Genetic differentiation among common and selected hatchery populations of flounder: Evidence from RAPD markers

Randomly amplified polymorphism DNA (RAPD) analysis was performed in order to evaluate one common population and two selected hatchery populations of flounder Paralichthys olivaceus. A total of 90 individuals belonging to three populations were screened using 12 different RAPD primers. A total of 71 loci were produced in the three studied populations, and 43.5%, 42.4% and 42.2% of these loci were polymorphic over all the genotypes tested in common, susceptible and resistant populations, respectively. The number of loci detected by single primers ranged from four to eight. The average heterozygosites of common, susceptible and resistant populations were 0.112, 0.103 and 0.111, respectively. Compared with the common population, the two selected hatchery populations, susceptible and resistant, showed some genetic differences including a smaller number of loci, a smaller number of polymorphic loci, a smaller number of genotypes and a smaller Shannon index. The present study confirmed that it is important to detect the genetic variability of the selected hatchery population for the conservation of natural flounder resources.     

雌雄异株稀有植物伞花木(Eurycorymbus caraleriei)自然居群的等位酶遗传多样性研究

伞花木（Eurycorymbus caraleriei）为中国特有的第三纪孑遗单种属植物,雌雄异株。采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对其5个自然居群和1个人工迁地保护居群的等位酶变异进行了初步研究。对7个酶系统中14个位点的等位酶居群遗传多样性及遗传结构分析结果表明：伞花木具有较高水平的遗传多样性,其每位点平均等位基因数A=1．6,平均多态位点比率P=42．9％,平均预期遗传杂合度Hr=0．216;各居群的遗传多样性无显著性差异,但都表现为严重偏离Hardy-Weinberg平衡的杂合子过量;其遗传变异主要发生在居群内（93．1％）,居群间分化较小（Gst=0．069）,居群问遗传一致度较高（I=0．965～1．000）。推断这可能是由于其古老孑遗性、雌雄异株、混和传粉方式的生物学特性以及其长寿命的生活史等原因所导致;同时,居群间的较高基因流（Nm=3．128）也可能起到很大的作用。还使用UPGMA聚类方法推断了武汉植物园迁地保护的野外居群来源,在对迁地保护居群的评价中发现迁地保护居群仅保存了该物种基因型多样性的16％,在此基础上提出了今后进一步的保育策略。     

雌雄异株稀有植物伞花木(Eurycorymbus caraleriei)自然居群的等位酶遗传多样性研究

伞花木(Eurycorymbuscaraleriei)为中国特有的第三纪孑遗单种属植物,雌雄异株。采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对其5个自然居群和1个人工迁地保护居群的等位酶变异进行了初步研究。对7个酶系统中14个位点的等位酶居群遗传多样性及遗传结构分析结果表明:伞花木具有较高水平的遗传多样性,其每位点平均等位基因数A=1.6,平均多态位点比率P=42.9%,平均预期遗传杂合度He=0.216;各居群的遗传多样性无显著性差异,但都表现为严重偏离Hardy-Weinberg平衡的杂合子过量;其遗传变异主要发生在居群内(93.1%),居群间分化较小(Gst=0.069),居群间遗传一致度较高(I=0.965~1.000)。推断这可能是由于其古老孑遗性、雌雄异株、混和传粉方式的生物学特性以及其长寿命的生活史等原因所导致;同时,居群间的较高基因流(N_m=3.128)也可能起到很大的作用。还使用UPGMA聚类方法推断了武汉植物园迁地保护的野外居群来源,在对迁地保护居群的评价中发现迁地保护居群仅保存了该物种基因型多样性的16%,在此基础上提出了今后进一步的保育策略。     

大针茅居群遗传分化和RAPD 位点多态性分布的分析

利用RAPD 分子标记技术对5 个居群的90 个大针茅个体间的遗传关系以及RAPD 多态性与所在生境的相关性进行了研究。16 个引物共扩增得到310 个RAPD 位点, 利用几种多元分析方法对所得位点进行分析, 结果显示: 主轴法分析能够在三维坐标下将90 个大针茅个体按居群来源进行分类, 前三个轴虽然只解释了总变异的21 . 91% , 却能将所研究的居群完全分开; 典范判别分析可以将97 .8%的大针茅个体正确地分类到已知居群, 且在二维功能轴下能够清晰地看到个体按居群来源进行了分类; Spearman 秩相关分析和多元逐步回归分析均得出大针茅RAPD 位点的Nei′s 基因多样性与气候因子( 包括年降水量、积温、年均温、一月份均温和七月份均温) 之间存在显著的关联性。基于以上结果我们可以得出: 大针茅地理居群分化显著; 大针茅RAPD 多样性并非随机分布而是与生境气候因子相联系; 气候差异的自然选择, 对大针茅遗传多样性和遗传结构的特点起决定作用。研究结果对大针茅种质资源的保护具有重要的指导意义。     

