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Results for “Genetic Structures”

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At least 811 records · Page 45Linked to original sources
PubMed1999

Genetic structure and transcriptional analysis of a mobilizable, antibiotic resistance transposon from Bacteroides.

Tn4555 is a 12.1-kb Bacteroides antibiotic resistance transposon representative of a novel class of transmissible genetic elements that can be transferred by resident conjugative tetracycline resistance transposons (Tc(r)-elements) but are not capable of self-transfer. Previously it was shown that Tn4555 transposes by a site-specific recombination mechanism that utilizes a circular intermediate. This circular form is induced by tetracycline and it also is the substrate for conjugation. To better understand the mechanism of transposition, the entire nucleotide sequence of Tn4555 was determined and a set of genes potentially involved in transposition was identified. The transposon was 12,105 bp including a variable 6-bp coupling sequence associated with one of the transposon termini. The element had a 44.3% G + C composition and nine potential protein coding regions were observed, eight of which were encoded on the forward strand. Two putative transposition genes were found. The int gene product had significant C-terminal homology to the lambda family of integrases and the xis gene product was similar to several excisionase proteins encoded by both plasmids and conjugative transposons. The mobA mobilization gene and cfxA beta-lactamase gene of Tn4555 had been previously identified, and the remaining five open reading frames had no significant matches with sequences in the available databases. Northern hybridization analysis revealed that all Tn4555 genes except for orf-9 were expressed and two sets of genes, tnpA, int and xis, orf-5, orf-6 were organized in operons. None of the genes seemed to be induced significantly by the addition of tetracycline to cultures. Although a small 0.4-kb xis-specific transcript appeared in tetracycline-treated cultures it was not clear if this was due to an induction or if it was a specific degradation product.

Amino Acid Sequence↗
PubMed2004

Genetic diversity and multilocus genetic structure in the relictual endemic herb Japonolirion osense (Petrosaviaceae).

Plant clonality may greatly reduce effective population size and influence management strategies of rare and endangered species. We examined genetic diversity and the extent of clonality in four populations of the monotypic herbaceous perennial Japonolirion osense, which is one of the most rare flowering plants in Japan. Allozyme analysis revealed moderate levels of genetic variation, and the proportion of polymorphic loci (P=66.7%) was higher than the value for species with similar life-history traits. With four polymorphic loci, 19 multilocus genotypes were observed among 433 aerial shoot samples and 10 (52%) were found only in single populations. The proportion of distinguishable genotypes (PD=0.10) and Simpson's index of diversity (D=0.52) also exhibited moderate levels of genotypic diversity compared to other clonal plants, with genotype frequencies at Hardy-Weinberg equilibrium. The distributions of genotypes were often localized and they were mostly found within a radius of 5 m. Spatial autocorrelation analysis showed that shoot samples located 4 m apart were expected to be genetically independent. The results suggest that the spatial extent of genets was relatively narrow and thus the clonality was not extensive.

Conservation of Natural Resources↗
PubMed2004

Genetic structuring of boll weevil populations in the US based on RAPD markers.

Abstract Randomly amplified polymorphic DNA (RAPD) analysis was performed to infer the magnitude and pattern of genetic differentiation among boll weevil populations from eighteen locations across eight US states and north-east Mexico. Sixty-seven reproducible bands from six random primers were analysed for genetic variation within and between weevil populations. Genetic and geographical distances among all populations were positively correlated, reflecting a pattern of isolation by distance within a larger metapopulation. Gene flow between south-central, western and eastern regions is limited, but migration between locations within regions appears to be relatively frequent up to distances of approximately 300-400 km. However, estimates of effective migration were much lower than those estimated from mtDNA-RFLP data reported previously.

Animals↗
PubMedDate not supplied

The origins of the Irish travellers and the genetic structure of Ireland.

Ireland's unique and well-documented history provides insight into the formation and origins of population subdivisions. Of particular interest, is the controversial ethnogenesis of an itinerant population of Ireland: the Travellers. The objectives of this study were: (1) to determine the genetic affinity of the Travellers to the general Irish population based on gene frequency data, subdivided by county, and (2) to explore the relationship between subpopulations of Ireland, given its turbulent history. The gene frequencies of standard genetic markers collected from populations residing in counties of Ireland and the Travellers were calculated and analysed using several multivariate methods. First, a relationship (R) matrix was used to ascertain the scaled variance covariance matrix of population similarity. Second, mean per locus heterozygosity (H) was regressed on distance of the region from the gene frequency centroid (r(ii)). The results of this study include: (1) the confirmation of Crawford's (1975, in Biosocial Interrelations in Population Adaptations, E. S. Watts et al. (eds), pp. 93-103) conclusions concerning the origins and genetic affinity of the Travellers; (2) based on several multivariate analyses, the major influence on population structure was unique historical events; and (3) Relethford and Crawford's (1995, American Journal of Physical Anthropology, 96, 25-38) hypothesis concerning the distinctiveness of the midland counties was verified by this study.

Emigration and Immigration↗
PubMed1999

Allozyme variation and genetic structure of calluna vulgaris (heather) populations in scotland: the effect of postglacial recolonization

Recent fragmentation of populations as well as historical postglacial recolonization may have significantly affected the population genetic diversity of temperate plant species. Regional allozymic variability was measured at seven loci within and among 12 populations of Calluna vulgaris in the previously glaciated region of Scotland. These results were compared with existing data on south-western continental populations. Low genetic differentiation (FST = 0.024) and lack of consistent geographical pattern were found at the regional level among Scottish populations, implying a high rate of gene flow (Nm = 10.2), probably favoured by the nearly continuous range of C. vulgaris across Scotland and characteristics of the Scottish environment. Scottish populations possessed lower mean allozymic diversity (PLP = 40.48, A = 1.95, He = 0.133) than populations from all the continental regions investigated previously. Belgian populations were genetically more closely related to Scottish than to other continental populations. These last two findings are interpreted with regard to the evolutionary history of the species revealed by palynological data.

