Evaluation of Genetic Variation in the Clown Knifefish, Chitala chitala, Using Allozymes, RAPD, and Microsatellites

Twenty-seven enzyme systems, six random amplified polymorphic DNA (RAPD) primers, and two microsatellite loci were tested to determine intraspecific divergence in the natural population of the endangered Indian featherback fish, Chitala chitala, for the first time. The 262 samples of C. chitala were collected from six riverine locations in India: the Satluj, Ganga (Ghagra, Bhagirathi, and Brahmaputra), Mahanadi, and Narmada river systems. The analysis revealed population subdivisions, with an F_ST value from 0.1235 (95% confidence 0.0868–0.1621) for RAPD and a combined F_ST of 0.0344 (95% confidence 0.0340–0.0350) for microsatellite loci. An analysis of 38 allozyme loci did not reveal any polymorphism in the samples from any of the riverine localities; a possible explanation for this could be that the ancestors of Chitala could have faced a population reduction in prehistoric periods, as low allozyme variation is also reported for other species of Chitala from south Asia.     

Microsatellite Variation in Red-Winged Blackbirds (Agelaius phoeniceus)

Territorial male red-winged blackbirds from five locations in the United States and Canada were genotyped using a suite of six microsatellite loci. Each population possessed unique alleles, but numbers of alleles per locus (range = 7.3-8.8) and expected multilocus heterozygosities (range = 0.76-0.80) were similar in all populations. Significant overall allele frequency differences were detected between some population pairs, and some pairwise Fst values were significant (but small). However, Fst among populations, although significant, was also small (0.009). Despite revealing low levels of population structure, the high multilocus polymorphism indicates these loci will be valuable in the genetic analysis of behavior and reproductive strategies in this species.     

Genetic structure of people from the Volga-Ural region and Central Asia from data of Alu-polymorphism

Nine Alu loci (Ya5NBC5, Ya5NBC27, Ya5NBC148, Ya5NBC182, YA5NBC361, ACE, ApoA1, PV92, TPA25) were analyzed in six ethnic populations (Trans-Ural Bashkirs, Tatars-Mishars, Mordovians-Moksha, Mountain Maris, Udmurts, and Komi-Permyaks) of the Volga-Ural region and in three Central Asian populations (Uzbeks, Kazakhs, and Uigurs). All Alu insertions analyzed appeared to be polymorphic in all populations examined. The frequency of insertion varied from 0.110 in Mountain Maris at the Ya5NBC5 locus to 0.914 in Tatars at the ApoA1 locus. The data on the allele frequency distribution at nine loci point to the existence of substantial genetic diversity in the populations examined. The value of the observed heterozygosity averaged over nine Alu insertions varied from 0.326 in Mountain Maris to 0.445 in Kazakhs and Uigurs. The level of the interpopulation genetic differences for the Volga-Ural population (Fst = 0.061) was higher than for the populations of Central Asia (Fst = 0.024), Europe (Fst = 0.02), and Southeastern Asia (Fst = 0.018). The populations examined were highly differentiated both in respect of linguistic characteristics and the geographical position. The data obtained confirmed the effectiveness of the marker system used for the assessment of genetic differentiation and the relationships between the ethnic groups.     

Cryptic divergence and strong population structure in the colonial invertebrate Pycnoclavella communis (Ascidiacea) inferred from molecular data

We studied sequence variation in the mitochondrial gene cytochrome c oxidase subunit I (COI) for 135 individuals from eight Mediterranean populations of the colonial ascidian Pycnoclavella communis across most of its presently known range of distribution in the Mediterranean. Three haplotypes from Atlantic locations were also included in the study. Phylogenetic, phylogeographic and population genetic analyses were used to unravel the genetic variability within and between populations. The study revealed 32 haplotypes for COI, 29 of them grouped within two Mediterranean lineages of P. communis (mean nucleotide divergence between lineages was 8.55%). Phylogenetic and network analyses suggest the possible existence of cryptic species corresponding to these two lineages. Population genetic analyses were restricted to the five populations belonging to the main genetic lineage, and for these localities we compared the information gleaned from COI sequence data and from eight microsatellite loci. A high genetic divergence between populations was substantiated using both kinds of markers (COI, global Fst=0.343; microsatellite loci, global Fst=0.362). There were high numbers of private haplotypes (COI) and alleles (microsatellites) in the populations studied. Restricted gene flow and inbreeding occur in the present range of distribution of the species. Microsatellite loci showed a strong incidence of failed amplifications, which we attribute to the marked intraspecies variability that hampered the application of these highly specific markers. Our results show important genetic variability at all levels studied, from within populations to between basins, possibly coupled to speciation processes. This variability is attributable to restricted gene flow among populations due to short-distance dispersal of the larvae.     

