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PubMed2002

[Genetic structure of STR in Naci ethnic group in China].

STR is a universal genetic marker that has changeable polymorphism and stable heredity in human genome. It is a specific DNA segment composed of 2-7 base pairs as its core sequence, and is formed through the repeated connection of the same one. Since it has the characteristics such as numerous allelic genes, highly heterozygosity and easy recognition and short PCR segment, it is employed as an ideal DNA marker in such practical fields as human genetics and forensic medicine. In this study, we investigated the polymorphism of STR of Naci minority with STR genescan marked by fluorescence. Seventy-two alleles of 9 STR in Naci were detected with their frequency 0.0052-0.5208 and 165 genotypes were found out with frequency 0.0104-0.3021. Hi-Square test indicated the distribution of genotypes agreed with Hardy-Weinberg equilibrium (P > 0.05). Statistical analysis showed the followings: the heterozygosity (H) > 0.6 in each locus, the average polymorphism information content (PIC) > 0.7, Mean discrimination power (DP) > 0.8, probability of paternity exclusion (EPP) > 0.5, indicating that the STR markers used in the study were of great value in the researches of minority genetics. This not only founds the base for genetic structures of STR of Chinese but also provides valuable information for anthropology, forensic medicine and ethnology.

China↗
PubMed2004

Genetic structuring of Patagonian toothfish populations in the Southwest Atlantic Ocean: the effect of the Antarctic Polar Front and deep-water troughs as barriers to genetic exchange.

The environmental and/or life history factors affecting genetic exchange in marine species with potential for high dispersal are of great interest, not only from an evolutionary standpoint but also with regard to effective management. Previous genetic studies have demonstrated substantial differentiation among populations of the Patagonian toothfish around the Southern Ocean, indicating breakdown of gene flow across large distances between inhabited shelf areas. The present study examined genetic structuring through analysis of microsatellite loci and restriction fragment length polymorphism (RFLP) of the mitochondrial ND2 gene and control region of the toothfish population in the SW Atlantic, allowing examination of the relative effects of the Antarctic Polar Front (APF), deep-water troughs and distance between sites. Mitochondrial DNA (mtDNA) data indicated a sharp genetic division between the Patagonian Shelf/North Scotia Ridge and the Shag Rocks/South Georgia samples, whereas microsatellite data showed much less distinct structuring and an intermediate position of the North Scotia Ridge samples. We suggest these data indicate that the APF, as a barrier to larval dispersal, is the major inhibitor of genetic exchange between toothfish populations, with deep-water troughs and distance between sites contributing to genetic differentiation by inhibiting migration of relatively sedentary adults. We also suggest that differences between mtDNA and nuclear DNA population patterns may reflect either genome population size effects or (putative) male-biased dispersal.

Animals↗
PubMed2004

Multilocus sequence typing of Streptococcus pyogenes representing most known emm types and distinctions among subpopulation genetic structures.

A long-term goal is to characterize the full range of genetic diversity within Streptococcus pyogenes as it exists in the world today. Since the emm locus is subject to strong diversifying selection, emm type was used as a guide for identifying a genetically diverse set of strains. This report contains a description of multilocus sequence typing based on seven housekeeping loci for 495 isolates representing 158 emm types, yielding 238 unique combinations of sequence type and emm type. A genotypic marker for tissue site preference (emm pattern) revealed that only 17% of the emm types displayed the marker representing strong preference for infection at the throat and that 39% of emm types had the marker for skin tropism, whereas 41% of emm types harbored the marker for no obvious tissue site preference. As a group, the emm types bearing the emm pattern marker indicative of no obvious tissue site preference were far less likely to have two distinct emm types associated with the same sequence type than either of the two subpopulations having markers for strong tissue tropisms (P < 0.002). In addition, all genetic diversification events clearly ascribed to a recombinational mechanism involved strains of only two of the emm pattern-defined subpopulations, those representing skin specialists and generalists. The findings suggest that the population genetic structure differs for the tissue-defined subpopulations of S. pyogenes. The observed differences may partly reflect differential host immune selection pressures.

