study.     

Assessment of genetic diversity among 16 promising cultivars of ginger using cytological and molecular markers

Ginger (Zingiber officinale Roscoe) is an economically important plant, valued all over the world. The existing variation among 16 promising cultivars as observed through differential rhizome yield (181.9 to 477.3 g) was proved to have a genetic basis using different genetic markers such as karyotype, 4C nuclear DNA content and random amplified polymorphic DNA (RAPD). The karyotypic analysis revealed a differential distribution of A, B, C, D and E type of chromosomes among different cultivars as represented by different karyotype formulas. A significant variation of 4C DNA content was recorded in ginger at an intraspecific level with values ranging from 17.1 to 24.3 pg. RAPD analysis revealed a differential polymorphism of DNA showing a number of polymorphic bands ranging from 26 to 70 among 16 cultivars. The RAPD primers OPC02, OPA02, OPD20 and OPN06 showing strong resolving power were able to distinguish all 16 cultivars. The extent of genetic diversity among these cultivars was computed through parameters of gene diversity, sum of allele numbers per locus and Shannon's information indices. Cluster analysis, Nei's genetic similarity and genetic distances, distribution of cultivars into special distance classes and principal coordinate analysis and the analysis of molecular variance suggested a conspicuous genetic diversity among different cultivars studied. The genetic variation thus detected among promising cultivars of ginger has significance for ginger improvement programs.