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PubMed1991

Analysis of population genetic structure by DNA fingerprinting.

DNA fingerprint similarity is now being used widely to make inferences about the genetic structure of natural and domesticated populations, often with little regard to the limitations of such data. This paper provides an overview of the statistical theory of DNA fingerprint analysis with special focus on applications to natural populations for which little if anything is known about the detailed genetics of the DNA profiles. Approaches to estimating individual and population homozygosity, effective population size, population subdivision, and relatedness are reviewed, and issues concerning the biases and sampling properties of the statistics are discussed.

DNA Fingerprinting↗

PubMed1984

Fine structure genetic map and complementation analysis of mutations in the dnaA gene of Escherichia coli.

A fine structure genetic map of several mutations in the dnaA gene of Escherichia coli was constructed by the use of recombinant lambda and M13 phages. The dnaA508 mutation was found to be the mutation most proximal to the promoter, while the dnaA203 mutation was found to be the most distal one. The order of mutations established in this analysis was: dnaA508, dnaA167, (dnaA5, dnaA46, dnaA211), dnaA205, dnaA204, dnaA203. The mutations dnaA601, dnaA602, dnaA603, dnaA604 and dnaA606 were found to map very close to each other and close to dnaA205 in the middle third of the dnaA gene. In analysing the dominance relationship all 13 dnaA mutations were found to be recessive to the wild type. Characteristic phenotypes of the dnaA(Ts) mutants, like reversibility of the temperature inactivation of the dnaA protein, cold sensitivity of haploid or of merodiploid strains and suppressibility by rpoB mutations, are found to correlate with clusters of mutations within the gene.

Bacterial Proteins↗

PubMed1989

Fine-structure genetic map of the maltose transport operon of Salmonella typhimurium.

We have constructed a fine-structure genetic map of the maltose transport operon in Salmonella typhimurium. We have isolated mal mutants by using indicator plates, penicillin selection, or a proton suicide technique. Mutants were obtained as spontaneous events or were induced by chemical mutagenesis and transposon insertion. Tn10 and Mu d(lac Ap)1 insertion mutations were used to create deletions. Mutations were also obtained in a gene that is equivalent to lamB in Escherichia coli, which codes for the lambda bacteriophage receptor. The gene products in the mutants were characterized by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis and immunoblotting. Our data indicate that the location of this operon on the Salmonella chromosome as well as the gene order and its orientation are the same as those in E. coli. This map will be useful in studying the mechanism of periplasmic transport in S. typhimurium.

ATP-Binding Cassette Transporters↗

PubMed2004

[Genetic structure of Tujia as revealed by Y chromosomes].

Tujia people call themselves "Bizika", which means aboriginal. Genetic study of Tujia is virtually absent. To characterize the genetic structure of Tujia,the distribution of 14 Y haplogroups was studied in Tujia populations sampled from Enshi, Hubei (31 males) and Jishou, Hunan (68 males). A total of eight haplogroups were observed in the Enshi and Jishou populations. The haplogroup frequencies of Tujia were compared with the frequencies of other related ethnic groups, including Northern Han, Southern Han, Tibetan-Burman speaking populations,Daic and Hmong-Mien. The principal component (PC) analysis was conducted and the PCs were plotted to explore the historical migrations. In addition, partial correlation analysis was performed to study the relationship between the first three PCs and the haplogroups. The PC2 revealed a cluster of Tujia groups including Longshan,Yongshun, and Enshi with Lahu, suggesting possible interaction between Tujia and the Di-Qiang groups. However,a similarity between Han and Tujia populations, though differentiated, were also observed. We postulated, by incorporating the results of archaeological and historical evidences, that the Ba people, the ancestors of the Tujia,might be related with Di-Qiang groups and inhabited the Tujia area initially before a substantial interaction with Han and other ethnic groups.

Asian People↗

PubMed1978

[Genetic structure of Staphylococcus epidermidis strain No. 17 possessing penicillinase and bacteriocinogenic activity].