色季拉山不同海拔高度的藏川杨种群遗传多样性的研究

为研究青藏高原海拔变化与藏川杨遗传多样性和群体遗传结构的关系,以青藏高原东南部色季拉山分布的藏川杨群体为材料,用24对微卫星标记对其进行遗传分析。在469个个体中共检测到126个等位基因,每个位点的平均等位基因数(Na)为5.25;多态性位点百分率(PPL)为100%,期望杂合度(He)在高、低海拔的群体中都处于较高水平,分别为0.48和0.49;分子方差分析(AMOVA)的结果表明,种群间分化占总变异的6.38%,遗传变异主要集中在群体内不同个体之间;基因分化系数(FST)为0.02,也证实群体分化处于较低水平,而检测到群体间的基因流动(Nm)处于较高水平,为9.89。上述结果表明,海拔因素未对生长在色季拉山高低海拔的藏川杨群体造成地理隔离,从而产生种群分化;在此地区藏川杨遗传背景一致,藏川杨种质资源的保存无需考虑海拔的差异。本研究结果为研究高海拔适应机制材料的选择提供了很大的便利,并为藏川杨的可持续利用与保护提供了一定的理论依据。     

云南西花蓟马rDNA-ITS2遗传多态性及其种群扩张

应用rDNA-ITS2基因序列对云南各地理种群西花蓟马Frankliniella occidentalis(Pergande)的遗传结构和遗传分化程度进行初步研究。经过比对112条序列,共发现了59个变异位点,定义了30种单倍型。云南省西花蓟马的单倍型多态性较高(Hd=0.90219),而核酸多态性较低(Pi=0.00891)。各地理种群西花蓟马的遗传分化指数Fst为0.00810,基因流Nm为30.61,表明各地理种群间遗传分化程度非常低,种群间存在充分的基因交流。对群体进行中性检验、错配分析表明西花蓟马群体曾经历过近期的种群扩张。分子方差分析(AMOVA)表明,云南西花蓟马的遗传变异主要来自于种群内部,种群间的遗传变异水平还非常低。从分子生物学的角度上也证实了西花蓟马近期入侵云南的事实。     

Morphological divergence and origin of sympatric populations of European whitefish (Coregonus lavaretus L.) in Lake Femund, Norway

Combining morphological and genetic analysis, we compared patterns of diversification within and between morphs among sympatric European whitefish (Coregonus lavaretus L.) populations in Lake Femund, Norway. Seven external populations, from potential colonization routes into Lake Femund were included. We found that deep-, shallow-, river- and bay spawning populations are distinct morphs in Lake Femund. Within morphs, populations range from being similar genetically (Fst=0-0.005) among deep-spawning populations to being highly differentiated (Fst=0.153) between bay-spawning populations. Between morphs, genetic differences ranged from a low (Fst=0.008-0.022) between deep- and shallow-spawning populations to high difference (Fst=0.125-0.143) between shallow- and bay-spawning populations. A higher proportion of molecular variance was seen among (3.9%) than within morphs (2.8%). The adaptive gene combinations behind the four morphs seem to have originated within the lake, although the lake could have been colonized from more than one source population.     

