Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genetic Structures”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10Linked to original sources
PubMed2004

Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Eurasia.

The genetic structure of populations of Turnip mosaic virus in Eurasia was assessed by making host range and gene sequence comparisons of 142 isolates. Most isolates collected in West Eurasia infected Brassica plants whereas those from East Eurasia infected both Brassica and Raphanus plants. Analyses of recombination sites (RSs) in five regions of the genome (one third of the full sequence) showed that the protein 1 (P1 gene) had recombined more frequently than the other gene regions in both subpopulations, but that the RSs were located in different parts of the genomes of the subpopulations. Estimates of nucleotide diversity showed that the West Eurasian subpopulation was more diverse than the East Eurasian subpopulation, but the Asian-BR group of the genes from the latter subpopulation had a greater nonsynonymous/synonymous substitution ratio, especially in the P1, viral genome-linked protein (VPg) and nuclear inclusion a proteinase (NIa-Pro) genes. These subpopulations seem to have evolved independently from the ancestral European population, and their genetic structure probably reflects founder effects.

Amino Acid Substitution↗
PubMed2007

Genetic structure in natural populations of barley/cereal yellow dwarf virus isolates from Alaska.

The genetic structure of natural populations of Alaskan barley yellow dwarf virus (BYDV)-PAV, BYDV-PAS, and cereal yellow dwarf virus (CYDV)-RPV from barley (Hordeum vulgare L.) and oats (Avena sativa L.) in Alaska were analyzed between 2002 and 2004. PCR products spanning the viral coat protein gene of 187 isolates were cloned and sequenced. The majority (78%) were similar to BYDV-PAS, 19% were similar to CYDV-RPV, and only about 3% resembled BYDV-PAV. The CYDV-RPV isolates clustered in three groups: 44, 17, and 39% resembled RPS-like CP from Mexico, resembled RPV-like CP from New York, or formed a unique clade that was RPV/RPS recombinant CP, respectively. The patterns of genetic variation of PAS and RPV varied little over time or with respect to host plant. The difference in spatial and temporal population genetic structures of the PAS and RPV isolates suggests that these two viruses are influenced by different agroecological factors. Sequence of PCR products spanning the carboxyl terminus of the polymerase gene, the intergenic region, and most of the coat protein gene of RPV revealed two probable ancestral recombination events for some isolates.

Alaska↗
PubMed2003

Migration and genetic structure of the grain aphid (Sitobion avenae) in Britain related to climate and clonal fluctuation as revealed using microsatellites.

Genetic structuring of populations reflects the interaction of genetic drift, mutation, migration and selection, with influences from life history. Aphids are interesting in this regard as they have the potential for unusually high levels of dispersal and natural selection, which typically counter each other. In the present study, winged grain aphids Sitobion avenae (F.) were collected in four 12.2-m high suction traps along a north-south transect in Britain in order to eliminate sampling bias from plant hosts (cereals and grasses; Poaceae), it being known that these insects show host adaptation demonstrable using molecular markers. Samples were analysed at four polymorphic microsatellite loci over two consecutive years. Population allele frequencies were similar nationally during the two years, although clonal diversity varied greatly between sites and years. In the first sampling year following a harsh winter, diversity was found to display a latitudinal clinal trend: the proportion of unique clones (genotypes) increased with latitude. However, this pattern was less apparent the following year, after a milder winter. Nonetheless, overall FST analysis showed that there was little spatial genetic structuring in either sampling year. These data support the view that the insect is highly migratory and also support a theoretical model and previous data suggesting that the reproductive mode is clinal in S. avenae. This appears to be because natural selection (reduced reproductive success of asexual genotypes under cold conditions) is sufficiently powerful to overcome the homogenizing effects of strong migration. There was no clear evidence for isolation by distance for the genetic data obtained. The data are compared with similar data from other aphid species and other insects. Only by the collection of such data sets can an accurate picture be built up relating genetic variability to flight behaviour, including migratory ambit in this group of insects since, due to their small size and rapid dilution in the air, other marking approaches are impracticable over large geographical distances.

Animal Migration↗
PubMed2004

Mating system and gene flow in the red seaweed Gracilaria gracilis: effect of haploid-diploid life history and intertidal rocky shore landscape on fine-scale genetic structure.