The studies on the genetic structure of Staphylococcus epidermidis, strain 17 showed that this strain possessed a factor of bactericinogenicity of the one type, which was an extrachromosomal element not bound with penicillinase activity. The loss of the bacteriocinogenicity factor spontaneously or under the effect of acridine orange at a temperature of 37 degrees C was not observed. Passages of the strain at a temperature of 44 degrees C for 5 days and acridine orange proved to be the most effective eliminating factors. The loss of the bacteriocinogenicity plasmid did not result in changing any biochemical properties of the strain but was accompanied by a loss of the immunity to bacteriocin of the initial strain. The study of the growth regularities of the initial strain and its variant deprived of the bacteriocinogenicity plasmid showed that multiplication of the cells in the presence of the plasmid practically started without the latent period.

Acridine Orange↗

PubMed2000

Genetic structure of the five-factor model of personality in a Japanese twin population.

Dimensional approaches have been used to describe the fundamental dimensions that underlie the entire domain of normal and pathological personality. We tested the five factor model of personality structure in a sample of Japanese twins, to clarify the contributions of genetic and environment. The revised NEO personality inventory (NEO-PI-R) was administered to 251 twin pairs, ranging in age from 15 to 27 years of age. The NEO-PI-R is a 240-item questionnaire which was developed to assess the dimensions of personality. Univariate genetic analysis showed that the AE model in which phenotypic covariances are explained only by additive genetic (A) and nonshared environment (E) is still a plausible model, and that the relative proportion of genetic influence was comparable to that reported by Loehlin (1992). Multivariate genetic analysis of the Japanese data suggested/revealed that the five factors are genetically dependent on each other and one common genetic factor mediates their interdependence. Previous studies have assumed that they are phenotypically independent and robust. Although there are sampling biases in the present study, it is noteworthy that the results for all five factors depicted by the NEO-PI-R were comparable to those reported by Western researchers, and the genetic structure of the five-factor model is complex.

Adolescent↗

PubMed2006

Is urbanization scrambling the genetic structure of human populations? A case study.

Recent population expansion and increased migration linked to urbanization are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from 22 Iranian populations. Potential changes in genetic diversity (theta) and genetic distance (F(ST)) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterized by massive immigration, increased theta and a large decrease in F(ST) over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies.

DNA, Mitochondrial↗

PubMed2002

Genetic structure of a greenhouse population of the spider mite Tetranychus urticae: spatio-temporal analysis with microsatellite markers.

The genetic structure of a greenhouse population of the mite Tetranychus urticae was studied by the analysis of five microsatellite loci. Genetic variation was compared during a crop season between periods of population foundation and rapid population increase and was investigated in two consecutive years. The population displayed significant heterozygote deficiency at all the sampling periods. However, inbreeding tended to decrease with increasing density (FIS coefficient between 0.13 and 0.25). No significant genetic differentiation between samples was found either at a spatial scale within the greenhouse or at a temporal scale between two growing seasons (FST between 0.008 and 0.09). Estimations of the genetic relatedness between pairs of individuals indicated that the distances between pairs of sisters and unrelated mites in the greenhouse were not significantly different, suggesting that mites do not tend to form patches that reside close to the point of birth.

Animals↗

PubMed2002

Genetic structure of Aedes aegypti populations in Chiang Mai (Thailand) and relation with dengue transmission.

We analysed the population genetic structure and differentiation regarding vector competence for a dengue virus of 15 Aedes aegypti samples collected from Chiang Mai in northern Thailand. Based on polymorphism of 10 isoenzyme loci, genetic differentiation was confirmed among samples collected in different subdistricts (high FST values and P < 0.05). Based on infection rate for a dengue 2 virus, susceptibilities were similar in mosquitoes collected in San Nuea subdistrict and in Choeng Doi subdistrict, and were heterogeneous in populations sampled in other subdistricts. These findings are discussed and related to insecticide treatments.

Aedes↗

PubMed2006

Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers.

Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic, Mediterranean and Black Sea populations are genetically disjunct. The present study used a higher sampling intensity and a combination of mitochondrial and four microsatellite markers to reveal population structuring between and within basins. Between basins, both marker sets indicated significant differentiation confirming earlier results that gene flow is probably absent between the respective S. setosa populations. At the within-basin scale, we found no evidence of spatial or temporal structuring within the NE Atlantic. In the Mediterranean basin, both marker sets indicated significant structuring, but only the mtDNA data indicated a sharp genetic division between Adriatic and all other Mediterranean populations. Data were inconclusive about population structuring in the Black Sea. The levels of differentiation indicated by the two marker sets differed substantially, with far less pronounced structure detected by microsatellite than mtDNA data. This study also uncovered the presence of highly divergent mitochondrial lineages that were discordant with morphology, geography and nuclear DNA. We thus propose the hypothesis that highly divergent mitochondrial lineages may be present within interbreeding S. setosa populations.

Atlantic Ocean↗

PubMed2003

Microsatellite markers to assess the influence of population size, isolation and demographic change on the genetic structure of the UK butterfly Polyommatus bellargus.

Five microsatellite DNA markers were isolated and used to quantify population genetic structure among a subset of UK populations of the Adonis blue (Polyommatus bellargus Rottemburg). Specifically, whether population size, degree of isolation or history of bottlenecking in 1976-1978 can explain current patterns of genetic variation. The butterfly is at its northern range limit in the UK, where it exists as a highly fragmented metapopulation on isolated pockets of calcareous grassland. Most populations were affected by a severe bottleneck in the late 1970s, when a drought caused the host plant (Hippocrepis comosa) to wilt. Mantel tests and spatial autocorrelation analysis indicated a significant effect of isolation by distance among the UK populations, a relationship that broke down at greater geographical scales (> 23.85 km), probably because of large areas of unsuitable habitat presenting barriers to gene flow. Similarly, amova revealed that variation among geographical regions was almost double that observed within regions. Larger populations were found to support significantly higher levels of genetic diversity, suggesting that small populations may lose genetic diversity through drift. If, as in other butterfly species, low genetic diversity increases the probability of population extinction, then these populations are likely to be under threat. Neither isolation nor a history of bottlenecks appeared to influence genetic diversity. The results indicate that adequate population size a crucial factor in the conservation of genetic diversity in P. bellargus in the UK.

Alleles↗

PubMed2006

Late Quaternary climate change and spatial genetic structure in the shrub Banksia hookeriana.

Spatial genetic variation within species is influenced by both contemporary and historical factors. We attempted to assess the impact of increased aridity and lower temperatures associated with the last glacial maximum on possible refugia and the structuring of genetic variation in Banksia hookeriana, a shrub species restricted to deep sands on the Eneabba sandplain and adjacent Gingin Scarp/Dandaragan Plateau, centred 300 km north of Perth, Western Australia. We used optically stimulated luminescence (OSL) dating to estimate the last time these sands were mobile, as well as amplified fragment length polymorphisms (AFLP) to infer spatial patterns and the phylogeographical history of genetic variation among 15 populations of B. hookeriana. While genetic variation at the species level was high, with 96.6% of 238 AFLP markers polymorphic, average within population gene diversity was low (H(pop) = 0.16). Of the total genetic variation, an analysis of molecular variance (amova) partitioned 70% within populations, 24% among populations within substrate and 6% between substrates. There was an isolation-by-distance effect among populations within the same substrate, but not across substrates, and ordination highlighted genetic differentiation between the sandplain and scarp/plateau populations. A neighbour-joining tree identified the sandplain populations as a distinct clade, with the exception of the most northern sandplain population, which clustered with two northern and eastern plateau populations. The most southern plateau populations formed a clade sister to the sandplain clade. OSL dating of sand at six extant populations suggested that dunes were last mobile 15,000-35,000 years ago, with no clear difference in the ages of sandplain and plateau dunes. These data are consistent with a historical scenario of (re)colonization from isolated refugia of smaller populations either within the patchily vegetated sandplain and/or refugia at the northern, eastern and southern sandplain/scarp margins following postglacial climate amelioration and dune stabilization. Historic interpretations were confounded by the possible effects of long-distance dispersal, natural selection by substrate, and weak and/or ancient introgression with the sister species, Banksia prionotes.