福建南北泥蚶种内分化的RAPD分析

采用随机扩增多态性DNA(RAPD)技术,对泥蚶在福建以南(广东汕头和湛江)和福建以北(浙江温岭和韩国)种群(分别合称南方类群和北方类群)做了遗传分化研究。由筛选出的20个随机引物共获得103个清晰可辨的RAPD标记,扩增片段长度在250—2500bp。汕头种群与湛江种群,韩国种群与温岭种群之间的最小遗传距离分别为0．0612和0．0692,而南、北类群间的遗传距离却在0．3261-0．4511。类群间近交系数也大于类群内。NJ和UPGMA法构建的系统树均显示汕头种群、湛江种群首先聚在一起,再与温岭种群和韩国种群聚合,说明两个类群发生了较明显的遗传分化,估计与地理隔离有关。     

Use of RAPD fingerprinting for discriminating two populations of Hilsa shad (Tenualosa ilisha Ham.) from inland rivers of Bangladesh

The Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) was applied to analyze the genetic variation of the Hilsa shad, Tenualosa ilisha Ham., from the two major inland rivers (Padma and Meghna) in Bangladesh. Twenty-eight random 10-mer primers were primarily scored in 8 individuals from each of the two locations. Fifteen primers, which gave polymorphism, were selected and used in the final analysis of 34 individuals from the two sites. Using these primers, 480 scorable DNA fragments were found, of which 98 (20.41%) were polymorphic. By comparing the RAPD banding patterns, variations were found between and within the populations. A dendrogram was constructed with the polymorphic fragments to analyze the genetic distances between the Hilsa shad populations. The results show two major clusters of Padma and Meghna, assuming different spawning populations with different stocks or races of Hilsa shad in the major Bangladesh rivers.     

Genetic variability and level of differentiation among Brazilian pantanal wood stork populations

The Wood Stork (Mycteria americana) is a colonial wading bird of the tropical and lower subtropical zones. We assessed genetic structure within and among five stork colonies from the Brazilian Pantanal and compared our data with those from North American populations. Samples of 234 individuals were studied using protein electrophoresis to evaluate genetic variability and interpopulation differentiation. Of 22 loci examined, 7 were polymorphic (mean heterozygosity = 0.068). The low Fst value (0.005) indicated little intraspecific variation among breeding colonies. Estimated number of migrants per generation based on private alleles (Nm = 11.3) and on Fst (48.8) suggests high gene flow. Nei's genetic distance values among Pantanal colonies ranged from 0.0001 to 0.0034, demonstrating low genetic divergence among populations. Our data can be explained by supposing high gene flow levels among Pantanal colonies, and between North and South American populations, intermediated by a probable interbreeding population in Central America.     

基于SSR分子标记的中国黄连木遗传多样性分析北大核心CSCD

该研究利用筛选出的7对SSR引物,对中国20个省、市、自治区的210份种质资源进行分子标记试验,分析中国黄连木种质资源遗传多样性、亲缘关系、遗传分化特点并构建DNA分子身份证,为黄连木的资源保护、种质利用提供理论依据,结果表明:(1)7对引物在210份种质中共扩增出158个等位基因位点,平均每对引物的等位基因数为22.571个。(2)基因多样性(GD)变化幅度为0.654~0.913,平均为0.804;期望杂合度(He)变化范围0.257~0.771,平均为0.532;多态信息含量(PIC)变化范围0.639~0.907,平均为0.784。(3)从不同地区黄连木群体的遗传多样性来看,观测杂合度(Ho)介于0.373~0.600之间,平均值为0.520;期望杂合度(He)介于0.632~0.811之间,平均值为0.737;从各群体间遗传分化指数(Fst)来看,黄连木各地区群体间的遗传分化值在0.015~0.099之间,各群体间的遗传分化处于中等以下水平。(4)分子方差分析(AMOVA)结果显示,黄连木的遗传分化变异以群体内为主,占总变异量的94%,群体间的变异占6%。(5)UPGMA聚类、群体遗传结构分析和PCoA分析结果相一致,全部种质被划分为两大类,西南地区群体单独为一类,其他地区单独为一类。(6)利用7对SSR引物构建了210份黄连木种质的DNA分子身份证。     

The application of RAPD markers in stock discrimination of the four-wing flyingfish, Hirundichthys affinis in the central western Atlantic