Journal Article↗
PubMed1986

The genetic structure of a tribal population, the Yanomama Indians. XV. Patterns inferred by autocorrelation analysis.

Fifteen allele frequencies have previously been determined for 50 villages of the Yanomama, an Amerindian tribe from southern Venezuela and northern Brazil. These frequencies were subjected to spatial autocorrelation analysis to investigate their population structure. There are significant spatial patterns for most allele frequencies. Clinical patterns, investigated by one-dimensional and directional spatial correlograms, were relatively few in number and were moderate in strength. Overall, however, there is a marked decline in genetic similarity with geographic distance. The results are compatible with a hierarchic population structure superimposed on the geography, and generated by a stochastic fission-fusion model of village propagation, followed by localized gene flow. Strong temporal autocorrelations of allele frequencies based on linguistic-historical distances representing time since divergence were also found. There appears to be a stronger relation between geography and linguistic-historical hierarchic subdivisions than between either feature and genetic distances. These findings confirm by different approaches the results of earlier analyses concerning the important roles of both stochastic and social factors in determining village allele frequencies and the occurrence within this tribe of some allele frequency clines most likely due to the operation of chance historical processes.

Alleles↗
PubMed1998

Spatial genetic structure of human populations in Japan.

We studied spatial patterns for 24 allele frequencies representing 15 systems (blood antigens, enzymes, serum proteins, color blindness, and cerumen) in Japan. The total number of samples over all systems and localities is 1125. We investigated patterns of genetic variation graphically as interpolated allele frequency surfaces, as one-dimensional and directional correlograms, and by testing for the direction of maximal genetic autocorrelation. We examined the allele frequency surfaces by various techniques of spatial autocorrelation analysis and found 13 allele frequency surfaces from 9 genetic systems exhibiting significant spatial patterns. Several surfaces have clinal patterns along the major axis of the Japanese archipelago; others tend toward a maximum or minimum in south-central Honshu. Yet other allele frequencies show long-distance differentiation or patchiness. We discovered seven areas of rapid genetic change by using the wombling method. These areas largely reflect maritime and montane barriers, and some are associated with dialectal boundaries in these populations. The observed patterns support the hybridization or dual structure hypothesis for the peopling of Japan.

Alleles↗
PubMed1994

The genetic structure of metapopulations and conservation biology.

A range of models describing metapopulations is surveyed and their implications for conservation biology are described. An overview of the use of both population genetic elements and demographic theory in metapopulation models is given. It would appear that most of the current models suffer from either the use of over-simplified demography or the avoidance of selectively important genetic factors. The scale for which predictions are made by the various models is often obscure. A conceptual framework for describing metapopulations by utilising the concept of fitness of local populations is provided and some examples are given. The expectation that any general theory, such as that of metapopulations, can make useful predictions for particular problems of conservation is examined and compared with the prevailing 'state of the art' recommendations.

Animals↗
PubMed2004

Analysis of the genetic structure of endangered bovine breeds from the Western Pyrenees using DNA microsatellite markers.

In the Western Pyrenees, three out of four native cattle breeds are in grave danger of extinction. Genetic variation of all four breeds was assessed by analyzing 478 animals using 11 microsatellite markers. A moderate/high within-breed variability was found, a favorable factor to consider when planning conservation and improvement programs. Interestingly, the only selected commercial breed, the Pirenaica, showed depressed heterozygosity levels and a low average number of alleles, perhaps explainable by intensive human selection exacerbated by a bottleneck effect. The Pirenaica also exhibited pronounced genetic differences and was the largest contributor of diversity among the breeds from the Western Pyrenees. Among endangered cattle breeds from this region, our results highlight the singularity of the Betizu. Geographic isolation among herds may be responsible for the large F(IS) value found in the Betizu breed. Lastly, our study suggests that the use of highly selected breeds may be one of the causes of distortion in phylogenetic analyses.

Alleles↗
PubMed2005

Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions.

To examine the performance and information content of different marker systems, comparative assessment of population genetic diversity was undertaken in nine populations of Athyrium distentifolium using nine genomic and 10 expressed sequence tag (EST) microsatellite (SSR) loci, and 265 amplified fragment length polymorphism (AFLP) loci from two primer combinations. In range-wide comparisons (European vs. North American populations), the EST-SSR loci showed more reliable amplification and produced more easily scorable bands than genomic simple sequence repeats (SSRs). Genomic SSRs showed significantly higher levels of allelic diversity than EST-SSRs, but there was a significant correlation in the rank order of population diversities revealed by both marker types. When AFLPs, genomic SSRs, and EST-SSRs are considered, comparisons of different population diversity metrics/markers revealed a mixture of significant and nonsignificant rank-order correlations. However, no hard incongruence was detected (in no pairwise comparison of populations did different marker systems or metrics detect opposingly significant different amounts of variation). Comparable population pairwise estimates of F(ST) were obtained for all marker types, but whilst absolute values for genomic and EST-SSRs were very similar (F(ST) = 0.355 and 0.342, respectively), differentiation was consistently higher for AFLPs in pairwise and global comparisons (global AFLP F(ST) = 0.496). The two AFLP primer combinations outperformed 18 SSR loci in assignment tests and discriminatory power in phenetic cluster analyses. The results from marker comparisons on A. distentifolium are discussed in the context of the few other studies on natural plant populations comparing microsatellite and AFLP variability.

Cluster Analysis↗