Genetic variation of apolipoproteins in North Indians

Genetic variation at three apolipoprotein loci (APOA4, APOH, and APOE) has been examined in nine endogamous populations of Punjab, North India. The overall pattern of allele frequency variation at different loci is compatible with that of European populations, but observed microvariation differentiates the populations according to their position in the Indian caste structure. The most common allele at the APOA4 locus was APOA4*1 with a narrow frequency range (89%-92%). APOH*2 allele frequency was highest in these populations (0.852-0.914). APOE*E4 allele frequency was relatively low (6%-10%) in the North Indian populations compared to its frequency in many European populations. The anthropological usage of these polymorphisms was evaluated using multivariate analyses. Genetic distance analysis and principal correspondence analysis showed that the North Indian populations are closest to Europeans, followed by Chinese and African populations. Overall, this study highlights the usefulness of apolipoproteins as genetic markers for clinical, population, and anthropological studies.     

Low genic variation in male-reproductive-tract proteins of Drosophila melanogaster and D. simulans

We report results, using two-dimensional gel electrophoresis (2DE), of natural population surveys of allelic variation in approximately 300 male-reproductive-tract polypeptides in both Drosophila melanogaster and its sibling species, D. simulans. Despite our efforts to maximize operational sensitivity of our 2DE gels to polymorphism, variation estimates in both species were low (proportion of polymorphic loci [P] = 9%, and average heterozygosity [H] = 1%-3%), compared with those by one-dimensional gel electrophoresis (1DE) (P = 29%-55%; H = 8%-19%) in the same populations. However, H of polymorphic loci was very similar for 2DE and 1DE proteins; and for 17 of a total of 54 polymorphic proteins, 2DE detected three or four distinct alleles. The results suggest that the differing levels of variability widely seen with 1DE and 2DE are real and reflect differing intensities of functional constraint between different classes of structural loci. However, the alternative possibility remains that 2DE has a greater between-locus unevenness of variant detection sensitivity than does 1DE.     

GENETIC VARIATION IN CACTOPHILIC DROSOPHILA FOR OVIPOSITION ON NATURAL YEAST SUBSTRATES

Theory predicts that environmental heterogeneity in space or in time can maintain genetic polymorphism. Stable polymorphisms are expected to be more readily maintained if there are genotype specific habitat preferences. Genotype specific preferences for oviposition sites in Drosophila could be a major factor promoting habitat selection, and thus the maintenance of genetic variation. This hypothesis is being tested using the cactophilic species, D. buzzatii and D. aldrichi, where available evidence indicates a potential for such habitat selection, the habitats (oviposition sites) being yeast species found in the natural environment of these flies (cactus rots). Genetic variation for oviposition preferences was tested using isofemale lines—for D. buzzatii, a total of 60 lines from seven localities widely distributed through the species range in Australia, and for D. aldrichi, 21 lines from three of these localities. Females were given a choice of five yeast species as oviposition sites. Genetic variation for oviposition preferences on these natural substrates was demonstrated. There was significant variation among isofemale lines within populations in their patterns of preferences for oviposition on the five yeast species. However, analyses of preferences for each yeast species separately showed that the genetic variation for preferences relates to only three of the five species. Heritabilities of individual female preferences for these three species were low, ranging up to 9%. Little geographic differentiation was apparent among populations, most likely due to similar selection regimes within each population. Within populations, this kind of habitat selection could act to maintain polymorphisms, both at loci determining the habitat preferences and at other loci in linkage disequilibrium with them.     