The polymerase chain reaction–random amplified polymorphic DNA (PCR–RAPD) technique was used to examine genetic variability and population structuring in the four-wing flyingfish, Hirundichthys affinis within the central western Atlantic. Three random decamer primers and pairs of these primers were used to amplify nuclear DNA from 360 fish sampled from six populations (at five locations) across the region. A total of 58 polymorphic RAPD markers were identified, 20 of which were population-specific and six of which were subregional or stock-specific markers. Cluster analysis of similarity indices indicated the presence of three genetically distinct subregional stocks located in the eastern Caribbean, southern Netherlands Antilles and Brazil, respectively. Estimates of gene diversity (φ) and gene flow ( Nm ) are consistent with this three-stock hypothesis. Furthermore, partially restricted gene flow was apparent among spatially and temporally separate sampled populations within the eastern Caribbean subregional stock, indicating the possible presence of different spawning groups. These results are entirely consistent with those obtained from PCR–RFLP analysis of the mtDNA D-loop in the same fish, indicating the presence of barriers to dispersal and interbreeding in both sexes. We conclude that the PCR–RAPD technique is suitable for determining population stock structure in this species and that a three-stock approach to managing H. affinis within the central western Atlantic would be appropriate.     

基于线粒体COⅡ基因序列的双斑长跗萤叶甲中国北方地理种群的遗传多样性研究

双斑长跗萤叶甲Monolepta hieroglyphica (Motschulsky)是自2001年以来在我国北方为害玉米呈加重趋势的一种害虫。为初步探讨中国北方不同地理种群间和种群内该害虫的遗传分化程度、 遗传多样性以及基因流水平, 对来自中国北方的26个不同地理种群的线粒体COⅡ (细胞色素C氧化酶亚基Ⅱ) 基因片段序列的核苷酸多态性进行了研究。结果表明： 在515头个体的长度为484 bp COⅡ片段中共发现了28个变异位点和15种单倍型。单倍型间的系统进化分析发现, 15种单倍型主要分为两大分支。总种群单倍型多样性指数Hd为0.257, 种群内单倍型多样度在0.100～0.515范围内。总种群的Fst为0.585, Gst为0.417, 基因流Nm为0.35。AMOVA分子变异分析结果发现, 双斑长跗萤叶甲的遗传分化主要来自种群之间, 占方差比率的58.58%。实验总种群及大部分种群的中性检验符合中性突变, 说明我国北方双斑长跗萤叶甲在近期没有出现种群扩张现象。研究结果揭示中国北方双斑长跗萤叶甲不同地理种群间基因流水平低, 种群间已发生明显的遗传分化, 分化主要来自种群之间。     

Genetic differences between Tunisian camel and sheep strains of the cestode Echinococcus granulosus revealed by SSCP

Ovine and dromedary Echinococcus granulosus isolates from Tunisia were identified as G1 and G6 strains based on polymorphism of the mitochondrial cytochrome C oxydase CO1. Single strand conformation polymorphism (SSCP) was used in order to examine the genetic variation within and between Tunisian G1 and G6 strains and to estimate the extent of selfing. The dromedary isolates are genetically distinct from sheep isolates (high value of genetic variation between populations: Fst= 0.46). No significant deficiency in heterozygotes was found in sheep isolates, whereas heterozygote deficiency (suggesting selfing) was found in a limited number of camel isolates.     

Genetic diversity and variance of Stentor coeruleus (Ciliophora: Heterotrichea) inferred from inter-simple sequence repeat (ISSR) fingerprinting

We used inter-simple sequence repeat fingerprinting to analyze the genetic structure of 16 populations of Stentor coeruleus from three lakes and three ponds in China. Using 14 polymorphic primers, a total of 99 discernible DNA fragments were detected, among which 76 (76.77%) were polymorphic, indicating median genetic diversity in these populations. Further, both Nei's gene diversity (h) and Shannon's information index (I) between the different populations revealed a median genetic diversity. At the same time, gene flow was interpreted to be low. The main factors responsible for the median level of diversity and low gene flow within populations are probably due to a low frequency of sexual recombinations. Analysis of molecular variance showed that there was high genetic differentiation among the five water bodies. Both cluster analysis and a nonmetric multidimensional scaling analysis suggested that genotypes isolated from the same locations displayed a higher genetic similarity than those from different ones, separating populations into subgroups according to their geographical locations. However, there is a weak positive correlation between the genetic distance and geographical distance.     

蕙兰SSR引物开发及渝贵川地区兰属遗传多样性研究

采用磁珠富集法对野生蕙兰DNA进行SSR引物开发,并以开发出的多态性引物为研究工具,选取来自渝、责、川3省(市)的9个野生兰属居群为研究对象,探讨遗传多样性与其地理位置分布的关系,从而在分子水平上为如何保护兰属植物提供有利参考.结果 显示:8对SSR引物共扩增出53个等位基因,平均每个位点的等位基因为6.6250个,平...     