Antigens, Bacterial↗
PubMedDate not supplied

Influence of religion and birthplace on the genetic structure of Northern Ireland.

The effect of geographic and religious subdivision on the genetic structure of Northern Ireland was assessed using data on 10 craniofacial measurements collected on 755 adult males that were born in five counties and belonged to one of three religious affiliations (Catholic, Church of Ireland, Presbyterian). Fifteen samples were defined based on birth county and religious affiliation. Two-way univariate and multivariate analysis of variance shows significant effects of birth county and religious affiliation, with somewhat greater subdivision due to religion. Distance matrix correlations reveal a small, but significant, effect of birth county and religious affiliation on the pattern of genetic distances between the 15 samples, with a slightly greater influence of religion. The Church of Ireland samples show the greatest differences. perhaps revealing the combined influence of differential population origins and religious differences as a barrier to gene flow. Overall, religion has a significant, though minor, influence on genetic variation in Northern Ireland.

Adult↗
PubMed2000

Microsatellite analysis of genetic structure in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae).

The level of genetic variation throughout the entire worldwide range of the mangrove species Avicennia marina (Forsk.) Vierh. was examined using microsatellite markers. Three microsatellite loci detected high levels of allelic diversity (70 alleles in total), essential for an accurate estimation of population genetic parameters. The informativeness of the microsatellite loci tended to increase with increasing average number of repeats. The levels of heterozygosity detected for each population, over all loci, ranged from 0.0 to 0.8, with an average of 0.407, indicating that some populations had little or no genetic variation, whereas others had a large amount. Populations at the extremes of the distribution range showed reduced levels of heterozygosity, and significant levels of inbreeding. This is not unexpected as these populations may be subject to founder effects and environmental constraints. The presence of genetic structure was tested in A. marina populations using three models: (i) a single panmictic model; (ii) the discrete subpopulation model; and (iii) the isolation by distance model. The discrete subpopulations model was supported by the overall measures of population differentiation based on the infinite alleles model (F-statistics), and the stepwise mutation model (R statistics). In addition, an analysis of molecular variance (AMOVA), using both theoretical models, found that most of the variation was between populations (41-71%), and within individuals in the total population (31-49%). There was little variation among individuals within populations (0-10%). There was no significant isolation by distance. The high levels of genetic differentiation observed among populations of A. marina may be due to environmental and ecological factors, particularly past sea level and climatic changes.

Alleles↗
PubMed2002

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers.

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.

Edible Grain↗
PubMed1990

Genetic structure of natural populations of the nitrogen-fixing bacterium Rhizobium meliloti.

The genetic structure of populations of the symbiotic nitrogen-fixing soil bacterium Rhizobium meliloti was examined by analysis of electrophoretically demonstrable allelic variation in 14 metabolic, presumably chromosomal, enzyme genes. A total of 232 strains were examined, most of which were isolated from southwest Asia, where there is an unsurpassed number of indigenous host species for R. meliloti. The collection consisted of 115 isolates recovered from annual species of Medicago in Syria, Turkey, and Jordan; 85 isolates cultured from two perennial species of Medicago (M. sativa [alfalfa] and M. falcata) in northern Pakistan and Nepal; and 32 isolates collected at various localities in North and South America, Europe, South Africa, New Zealand, and Australia, largely from M. sativa. Fifty distinctive multilocus genotypes (electrophoretic types [ETs]) were identified, and cluster analysis revealed two primary phylogenetic divisions separated at a genetic distance of 0.83. By the criterion of genetic differentiation conventionally applied in defining species limits among members of the family Enterobacteriaceae and certain other bacteria, the two primary divisions of R. meliloti represent distinct evolutionary species. Division A included 35 ETs represented by 209 strains from the eastern Mediterranean basin, northern Pakistan, Nepal, and various other localities worldwide. This division contained the nine commercial alfalfa inoculant strains examined. Division B included 15 ETs represented by 23 isolates, 21 of which were isolated from annual medic species growing in previously uninoculated soils in the eastern Mediterranean basin. The two remaining strains in division B, both representing the same ET, were isolated in the United States and Australia.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed2006

RAPD analysis of genetic diversity and population genetic structure of Stipa krylovii Reshov. in Inner Mongolia steppe.