Serial population bottlenecks and genetic variation: Translocated populations of the New Zealand Saddleback (<Emphasis Type="Italic">Philesturnus carunculatus rufusater</Emphasis>)

The genetic effects of population bottlenecks have been well studied theoretically, in laboratory studies, and to some extent, in natural situations. The effects of serial population bottlenecks (SPBs), however, are less well understood. This is significant because recurrent population bottlenecks are likely to be a common feature of the life history of many species. The lack of understanding of SPBs in natural populations has certainly been hampered by a lack of good examples where it can be studied. We report the results of a study into island populations of North Island Saddleback (Philesturnus carunculatus rufusater) that have undergone 13 translocations since 1964, all but one of these has been deliberate and for which detailed records are available. We have examined nine island populations of this passerine bird, from the source population, three first-order bottlenecked and five second-order bottlenecked populations. We examine variation in these nine populations using multilocus minisatellite DNA markers, together with Mendelian loci comprising six microsatellite DNA loci and a variable isozyme locus. Despite the generally low level of genetic variation in the Saddleback source population, we were able to detect a pattern of significant changes in both the mean number of minisatellite DNA bands per individual and the frequency of alleles at the Mendelian loci, with increasing population bottlenecks. This study generally shows that in a natural population, SPBs result in more pronounced genetic changes than do single population bottlenecks by themselves, thereby highlighting their importance for the conservation of rare and endangered species.     

Gene Flow in Natural Populations of DROSOPHILA MELANOGASTER with Special Reference to Lethal Allelism Rates and Protein Variation

A simultaneous survey of 14 protein loci, together with frequencies and within- and between-population allelism rates of lethal chromosomes, was carried out in five (four Japanese and one Korean) natural populations and one cage population of Drosophila melanogaster. It was found that lethal allelism rates decrease rapidly as geographic distance between two populations increases, while variation at protein loci shows a remarkable similarity over all populations examined. These findings suggest that there are very high levels of gene flow in these natural populations and that selection at protein loci which can maintain substantial geographic variation, if present, is overshadowed by gene flow. There is no indication that invasion of D. melanogaster to the Far East occurred so recently that the frequencies of lethal chromosomes are still in nonequilibrium.     

Ecologically and evolutionarily important SNPs identified in natural populations

Evolution by natural selection acts on natural populations amidst migration, gene-by-environmental interactions, constraints, and tradeoffs, which affect the rate and frequency of adaptive change. We asked how many and how rapidly loci change in populations subject to severe, recent environmental changes. To address these questions, we used genomic approaches to identify randomly selected single nucleotide polymorphisms (SNPs) with evolutionarily significant patterns in three natural populations of Fundulus heteroclitus that inhabit and have adapted to highly polluted Superfund sites. Three statistical tests identified 1.4-2.5% of SNPs that were significantly different from the neutral model in each polluted population. These nonneutral patterns in populations adapted to highly polluted environments suggest that these loci or closely linked loci are evolving by natural selection. One SNP identified in all polluted populations using all tests is in the gene for the xenobiotic metabolizing enzyme, cytochrome P4501A (CYP1A), which has been identified previously as being refractory to induction in the three highly polluted populations. Extrapolating across the genome, these data suggest that rapid evolutionary change in natural populations can involve hundreds of loci, a few of which will be shared in independent events.     

Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?

The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here, we use both neutral and major histocompatibility complex (MHC) markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled 11 different populations; five continuous, three isolated, and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs) which both were found to be neutral, and two functional MHC genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented.     

A Direct Assessment of the Role of Genetic Drift in Determining Allele Frequency Variation in Populations of EUPHYDRYAS EDITHA

Estimates of allele frequencies at six polymorphic loci were collected over eight generations in two populations of Euphydryas editha. We have estimated, in addition, the effective population size for each generation for both populations with results from mark-recapture and other field data. The variation in allele frequencies generated by random genetic drift was then studied using computer simulations and our direct estimates of effective population size. Substantial differences between observed values and computer-generated expected values assuming drift alone were found for three loci (Got, Hk, Pgi) in one population. These observations are consistent with natural selection in a variable environment.     