利用30个微卫星标记分析长江中下游鲢群体的遗传多样性

摘要: 利用30对微卫星分子标记对长江中下游5个鲢群体进行了遗传多样性分析。结果表明: 在30个基因座中, 共检测到144个等位基因, 每个座位检测到的等位基因数为1～10个, 其中有25个座位具有多态性, 多态位点百分率为83.33,5个群体的平均等位基因数A为4.0/4.1, 平均有效等位基因数Ne为2.4445～2.6332, 平均观察杂合度Ho为0.3233～0.3511, 平均期望杂合度He为0.4421～0.4704, 平均多态信息含量PIC为0.4068～0.4286。对数据进行F-检验, Fst值表明群体间的遗传分化程度中等, 并对基因型进行了基于Hardy-Weinberg平衡的卡方检验, 所得P值说明5个群体均一定程度上偏离了平衡。5个群体间的遗传相似系数为0.8466～0.9146,遗传距离为0.0893～0.1665, 并根据Nei氏标准遗传距离用UPGMA方法对5个鲢群体进行亲缘关系聚类。     

Genetic Diversity Within and Among Lepidium draba Populations from Eastern Anatolia Based on RAPD Analysis

Genetic variation and structure of six natural populations of Lepidium draba L. from Eastern Anatolia were assessed using random amplified polymorphic DNA (RAPD) markers. For RAPD analysis, 12 primers generated 218 reproducible bands across the six populations analyzed, of which 73 bands (33.3%) were polymorphic. The mean Nei’s gene diversity value for all six populations was 0.1771. Shannon’s information index varied with population (0.2278–0.3082), averaging 0.2608. Analysis of molecular variance (AMOVA) showed that genetic diversity was greater within populations (58.66%) than among populations (30.68%). In addition, the variation between groups was 10.33%. The genetic differentiation among populations (G _ST) was 0.3210, indicating that most genetic diversity occurs within populations. Gene flow (Nm) was low, at only 0.5288.     

Allozyme and RAPD polymorphism in Tylophora indica (Burm.f.) Merr.

Tylophora indica (Burm.f.) Merr (syn. T. asthmatica), is being indiscriminately collected for medicinal use which is not sustainable. Conservation of the species requires information on existing genetic content and its distribution in different populations. In the present study, polymorphism in allozyme and RAPD profiles of five populations were analysed using six enzyme systems and ten random primers. Genetic content in terms of allozymes and RAPDs as revealed by Shannon-Weiner index was more or less same in all the populations. Evenness as calculated from observed diversity (Shannon-Weiner index, H’) and the maximum expected diversity (H^max) for the allozymes and RAPDs was high for individual populations indicating that the distribution of genetic content was fairly uniform. From the results, it was concluded that collection of few genotypes from geographically distinct locations rather than intensive collection within one or two locations would be representative of the genetic variability present in this species.     

Random Amplified Polymorphic DNA Analysis of Heterodera cruciferae and H. schachtii populations

Heterodera schachtii and H. cruciferae are sympatric in California and frequently occur in the same field upon the same host. We have investigated the use of polymerase chain reaction (PCR) amplification of nematode DNA sequences to differentiate H. schachtii and H. cruciferae and to assess genetic variability within each species. Single, random oligodeoxyribonucleotide primers were used to generate PCR-amplified fragments, termed RAPD (random amplified polymorphic DNA) markers, from genomic DNA of each species. Each of 19 different random primers yielded from 2 to 12 fragments whose size ranged from 200 to 1,500 bp. Reproducible differences in fragment patterns allowed differentiation of the two species with each primer. Similarities and differences among six different geographic populations of H. schachtii were detected. The potential application of RAPD analysis to relationships among nematode populations was assessed through cluster analysis of these six different populations, with 78 scorable markers from 10 different random primers. DNA from single cysts was successfully amplified, and genetic variability was revealed within geographic populations. The use of RAPD markers to assess genetic variability is a simple, reproducible technique that does not require radioisotopes. This powerful new technique can be used as a diagnostic tool and should have broad application in nematology.