Random amplified polymorphic DNA (RAPD) analysis was used to characterize the genetic diversity and population genetic structure of Stipa krylovii populations in Inner Mongolia steppe of North China. Thirteen 10 bp oligonucleotide primers, which generated 237 RAPD bands, were used to analyze 90 plants of five populations from three regions, meadow steppe, typical steppe and desert steppe, from the east to the west. The genetic diversity of Stipa krylovii that was revealed by observed number of alleles (na), expected number of alleles (ne), Nei's diversity index (h), Shannon's diversity index (H), amplificated loci, polymorphic loci and the percentage of polymorphic loci (PPB) increased from the east to the west. The Pearson's correlation analysis between genetic diversity parameters and ecological parameters indicated that the genetic diversity of Stipa krylovii was associated with precipitation and cumulative temperature variations along the longitude (humidity were calculated by precipitation and cumulative temperature). Dendrogram based on Jaccard's genetic distance showed that the individuals from the same population formed a single sub-group. Although most variation (56.85%) was within populations, there was high genetic differentiation among populations of Stipa krylovii, high differentiation within and between regions by AMOVA analysis. Either Nei's unbiased genetic distance (G(ST)) or gene flow (Nm) among pairwise populations was not correlated with geographical distance by Mantel's test (P > 0.05), suggesting that there was no consistency with the isolation by distance model in these populations. Natural selection may have played a role in affecting the genetic diversity and population structure, but habitat destruction and degradation in northern grassland in China may be the main factor responsible for high genetic differentiation among populations, within and among regions.

China↗
PubMed1999

Genetically structured modeling of protein production in filamentous fungi.

A general framework for a genetically structured model is presented. The framework allows description of the interactions in a system of regulatory and structural genes. The model assumes equilibrium kinetics for the binding of regulatory proteins to the promoter regions of the genes and includes the possible activation of proteins following their synthesis. The model is evaluated by simulating the alcA-expression (alcohol dehydrogenase I) in Aspergillus nidulans which is an inducible system subject to glucose repression. The intracellular enzyme levels in strains with different regulatory mutations are simulated during various growth conditions. The model gives a good description of the experimental data with changes in only a few parameter values which have a mechanistic interpretation.

Alcohol Dehydrogenase↗
PubMed2002

[Genetic structure of a diploid-polyploid complex of the spined loach Cobitis taenia (Cypriniformes: Cobitidae) from the middle Dnieper bassin].

Biochemical genetic typing and cytometry showed that polyploid females account for 87% of the spined loach Cobitis taenia population from the middle Dnieper basin. The polyploidy series included triploids, tetraploids, and, possibly, a few pentaploids. A characteristic feature of the genetic structure of polyploids was that their genetic variation was due to the clonal variation in the haploid portion of the genome originating from Cobitis sp. and to polymorphism of the diploid portion originating from C. taenia. The results are discussed with regard to comparative evolution of alloploid complexes in fish and terrestrial vertebrates.

Animals↗
PubMed2006

Microsatellite typing reveals strong genetic structure of Schistosoma mansoni from localities in Kenya.

Genetic diversity and population structure of seven populations of Schistosoma mansoni sampled in Kenya were assessed using five microsatellite markers. The mean number of alleles per locus, expected heterozygosity in Hardy-Weinberg equilibrium and pairwise F(ST) values ranged from 5.2 to 10.7, 0.5-0.8 and 3.6-27.3%, respectively. These data reveal that S. mansoni populations in Kenyan have relatively high levels of genetic diversity and is significantly differentiated. Our data combined with information on biogeography support the hypothesis that the strong genetic structure in Kenyan schistosomes is as a result of limited gene flow and large population sizes. Resistance to anthelminthics has not been reported among the Kenyan schistosomes, we hypothesize that this is probably due to the very little gene flow among populations, thereby limiting opportunities for the spread of rare alleles that might confer resistance to the drugs.