湖北3种药用淫羊藿植物等位酶多样性与居群遗传结构

采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对湖北3种淫羊藿属（Epimedium L．）药用植物：柔毛淫羊藿（E．pubescens Maxim．）、箭叶淫羊藿（Esagittatum（Sieb．＆Zucc．）Maxim．）和巫山淫羊藿（Ewushanense T.S．Ying）的11个自然居群进行了等位酶种内遗传多样性和居群遗传结构以及种间遗传关系的研究。6个酶系统在3种淫羊藿植物中检测到13个酶位点共45个等位基因,分析结果表明：1）3种淫羊藿均具有较高的遗传多样性水平（A=2．6-3．2,P=69．2％-84．6％,Ho=0．274-0．377,HE=0．282-0．369）,远高于多年生草本植物和依靠动物传粉植物的平均水平;2）所有居群都显著偏离Hardy—Weinberg平衡,大多数多态位点固定指数（F）明显偏离于0且正负值各半,暗示该属植物可能具有复杂的繁育系统;3）种内和种间的遗传分化度均较低,分别为GST=0．0246-0．0409和0．0495-0．1213,表明种内居群间存在较高的基因流和种间较近的遗传关系;4）聚类分析表明柔毛淫羊藿与箭叶淫羊藿的亲缘关系更近,这与形态学特征、花瓣演化趋势及系统发育分析等方面的研究的结果相吻合。讨论分析认为3种淫羊藿植物的遗传变异特性是由淫羊藿属植物异交与克隆繁殖的混合繁育系统、多年生的生活特性、古老的进化历史和种子的蚁播特性等多因素共同决定的。     

Use of RAPD and ITE molecular markers in studying the genetic structure of the Crimean population of T. boeoticum Boiss

The influence of ecological factors on variation of random PCR markers (RAPD and inter-MITE polymorphism (IMP) primers) was evaluated in two wild Triticum boeoticum populations with contrasting climatic conditions in Crimea. The proportion of variation that undergoes natural selection was compared for these two types of molecular markers. The Sapun Mountain and Baidar Valley populations differed significantly in 24.7% of the analyzed loci, with a low Nei distance between these populations (0.0324). The number of significantly different RAPD and IMP markers in the two populations was nearly equal. Testing for evolutionary neutrality showed that 13 loci (17.8%) were influenced by natural selection. The Sapun Mountain population was more dependent on natural selection (ten loci, 13.7%) than the Baidar Valley population (four loci, 5.5%). Eleven out of the 13 loci undergoing selection were amplified with IMP primers.     

大王马先蒿云南五个居群遗传变异研究

采用随机扩增多态DNA(RAPD)分子标记方法,对大王马先蒿(PedicularisrexL.)分布在云南中甸、丽江、大理、武定和昆明的5个居群(其中中甸居群有3个亚居群)的遗传多样性和遗传结构进行了研究。结果表明,大王马先蒿居群具有较高的遗传多样性,多态位点百分率P、Shannon表型多样性指数I和Nei的基因多样性指数h分别为82.0%、0.361和0.240,遗传多样性水平与居群的地理分布范围相关;大王马先蒿居群间的遗传变异较高,遗传变异主要发生在居群之间,而不是居群内部;居群间遗传分化系数Gst为0.747,遗传分化明显,居群间基因交流较少。居群间的遗传距离与居群间的相对地理距离具有一定的相关性。对云南西北部中甸居群的3个亚居群的遗传多样性分析表明,居群的遗传多样性水平与海拔高度有一定的相关性。居群间遗传变异较高可能是由于大王马先蒿为短命多年生植物,繁育系统为混交型,且自交占较大比例等原因造成的。     

Allozyme variation of Cyclobalanopsis championii (Fagaceae), a narrowly distributed species in southern Taiwan

Allozyme genetic variability in five natural populations of Cyclobalanopsis championii (Fagaceae) in Taiwan was investigated using 12 loci from 9 enzyme systems. The average values of parameters describing within-population variation, expected heterozygosity (He = 0.151), the percentage of polymorphic loci per individual (P = 50%), the average number of alleles per locus (A = 1.7), effective number of alleles per locus (Ae = 1.25), and the average number of alleles per polymorphic loci (AP = 2.2) are comparable to those of other long-lived woody plants. The overall fixation index (Fis = 0.208) indicates a significant deficiency of heterozygotes at the population level. Allelic frequency deviation from Hardy-Weinberg equilibrium was found for different loci in different populations. An exact test for population differentiation using the Tools for Population Genetic Analyses program also indicates that allelic frequencies among populations are significantly different (P < .001). Among-population variation, Gst, accounted for 9.2% of the total heterozygosity. The population at Shouchia and the southernmost population Nanjenshan had higher inbreeding coefficients (0.177 and 0.153, respectively) than did the northern populations. Genetic drift is supported by the observations of the variance components of linkage disequilibrium and a large proportion of loci in Nanjenshan and Shouchia that show pairwise locus disequilibrium. We believe continuous genetic drift in the southern populations will increase genetic divergence among populations of C. championii in Taiwan. Significant correlation was found between elevation and expected heterozygosity. We therefore inferred that temperature is the most important ecological factor to influence the genetic diversity of C. championii.     

Chromosomal regions associated with segregation distortion of molecular markers in F2 , backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.)

Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps. Mapping populations were derived from one interspecific backcross and five intersubspecific (indica?/?japonica) crosses, including two F₂ populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population consisted of 129–629 markers. Segregation distortion was determined based on chi-square analysis (P?<?0.01) and was observed at 6.8–31.8% of the mapped marker loci. Marker loci associated with skewed allele frequencies were distributed on all 12 chromosomes. Distortion in eight chromosomal regions bracketed previously identified gametophyte (ga) or sterility genes (S). Distortion in three other chromosomal regions was found only in DH populations, where japonica alleles were over-represented, suggesting that loci in these regions may be associated with preferential regeneration of japonica genotypes during anther culture. Three additional clusters of skewed markers were observed in more than one population in regions where no gametophytic or sterility loci have previously been reported. A total of 17 segregation distortion loci may be postulated based on this study and their locations in the rice genome were estimated.     

Genetic variation in original and colonizing Drosophila buzzatii populations analysed by microsatellite loci isolated with a new PCR screening method

A new polymerase chain reaction-based screening method for microsatellites is presented. Using this method, we isolated 12 microsatellite loci from Drosophila buzzatii, two of which were X-linked. We applied the other 10 microsatellite loci to the analysis of genetic variation in five natural populations of D. buzzatii. Two populations were from the species' original distribution in Argentina, whereas the other three were from Europe (two) and Australia that were colonized 200 and 65 years ago, respectively. Allelic variation was much larger in the original populations than in the colonizing ones and there was a tendency to decreased heterozygosity in the colonizing populations. We used three different statistical procedures for detecting population bottlenecks. All procedures suggested that the low variability in the populations in the Old World was not the result of the recent population decline, but was due to a founder effect followed by a population expansion. In fact, one procedure which detects population expansions and declines based on the genealogical history of microsatellite data suggested that an expansion had taken place in all the colonized populations.     

Genetic polymorphism study at four minisatellite loci (D1S80, D17S5, D19S20, and APOB) among five Indian population groups

The present study reports the genetic variation observed among five anthropologically distinct population groups of India, using four highly polymorphic minisatellite loci (D1S80, D17S5, D19S20, and APOB 3' VNTR) in order to examine the effect of geographical and linguistic affiliations on the genetic affinities among these groups. Random individuals from five ethnic groups were studied; the sample size ranged from 235 to 364. The population groups belong to two geographically separated regions of India, the state of Maharashtra (western India) and the state of Kerala (southern India). The two Maharashtrian groups (Konkanastha Brahmins and Marathas) speak "Marathi," an Indo-European language, whereas the three Kerala population groups (Nairs, Ezhavas, and Muslims) speak "Malayalam," an Indo-Dravidian language. Genomic DNA was extracted from peripheral blood samples and analyzed using amplified fragment length polymorphism (Amp-FLP) technique. All four loci displayed high heterozygosity with average heterozygosity in the range of 0.82 to 0.84. The Polymorphic Information Content and Power of Discrimination were > or = 0.75 and > or = 0.80, respectively. The coefficient of gene differentiation was found to be low (average G(ST) = 1.2%; range between 0.6% at D1S80 locus to 1.6% at APOB 3' VNTR locus) across the loci, indicating close affinity among the population groups. The neighbor-joining tree revealed two clear clusters, one for the two Maharashtrian population groups and the other for the three Kerala population groups. The results obtained are in conformity with the geographical and linguistic backgrounds of the studied populations.     

Genetic differentiation ofDrosophila melanogaster populations as assessed by two-dimensional electrophoresis

Seven populations ofDrosophila melanogaster, representing a worldwide distribution, were compared using two-dimensional protein gel electrophoresis. A total of 611 protein spots was scored, which probably represent a sample of over 500 loci that were surveyed. Of the protein spots scored, 521 spots were found to be invariant, but another 90 spots were found to be variable among the populations. Of these variable protein spots, 12 were found to be present in only one population. All the populations, except one, had at least one protein spot restricted to itself. However, the Japanese population had by far the most, with five protein spots restricted to this one population, which has been observed in previous studies of private alleles in oriental populations. The mean genetic similarity (F) found among the seven populations was 0.965, with a range of between 0.956 and 0.977. This is similar to previous reports of lower variation found in population genetic surveys using two-dimensional electrophoresis. It was found that the historical relationships among these populations was somewhat congruent with the geographic distribution of the populations, but as in previous studies, it was not exactly coincident.