The impact of haploid-diploidy and the intertidal landscape on a fine-scale genetic structure was explored in a red seaweed Gracilaria gracilis. The pattern of genetic structure was compared in haploid and diploid stages at a microgeographic scale (< 5 km): a total of 280 haploid and 296 diploid individuals located in six discrete, scattered rock pools were genotyped using seven microsatellite loci. Contrary to the theoretical expectation of predominantly endogamous mating systems in haploid-diploid organisms, G. gracilis showed a clearly allogamous mating system. Although within-population allele frequencies were similar between haploids and diploids, genetic differentiation among haploids was more than twice that of diploids, suggesting that there may be a lag between migration and (local) breeding due to the long generation times in G. gracilis. Weak, but significant, population differentiation was detected in both haploids and diploids and varied with landscape features, and not with geographic distance. Using an assignment test, we establish that effective migration rates varied according to height on the shore. In this intertidal species, biased spore dispersal may occur during the transport of spores and gametes at low tide when small streams flow from high- to lower-shore pools. The longevity of both haploid and diploid free-living stages and the long generation times typical of G. gracilis populations may promote the observed pattern of high genetic diversity within populations relative to that among populations.

Diploidy↗
PubMed1999

Genetic structure of Helianthus occidentalis (Asteraceae) in a preserve withfragmented habitat.

We examined the spatial genetic structure of Helianthus occidentalis Riddell ssp. occidentalis Riddell (western sunflower) to determine whether this species is highly clonal and whether the distance between prairie patches influences genetic differentiation. In the Edge of Appalachia Preserve System, Ohio, this species is restricted to prairie patches that have a clumped distribution in the forest matrix. Data from this insect-pollinated forb with gravity-dispersed seed were compared to data from the same patches for Asclepias verticillata, an insect-pollinated species with wind-dispersed seed. Allozyme electrophoresis was used to collect genetic data from H. occidentalis samples from eight patches in four regions. Genetic data from three polymorphic loci indicted that this species is not highly clonal. Genetic differentiation was greater among patches within a region than among regions, suggesting that gene flow among patches is more limited in H. occidentalis than in A. verticillata. Founder effect may also have contributed to observed genetic differences among patches as some of these populations may have re-established after release from human use. As habitat fragmentation is increasing in the preserve, it is also likely that genetic differentiation may be increasing. Therefore, monitoring of genetic structure is necessary to further assess the effect of fragmentation.

Journal Article↗
PubMed1994

[Genetic structure of populations and characteristics of geographic distribution of autosomal recessive diseases in the Kirov region].

The genetic structure of human populations inhabiting Kirov region is described. The effect of genetic drift on geographical distribution of families with autosomal recessive diseases is analyzed. Genetic distances were calculated from frequencies of occurrence of certain family names and frequencies of autosomal recessive genes encoding hereditary diseases. Cluster analysis based on matrices of genetic distances showed that descriptions of the genetic structure obtained using these two methods are in good agreement with one another. It is shown that genetic drift is the principal factor determining the territorial distribution of autosomal recessive genes within population of Kirov region. This conclusion is based on local accumulation of families suffering from autosomal recessive diseases.

Cluster Analysis↗
PubMed1998

The significance of relatedness and gene flow on population genetic structure in the®subsocial spider Eresus cinnaberinus (Araneae: Eresidae)

Interdemic selection, inbreeding and highly structured populations have been invoked to explain the evolution of cooperative social behaviour in the otherwise solitary and cannibalistic spiders. The family Eresidae consists of species ranging from solitary and intermediate subsocial to species exhibiting fully cooperative social behaviour. In this study we, in a hierarchical analysis, investigated relatedness of putative family clusters, inbreeding and population genetic structure of the subsocial spider Eresus cinnaberinus. Five hierarchical levels of investigation ranging from large scale genetic structure (distances of 250 and 50 km level 1 and 2) over microgeographic structure (20 km2 and 4 km2, level 3 and 4) to a single hill transect of 200 m (level 5) were performed. The purpose of level 5 was two-fold: (1) to investigate the relatedness of putative family groups, and (2) to evaluate the influence of both family living and sampling design on higher level estimates. Relatedness estimates of putative family groups showed an average relatedness of R=0.26. There was no indication of inbreeding. In contrast to social spiders, genetic variation was abundant, Heapproximately0.10. The population genetic structure was intermediate between social and asocial spiders. Genetic variance increased continually across hierarchical levels. Family structured neighbourhoods biased differentiation estimates among level 5 samples (FST=0.04) and level 3 and 4 samples (0.07 0, was caused by disjunct sampling from separate neighbourhoods. Larger scale samples were highly differentiated 0.12<FST<0.26, depending on level and sampling design. Due to a distance effect family living did not influence estimates of the higher level 1. Although the dispersing sex among social spiders and the subsocial E. cinnebarinus differ, females versus males, female behaviour of both sociality classes lead to high genetic variance.Copyright 1998 The Linnean Society of London

Journal Article↗
PubMed1995

[Genetic structure of soil population of the fungus Fusarium oxysporum Schlechtend.: Fr.: molecular reidentification of the species and genetic differentiation of isolates using polymerase chain reaction with universal primers (UP-PCR)].