Analysis of Variance↗

PubMed2003

[Analysis of genetic structure of Magnaporthe grisea in the fields of different rice varieties].

The DNA of 251 Magnaporthe grisea isolates from Shiping County, which originated from monoculture and mixture fields, was extracted and amplified by rep-PCR which primer was from palindromes Pot2 of Magnaporthe grisea. The result showed that all isolates were amplified 9-17 DNA bands, the size was about from 400 bp to 23 kb, but mainly between 5-10 kb. 65% bands were polymorphism bands, and 35% were the same bands. Genetic structures of Magnaporthe grisea in the different rice varieties fields were compared by clustering analysis. The complexions of isolates genetic lineages were related to culture patterns. There were more genetic lineages in mixture field than in monoculture one. The dominant lineages were not distinct in mixture field. The result proved that biodiversity might provide a convincing basis for the steady selection of rice variety to pathogen.

Genetic Structures↗

PubMed2001

Population genetic structure of the endangered freshwater crayfish Austropotamobius pallipes, assessed using RAPD markers.

Random amplified polymorphic DNA (RAPD) analysis was performed to characterize the genetic diversity of Austropotamobius pallipes, a threatened freshwater crayfish native to Europe. Four decamer primers which generated six unambiguous polymorphic bands were used to analyse crayfish from 21 populations sampled in the major part of its range. Genetic diversity within populations of A. pallipes, estimated by Shannon's diversity index, ranged from 0 to 0.446 with a mean of 0.159. A UPGMA dendrogram constructed from pairwise PhiST values between populations, revealed three clusters corresponding to populations sampled in the southern, northwestern and eastern part of its range. AMOVA analysis revealed a high genetic structure of A. pallipes populations PhiST=0.814, with 73.11% of the genetic variation distributed between these clusters. It suggests a historical geographical separation of these groups into three refugial areas, probably in the Rhine, Mediterranean and Atlantic basins during recent glaciations. The close genetic relationships between English and western French populations are in accordance with a natural postglacial origin of English populations from individuals having survived in an Atlantic refugium. However, the present results suggest that the Irish stock originated from a human translocation of individuals from an Atlantic refugium.

Animals↗

PubMed2006

Multilocus sequence typing and genetic structure of Cryptosporidium hominis from children in Kolkata, India.

Endemicity of cryptosporidiosis in India has been documented with little genetic characterization of the parasites. Fifty Cryptosporidium-positive specimens collected between 2001 and 2004 from pediatric patients in Kolkata, India were analyzed for parasite genetic structure using multilocus sequence typing (MLST). Genotype analyses showed the presence of Cryptosporidium hominis, Cryptosporidium meleagridis and Cryptosporidium felis in 49, 2 and 1 patients, respectively (two patients had mixed infections of C. hominis and C. meleagridis). To assess the extent of genetic heterogeneity of C. hominis, minisatellites, microsatellites and polymorphic markers in three different chromosomes were sequenced, including genes encoding the 60kDa glycoprotein (GP60), a 47kDa protein (CP47), a mucin-like protein (Mucin1), a serine repeat antigen (MSC6-7), and a 56kDa trans-membrane protein (CP56) in chromosome 6, the 70kDa heat shock protein (HSP70) in chromosome 2, and a T-rich gene fragment (Chrom3T) in chromosome 3. Population sub-structure of C. hominis based on multilocus gene sequences showed that there were 25 multilocus subtypes defined by combined sequence length and nucleotide polymorphism, which formed four distinct groups in this population. Significant intra- and inter-genic linkage disequilibria were observed with minimum recombination or expansion of limited subtypes, all indicative of a mostly clonal population structure. The results highlight the importance of high resolution MLST in studying Cryptosporidium population sub-structure especially when length polymorphism may be inadequate in identifying unique subtypes. The significance of the diverse MLST within C. hominis in relation to geographical and temporal factors and clinical manifestations of disease warrants further investigations.