Animals↗
PubMed1997

Hierarchical analysis of genetic structure in native fire ant populations: results from three classes of molecular markers.

We describe genetic structure at various scales in native populations of the fire ant Solenopsis invicta using two classes of nuclear markers, allozymes and microsatellites, and markers of the mitochondrial genome. Strong structure was found at the nest level in both the monogyne (single queen) and polygyne (multiple queen) social forms using allozymes. Weak but significant microgeographic structure was detected above the nest level in polygyne populations but not in monogyne populations using both classes of nuclear markers. Pronounced mitochondrial DNA (mtDNA) differentiation was evident also at this level in the polygyne form only. These microgeographic patterns are expected because polygyny in ants is associated with restricted local gene flow due mainly to limited vagility of queens. Weak but significant nuclear differentiation was detected between sympatric social forms, and strong mtDNA differentiation also was found at this level. Thus, queens of each form seem unable to establish themselves in nests of the alternate type, and some degree of assortative mating by form may exist as well. Strong differentiation was found between the two study regions using all three sets of markers. Phylogeographic analyses of the mtDNA suggest that recent limitations on gene flow rather than longstanding barriers to dispersal are responsible for this large-scale structure.

Animals↗
PubMed2006

A case study: looking at the effects of fragmentation on genetic structure in different life history stages of old-growth mountain hemlock (Tsuga mertensiana).

We examined fine-scale genetic structure of mountain hemlock (Tsuga mertensiana) in an old-growth stand and an adjacent seedling population, with the goal of detecting the effects of fragmentation. Three hundred and six old-growth trees and 195 naturally regenerating seedlings were genotyped at 5 microsatellite loci. Genetic diversity was similar across old-growth life stages and within the clear-cut seedlings. Significant inbreeding was found in the adult class (30+ cm diameter at breast height) of old-growth seedlings and in the adjacent natural regeneration. Relatedness was significantly associated with physical distance for both the oldest age class and for regenerating seedlings in the adjacent clear-cut, whereas intermediate classes showed no such association. As intermediate classes show no isolation by distance, the associations that arise probably occur from single cohort regeneration that clearly has taken place in the clear-cut, and possibly when the oldest old-growth trees were established. Parentage analysis suggested that large-scale fragmentation, such as this clear-cut, allowed for increased long-distance seed dispersal. We conclude that long-lived tree populations can consist of a cohort mosaic, reflecting the effects of fragmentation, and resulting in a complex, age-dependent, local population structure with high levels of genetic diversity.

Aging↗
PubMedDate not supplied

[Genetic structure of the spawning population of Danube shad, Alosa pontica, Eichwaldt 1838 (Clupeiformes, Alosiinae)].

The genetic structure of the population of Danube shad, Alosa pontica, has been studied by means of analysis of 3 polymorphic biochemical gene loci. The results of the study provide evidence of its genetic heterogeneity which is expressed by: firstly, an unbalanced ratio of genotype loci manifested by an excess of rare homozygotes and deficite of the correspoding heterozygotes, and secondly, differences in the allele frequencies between shad populations arriving for spawning in March-April and May-June. It is suggested that there could be two causes of heterogeneity: one due to the introgressive hybridization between various forms of A. pontica and another to the differences between early and late spring races of shad which to a certain extent are reproductively autonomous.

Alleles↗
PubMed1997

Genetic structure of Trypanosoma cruzi in Central America and its comparison with South American strains.