The genetic structure of three soil populations of fungus Fusarium oxysporum was analyzed using polymerase chain reaction with universal primers (UP-PCR). Distinct UP-PCR variants revealed by means of cross-dot hybridization of amplified DNA and restriction analysis of nuclear ribosomal DNA represent subspecies or sibling species of F. oxysporum. The remaining isolates of F. oxysporum showed moderate UP-PCR polymorphism characterized by numerous types, whose relatedness was analyzed by computer treatment of the UP-PCR patterns. The genetic distance trees based on the UP-PCR patterns, which were obtained with different universal primers, demonstrated similar topology. This suggests that evolutionarily important genome rearrangements correlatively occur within the entire genome. Isolates representing different UP-PCR polymorphisms were encountered in all populations, being distributed asymmetrically in two of these. In general, soil populations of F. oxysporum were represented by numerous genetically isolated groups with a similar genome structure. The genetic heterogeneity of the isolates within these groups is likely to be caused by the parasexual process. The usefulness of the UP-PCR technique for population studies of F. oxysporum was demonstrated.

Base Sequence↗
PubMed2004

Population genetic structure of North American thinhorn sheep (Ovis dalli).

The thinhorn sheep (Ovis dalli ssp.) provides a rare example of a North American large mammal that occupies most of its native range and maintains close to ancestral population size. There are currently two recognized subspecies, Dall's sheep (O. d. dalli) and Stone's sheep (O. d. stonei), the validity of which remains uncertain. We investigated the spatial genetic structure of thinhorn sheep populations representing both subspecies by genotyping individuals (n = 919) from across the species range at 12 variable microsatellite loci. We found high levels of genetic diversity within (HE = 0.722) and significant genetic structure among the 24 sampled areas (FST = 0.160). Genetic distance measures and Bayesian clustering analyses revealed the presence of at least eight subpopulations that are delineated by mountain range topology. A strong overall pattern of isolation-by-distance is evident across the sampling range (r = 0.75, P < 0.001) suggesting limited dispersal and extensive philopatry. Partial Mantel tests of this relationship showed mountain range distinctions represent significant barriers to gene flow (P = 0.0001), supporting the Bayesian analyses. Genetic structure was more strongly pronounced in southern Yukon and Alaska than elsewhere. We also show evidence for genetic differences between the two currently recognized thinhorn subspecies.

Alaska↗
PubMed2002

Population genetic structure and male-biased dispersal in the queenless ant Diacamma cyaneiventre.

In this study we investigated the population genetic structure of the queenless ant Diacamma cyaneiventre. This species, lacking winged queens, is likely to have a restricted female dispersal. We used both mitochondrial and microsatellite markers to assess the consequence of such restricted female dispersal at three geographical scales: within a given locality (< 1 km), between localities within a given region (< 10 km) and between regions (> 36 km). Within a locality, a strong population structure was observed for mitochondrial DNA (mtDNA) whereas weak or nonexistent population genetic structure was observed for the microsatellites (around 5% of the value for mtDNA). Male gene flow was estimated to be about 20-30 times higher than female gene flow at this scale. At a larger spatial scale, very strong genetic differentiation for both markers was observed between localities - even within a single region. Female dispersal is nonexistent at these scales and male dispersal is very restricted, especially between regions. The phylogeographical structure of the mtDNA haplotypes as well as the very low genetic diversity of mtDNA within localities indicate that new sites are colonized by a single migration event from adjacent localities, followed by successive colony fissions. These patterns of genetic variability and differentiation agree with what is theoretically expected when colonization events are kin-structured and when, following colonization, dispersion is mainly performed by males.

Animals↗
PubMed2006

Dispersal and genetic structure in the American marten, Martes americana.

Natal dispersal in a vagile carnivore, the American marten (Martes americana), was studied by comparing radio-tracking data and microsatellite genetic structure in two populations occupying contrasting habitats. The genetic differentiation determined among groups of individuals using F(ST) indices appeared to be weak in both landscapes, and showed no increase with geographical distance. Genetic structure investigated using pairwise genetic distances between individuals conversely showed a pattern of isolation by distance (IBD), but only in the population occurring in a homogeneous high-quality habitat, therefore showing the advantage of individual-based analyses in detecting within-population processes and local landscape effects. The telemetry study of juveniles revealed a leptokurtic distribution of dispersal distances in both populations, and estimates of the mean squared parent-offspring axial distance (sigma2) inferred both from the genetic pattern of IBD and from the radio-tracking survey showed that most juveniles make little contribution to gene flow.