Animals↗

PubMed2006

The genetic structure of Australasian green turtles (Chelonia mydas): exploring the geographical scale of genetic exchange.

Ecological and genetic studies of marine turtles generally support the hypothesis of natal homing, but leave open the question of the geographical scale of genetic exchange and the capacity of turtles to shift breeding sites. Here we combine analyses of mitochondrial DNA (mtDNA) variation and recapture data to assess the geographical scale of individual breeding populations and the distribution of such populations through Australasia. We conducted multiscale assessments of mtDNA variation among 714 samples from 27 green turtle rookeries and of adult female dispersal among nesting sites in eastern Australia. Many of these rookeries are on shelves that were flooded by rising sea levels less than 10 000 years (c. 450 generations) ago. Analyses of sequence variation among the mtDNA control region revealed 25 haplotypes, and their frequency distributions indicated 17 genetically distinct breeding stocks (Management Units) consisting either of individual rookeries or groups of rookeries in general that are separated by more than 500 km. The population structure inferred from mtDNA was consistent with the scale of movements observed in long-term mark-recapture studies of east Australian rookeries. Phylogenetic analysis of the haplotypes revealed five clades with significant partitioning of sequence diversity (Phi = 68.4) between Pacific Ocean and Southeast Asian/Indian Ocean rookeries. Isolation by distance was indicated for rookeries separated by up to 2000 km but explained only 12% of the genetic structure. The emerging general picture is one of dynamic population structure influenced by the capacity of females to relocate among proximal breeding sites, although this may be conditional on large population sizes as existed historically across this region.

Animal Migration↗

PubMedDate not supplied

[Genetic structure of species complex of the spined loach Cobitis auc. (Cypriniformes: Cobitidae) in Severskiĭ Donets river basin].

Biochemical, genetic, cytometric and morphological analyses of spined loaches of the middle stream of Severskiy Donetz river revealed 3 bisexual species: Cobitis taenia s.l. (68% of the sample); C. melanoleuca (11%); Sabanejewia aurata (9%) and 2 hybrid forms: triploid C. taenia(2)-sp. (9%) and diploid C. taenia-melanoleuca (3%). Distinctive features of genetic structure of polyploid hybrids C. taenia(2)-sp. as well as taxonomic identity of diploid C. taenia s.l. of Severskiy Donetz river were discussed in regard to the Dnieper population ones.

Animals↗

PubMed2005

Within-population spatial genetic structure, neighbourhood size and clonal subrange in the seagrass Cymodocea nodosa.

Abstract The extent of clonality within populations strongly influences their spatial genetic structure (SGS), yet this is hardly ever thoroughly analysed. We employed spatial autocorrelation analysis to study effects of sexual and clonal reproduction on dispersal of the dioecious seagrass Cymodocea nodosa. Analyses were performed both at genet level (i.e. excluding clonal repeats) and at ramet level. Clonal structure was characterized by the clonal subrange, a spatial measure of the linear limits where clonality still affects SGS. We show that the clonal subrange is equivalent to the distance where the probability of clonal identity approaches zero. This combined approach was applied to two meadows with different levels of disturbance, Cadiz (stable) and Alfacs (disturbed). Genotypic richness, the proportion of the sample representing distinct genotypes, was moderate (0.38 Cadiz, 0.46 Alfacs) mostly due to dominance of a few clones. Expected heterozygosities were comparable to those found in other clonal plants. SGS analyses at the genet level revealed extremely restricted gene dispersal in Cadiz (Sp = 0.052, a statistic reflecting the decrease of pairwise kinship with distance), the strongest SGS found for seagrass species, comparable only to values for selfing herbaceous land plants. At Cadiz the clonal subrange extended across shorter distances (20-25 m) than in Alfacs (30-35 m). Comparisons of sexual and vegetative components of gene dispersal suggest that, as a dispersal vector within meadows, clonal spread is at least as important as sexual reproduction. The restricted dispersal and SGS pattern in both meadows indicates that the species follows a repeated seedling recruitment strategy.

Demography↗