Genetic characterization by isozyme analysis was performed on 68 isolates of Trypanosoma cruzi; 57 from Guatemala in Central America and 11 from South American countries. Ten zymodemes (isozyme patterns) were identified by examining zymograms of 12 enzymes (13 loci). These zymodemes were classified to 3 major distinctive groups: (1) major Guatemalan, (2) minor Guatemalan and (3) unique South American, by the genetic distances and the phylogenetic dendrogram drawn by UPGMA. Based on the results obtained, genetic structures and phylogenetic relations of T. cruzi in Guatemala and South America are discussed. Clonal reproduction seemed to be consistent with the observation of deviation from Hardy-Weinberg equilibrium in several loci.

Animals↗
PubMed1981

Genetic structure, transforming sequence, and gene product of avian sarcoma virus UR1.

We analyzed the genetic structure and gene products of the newly isolated avian sarcoma virus UR1, which recently has been shown to be replication defective and to contain no sequences homologous to the src gene of Rous sarcoma virus. The sizes of the genomic RNAs of UR1 and its associated helper virus, UR1AV, were determined to be 29S and 35S (5.9 and 8.5 kilobases), respectively, by gel electrophoresis and sucrose gradient sedimentation. RNase T1 oligonucleotide mapping of purified viral RNAs indicated that UR1 RNA contains eight unique oligonucleotides in the middle of the genome and shares four 5'-terminal and three 3'-terminal oligonucleotides with UR1AV RNA. The unique sequences of UR1 and Fujinami sarcoma virus were found to be closely related to each other by molecular hybridization of UR1 RNA with DNA complementary to the unique sequence of Fujinami sarcoma virus RNA, but minor differences were found by oligonucleotides fingerprinting. In the regions flanking the unique sequences, UR1 and Fujinami sarcoma viral RNAs contain distinct oligonucleotides, which are shared with oligonucleotides of the respective helper viral RNAs. Cell transformed with UR1 produce a single 29S RNA species which contains a UR1 unique sequence; this species is most likely the mRNA coding for the transforming protein. In UR1-transformed cells, a phosphoprotein fo 150,000 daltons (p150) was detected by immunoprecipitation with antiserum against gag proteins. p150 was associated with a protein kinase activity that was capable of phosphorylating p150 itself, immunoglobulin G of antiserum, and a soluble substrate, alpha-casein. This enzyme transferred phosphate exclusively to tyrosine residues of substrates in vitro, but p 150 labeled in vivo with 32P contained both phosphoserine and phosphotyrosine. The in vitro kinase reaction was not affected by the presence of cyclic AMP or cyclic GMP and strongly preferred Mn2+ over Mg2+. Thus, the properties of UR1 protein are almost identical to those of Fujinami sarcoma virus protein.

Alpharetrovirus↗
PubMed1986

Genetic structure of Anisakis physeteris, and its differentiation from the Anisakis simplex complex (Ascaridida: Anisakidae).

The genetic structure of Anisakis physeteris from the Mediterranean Sea has been analysed electrophoretically at 22 enzyme loci. The samples studied, although differing in the life-stage (larvae and adults), and in the host (the fishes Micromesistius poutassou and Trachurus trachurus, and the sperm whale Physeter macrocephalus) were genetically homogeneous. Of these loci 11 (Ldh, Sod, Np, Adk-2, Pgm-1, Est-1, Est-2, Acph-1, Acph-2, Lap-2 and Ca) were found to be monomorphic, while the other 11 (Sdh, Mdh, Idh, 6-Pgdh, G3pdh, Got, Adk-1, Pgm-2, Lap-1, Mpi and Gpi) showed from 2 to 7 alleles. The following values of genetic variability were estimated: He = 0.11, P = 0.50, A = 1.95. Distinct alleles were found between A. physeteris and the A. simplex complex at 19 out of the 22 loci studied, and only few rare alleles were shared at the remaining 3 loci. The genetic divergence between A. physeteris and A. simplex A and B is therefore very high, the values of Nei's index D being 7.384 and 6.443 respectively (I = 0.001 and 0.002). The assignation of A. physeteris and the A. simplex complex to two distinct subgenera, Skrjabinisakis and Anisakis, as proposed by Mosgovoy on a morphological basis, appears to be fully justified according to our genetic data.

Alleles↗