Animal Migration↗
PubMed2005

Genetic structure in the coral-reef-associated Banggai cardinalfish, Pterapogon kauderni.

In this study, we used 11 polymorphic microsatellite loci to show that oceanic distances as small as 2-5 km are sufficient to produce high levels of population genetic structure (multilocus F(ST) as high as 0.22) in the Banggai cardinalfish (Pterapogon kauderni), a heavily exploited reef fish lacking a pelagic larval dispersal phase. Global F(ST) among all populations, separated by a maximum distance of 203 km, was 0.18 (R(ST) = 0.35). Moreover, two lines of evidence suggest that estimates of F(ST) may actually underestimate the true level of genetic structure. First, within-locus F(ST) values were consistently close to the theoretical maximum set by the average within-population heterozygosity. Second, the allele size permutation test showed that R(ST) values were significantly larger than F(ST) values, indicating that populations have been isolated long enough for mutation to have played a role in generating allelic variation among populations. The high level of microspatial structure observed in this marine fish indicates that life history traits such as lack of pelagic larval phase and a good homing ability do indeed play a role in shaping population genetic structure in the marine realm.

Animals↗
PubMedDate not supplied

[Genetic structure of Corynebacterium diphtheriae strains isolated in Russia during epidemics of various intensity].

The genetic structure of C. dipthteriae toxigenic strains isolated in Russia during the period of more than 50 years was analysed. The use of the method of ribotyping made it possible to register 17 C. diphtheriae ribotypes. The study revealed that the genetic structure of C. diphtheriae population varied in the dynamics of the epidemic process: each epidemic cycle characterized by predominant spread of epidemic strains of definite biovars and ribotypes. Thus, C. diphtheriae strains of biovar gravis, ribotype M11, dominated in the 40-60 years and C. diphtheriae strains of biovar mitis, closely related ribotypes M1 and M1v, dominated in the 80 years. During the last epidemic rise of diphtheriae morbidity in the 90 s C. diphtheriae strains of biovar gravis, closely related ribotypes G1 and G4, dominated among circulating strains. The proportion of these ribotypes began to increase 3 years before the rise of morbidity. The data of microbiological monitoring are recommended for use in the prognostication of the development of the epidemic process of diphtheria infection.

Corynebacterium diphtheriae↗
PubMed2001

Assessment of genetic structure within and among Bulgarian populations of the common ash (Fraxinus excelsior L.).

We analysed genetic variation within and between populations of the common ash from Bulgaria in order to extract biological information useful in the context of conservation management of eastern European genetic resources of noble hardwood species. A total of 321 trees from three regions of Bulgaria were typed at six highly polymorphic microsatellite loci. Analysis of within-population inbreeding suggests an upper boundary value of 2.7% for the selfing rate. Significant spatial genetic structure consistent with models of isolation by distance was detected within four out of 10 populations as well as among populations. Estimates of neighbourhood size in the range 38-126 individual trees were obtained based on spatial genetic structure analyses at either the intrapopulation or interpopulation level. Differentiation among populations explained only about 8.7% of total genetic diversity. These results are discussed in comparison with data from social broad-leaved species such as oak and beech.

Alleles↗
PubMed2002

Nestmate relatedness and population genetic structure of the Australian social crab spider Diaea ergandros (Araneae: Thomisidae).

We characterized the population genetic structure of the Australian social spider Diaea ergandros using polymorphic allozyme markers. Our main objectives were to understand the social organization of D. ergandros and discern patterns of gene flow across distantly separated geographical areas. Spiders were sampled from nests located within 100 m wide locales, which were distributed within larger 50 km wide regions. Our results indicated that nestmates could have been produced by a single mother and father in 88.9% of D. ergandros nests. The remainder of nests contained spiders that were probably produced by polyandrous females or were immigrants from foreign nests. Nestmate relatedness was relatively high (r = 0.44) and did not differ significantly between the sexes or among juvenile, subadult and adult life stages. We also discovered that D. ergandros populations were highly structured, with significant differentiation detected among locales (FLR = 0.23) and regions (FRT = 0.081). Spiders within locales were also substantially inbred (FIL = 0.15). Overall, our data show that significant population subdivision exists in D. ergandros populations, and we suggest that the poor dispersal ability of Diaea spiders can account for the observed genetic structure.

Animals↗
PubMed2003

Host-associated genetic structure of Mexican populations of the cabbage aphid Brevicoryne brassicae L. (Homoptera: Aphididae).

Phytophagous insects can use different host plant species across their geographic distribution. Within a locality, however, their feeding can be restricted to one or two plant species. If host species constitute different selective regimes to herbivorous insects, genetic differentiation and host-associated local adaptation may occur. In this study, we describe the genetic structure of the aphid Brevicoryne brassicae L. associated to Brassica campestris L. and B. oleraceae var. capitata L., two plant species that occur sympatrically in four localities in the highlands of Chiapas, Mexico. The aim was to determine if the aphid populations are genetically structured in relation to the plant host species, and if such differentiation is consistent among localities. The genetic description of populations was made using 11 enzyme loci using cellulose acetate electrophoresis. Aphid genotypes were surveyed in two host plant species-associated populations within each of four localities at seven polymorphic loci (eight subpopulations in total). The genetic structure was assessed at the level of subpopulations, among localities, between hosts, and pairwise comparisons of hosts within locality, using Wright F-statistics. Genetic distance among localities and between host-associated populations within each locality was also estimated. We found that overall genetic differentiation was high (FST=0.22), and that differentiation among localities (FST=0.13) was higher than differentiation between hosts (FST=0.03). All FST estimates were statistically significant. Pairwise comparisons of FST between hosts in each locality suggest high differentiation in two of them, and low but still significant differentiation in two other localities. Given that general environmental conditions are similar within localities, selection on each host species may produce genetic divergence within and among subpopulations of B. brassicae.

Animals↗
PubMed2005

Wide-range analysis of genetic structure of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in the cool temperate zone of Japan.

Betula maximowicziana is a long-lived pioneer tree species in Japanese cool temperate forests that plays an important role in maintenance of the forest ecosystem and has high economic value. Here we assess the wide-range genetic structure of 23 natural populations of B. maximowicziana using 11 simple sequence repeat (SSR) loci. Genetic diversity within populations was relatively low in all populations (mean H(E), 0.361; mean allelic richness, 2.80; mean rare allelic richness, 1.02). The population differentiation was also relatively low (F(ST), 0.062). Genetic distance-based and Bayesian clustering analysis revealed that the populations examined here could be divided into a southern group and a northern group. Analysis of rare allelic richness and Bayesian clustering revealed evidence for both southern and northern refugia during the last glacial period. Furthermore, a comparison of regional genetic diversity revealed significant clines in allelic richness. In spatial genetic structure evaluation, significant isolation by distance (IBD) was detected among the 23 populations, but not within regions. Moreover, significant population bottlenecks were found in all populations under infinite allele model (IAM) assumptions. These unusual, significant bottlenecks might be because of the processes of postglacial colonization and the species' characters and/or life history as a long-lived pioneer tree species. The wide-range, regional genetic structure found in this study provides an important baseline for conservation and forest management, including the identification of evolutionarily significant units (ESUs) and/or management units (MUs) of B. maximowicziana.

Bayes Theorem↗
PubMed2001

Fine-scale genetic structure, estuarine colonization and incipient speciation in the marine silverside fish Odontesthes argentinensis.

The identification of incipient ecological species represents an opportunity to investigate current evolutionary process where adaptive divergence and reproductive isolation are associated. In this study we analysed the genetic structure of marine and estuarine populations of the silverside fish Odontesthes argentinensis using nine microsatellite loci and 396 bp of the mitochondrial DNA (mtDNA) control region. Our main objective was to investigate the relationship among estuarine colonization, divergent selection and speciation in silversides. Significant genetic structure was detected among all marine and estuarine populations. Despite the low phylogeographic structure in mtDNA haplotypes, there was clear signal of local radiations of haplotypes in more ancient populations. Divergence among marine populations was interpreted as a combined result of homing behaviour, isolation by distance and drift. On the other hand, ecological shifts due to the colonization of estuarine habitats seem to have promoted rapid adaptive divergence and reproductive isolation in estuarine populations, which were considered as incipient ecological species. This conclusion is supported by the existence of a set of environmental factors required for successful reproduction of estuarine ecotypes. The pattern of genetic structure indicates that phenotypic and reproductive divergence evolved in the face of potential gene flow between populations. We suggest that the 'divergence-with-gene-flow' model of speciation may account for the diversification of estuarine populations. The approach used can potentially identify 'incipient estuarine species', being relevant to the investigation of the evolutionary relationships of silversides in several coastal regions of the world.

Animals↗